From fe9bc1410366ce33ebf4ac909ae04397c3f81a39 Mon Sep 17 00:00:00 2001
From: fubar2 <ross.lazarus@gmail.com>
Date: Thu, 14 Mar 2024 14:53:12 +1100
Subject: [PATCH 01/27] add sam output - means no delta.out so some filters and
 a new test. Fixed many parameters with both name and argument making planemo
 lint upset.

---
 tools/mummer4/macros.xml           |   6 +--
 tools/mummer4/nucmer.xml           |  65 ++++++++++++++++++++---------
 tools/mummer4/test-data/nucmer.txt |   2 +-
 tools/mummer4/test-data/plot.png   | Bin 6147 -> 0 bytes
 4 files changed, 49 insertions(+), 24 deletions(-)

diff --git a/tools/mummer4/macros.xml b/tools/mummer4/macros.xml
index d5433d987e9..611ef8d8d9c 100644
--- a/tools/mummer4/macros.xml
+++ b/tools/mummer4/macros.xml
@@ -34,9 +34,9 @@
             <option value="">Dotplot</option>
             <option value="-c">Coverage Plot (-c)</option>
         </param>
-        <param name="filter" type="boolean" argument="--filter" truevalue="--filter" falsevalue="" label="Filter"
+        <param type="boolean" argument="--filter" truevalue="--filter" falsevalue="" label="Filter"
             help="Only display .delta alignments which represent the 'best' hit to any particular spot on either sequence, i.e. a one-to-one mapping of reference and query subsequences. (--filter)" />
-        <param name="fat" type="boolean" argument="--fat" truevalue="--fat" falsevalue="" label="Layout sequences using fattest alignment only" help="(--fat)" />
+        <param type="boolean" argument="--fat" truevalue="--fat" falsevalue="" label="Layout sequences using fattest alignment only" help="(--fat)" />
         <conditional name="labels" >
             <param name="IDs" type="select" label="Plot a particular reference or query sequence?" help="For alignments that used more than one reference/query." >
                 <option value="no">NO</option>
@@ -54,7 +54,7 @@
             <option value="large">Large</option>
         </param>
         <param name="snp" type="boolean" argument="--SNP" truevalue="--SNP" falsevalue="" label="SNPs" help="Highlight SNP locations in each alignment. (--SNP)" />
-        <param name="title" type="text" argument="-title" value="Title" label="Plot Title" help="(-title)" />
+        <param type="text" argument="-title" value="Title" label="Plot Title" help="(-title)" />
         <conditional name="range" >
             <param name="custom" type="select" label="Choose custom X and Y axis ranges?" >
                 <option value="no">NO</option>
diff --git a/tools/mummer4/nucmer.xml b/tools/mummer4/nucmer.xml
index a859d2c2f8d..03f16403d75 100644
--- a/tools/mummer4/nucmer.xml
+++ b/tools/mummer4/nucmer.xml
@@ -11,8 +11,11 @@
         <![CDATA[
         ln -s $reference_sequence reference.fa &&
         ln -s $query_sequence query.fa &&
-        nucmer 
+        nucmer
             $anchoring
+            #if $out_format != "delta":
+                  $out_format
+            #end if
             -b '$breaklen'
             -c '$mincluster'
             -D '$diagdiff'
@@ -31,8 +34,8 @@
                 $options.genome
                 -M '$options.max_chunk'
             #end if
-            'reference.fa' 'query.fa' 
-            #if $mumplot.plot == 'yes':
+            'reference.fa' 'query.fa'
+            #if $mumplot.plot == 'yes' and $out_format == "delta":
                 && mummerplot
                     #if $mumplot.sequences.seq_input == 'yes':
                         -R '$reference_sequence'
@@ -60,15 +63,21 @@
                     @MUMMER_GNUPLOT_MANUAL@
             #end if
         ]]>
-    </command> 
+    </command>
     <inputs>
         <param name="reference_sequence" type="data" format="fasta" label="Reference Sequence" help="FastA or multi-FastA" />
         <param name="query_sequence" type="data" format="fasta" label="Query Sequence" help="FastA or multi-FastA" />
+        <param name="out_format" type="select" label="Output format" help="Default is delta format. Use sam-long or sam-short if downstream processing is needed in Galaxy">
+            <option value="delta">Use default</option>
+            <option value="--sam-short sam.out">Sam short format output</option>
+            <option value="--sam-long sam.out" >Sam long format output</option>
+        </param>
         <param name="anchoring" type="select" label="Anchoring" help="Choose a match anchoring strategy">
             <option value="">Use default</option>
             <option value="--mum">Unique matches only (--mum)</option>
             <option value="--maxmatch">All matches (--maxmatch)</option>
         </param>
+
         <param name="breaklen" type="integer" argument="-b" value="200" label="Break Length"
             help="Set the distance an alignment extension will attempt to extend poor scoring regions before giving up. (-b)" />
         <param name="mincluster" type="integer" argument="-c" value="65" label="Minumum Cluster Length" help="Sets the minimum length of a cluster of matches. (-c)" />
@@ -76,7 +85,7 @@
             help="Set the maximum diagonal difference between two adjacent anchors in a cluster. (-D)" />
         <param name="diagfactor" type="float" argument="-d" value="0.12" label="Maximum Diagonal Difference"
             help="Set the maximum diagonal difference between two adjacent anchors in a cluster as a differential fraction of the gap length. (-d)" />
-        <param name="noextend" type="boolean" argument="--noextend" truevalue="--noextend" falsevalue="" label="No Extend" help="Do not perform cluster extension step. (--noextend)" />
+        <param type="boolean" argument="--noextend" truevalue="--noextend" falsevalue="" label="No Extend" help="Do not perform cluster extension step. (--noextend)" />
         <param name="direction" type="select" label="Direction" help="Choose a direction of Query Sequence to Use">
             <option value="">Use foward and reverse sequences</option>
             <option value="-f">Use only forward sequence of query (-f)</option>
@@ -85,9 +94,9 @@
         <param name="maxgap" type="integer" argument="-g" value="90" label="Maximum Gap Distance" help="Set the maximum gap between two adjacent matches in a cluster. (-g)" />
         <param name="minmatch" type="integer" argument="-l" value="20" label="Minimum Match Length" help="Set the minimum length of a single exact match. (-l)" />
         <param name="minalign" type="integer" argument="-L" value="0" label="Minumum Alignment Length" help="Minimum length of an alignment, after clustering and extension. (-L)" />
-        <param name="nooptimize" type="boolean" argument="--nooptimize" truevalue="--nooptimize" falsevalue="" label="No Alignment Score Optimization"
+        <param type="boolean" argument="--nooptimize" truevalue="--nooptimize" falsevalue="" label="No Alignment Score Optimization"
             help="No alignment score optimization, i.e. if an alignment extension reaches the end of a sequence, it will not backtrack to optimize the alignment score and instead terminate the alignment at the end of the sequence. (--nooptimize)" />
-        <param name="nosimplify" type="boolean" argument="--nosimplify" truevalue="--nosimplify" falsevalue="" label="Don't Simplify Alignments"
+        <param type="boolean" argument="--nosimplify" truevalue="--nosimplify" falsevalue="" label="Don't Simplify Alignments"
             help="Don't simplify alignments by removing shadowed clusters. Use this option when aligning a sequence to itself to look for repeats. (--nosimplify)" />
         <conditional name="options">
             <param name="advanced" type="select" label="Additional options">
@@ -95,16 +104,16 @@
                 <option value="enable">Select additional options</option>
             </param>
             <when value="enable">
-                <param name="banded" type="boolean" argument="--banded" truevalue="--banded" falsevalue="" label="Banding"
+                <param type="boolean" argument="--banded" truevalue="--banded" falsevalue="" label="Banding"
                     help="Enforce absolute banding of dynamic programming matrix based on diagdiff parameter. (--banded)" />
-                <param name="large" type="boolean" argument="--large" truevalue="--large" falsevalue="" label="Offsets" help="Force the use of large offsets. (--large)" />
+                <param  type="boolean" argument="--large" truevalue="--large" falsevalue="" label="Offsets" help="Force the use of large offsets. (--large)" />
                 <param name="genome" type="boolean" argument="-G" truevalue="-G" falsevalue="" label="Map genome to genome" help="For long query sequences. (-G)" />
                 <param name="max_chunk" type="integer" argument="-M" value="50000" label="Max Chunk" help="Stop adding sequence for a thread if more than MAX already. (-M)" />
             </when>
             <when value="defaults" />
         </conditional>
         <conditional name="mumplot" >
-            <param name="plot" type="select" label="Do you want to output a 2-D dotplot of the input sequences? (mummerplot)" >
+            <param name="plot" type="select" label="If output file is in delta (not sam) format, make a 2-D dotplot of the input sequences? (mummerplot)" >
                 <option value="yes">YES</option>
                 <option value="no">NO</option>
             </param>
@@ -118,7 +127,7 @@
                         <when value="yes">
                             <param name="reference_sequence" type="data" format="fasta" label="Reference Sequence" help="(-R)" />
                             <param name="query_sequence" type="data" format="fasta" multiple="True" label="Query Sequence(s)" help="(-Q)" />
-                            <param name="layout" type="boolean" argument="--layout" truevalue="--layout" falsevalue="" label="Layout" help="Layout a .delta multiplot in an intelligible fashion. (--layout)" />
+                            <param type="boolean" argument="--layout" truevalue="--layout" falsevalue="" label="Layout" help="Layout a .delta multiplot in an intelligible fashion. (--layout)" />
                         </when>
                         <when value="no" />
                     </conditional>
@@ -128,14 +137,20 @@
         </conditional>
     </inputs>
     <outputs>
-        <data name="delta_output" format="tabular" from_work_dir="out.delta" label="${tool.name} on ${on_string}: alignment" />
+        <data name="delta_output" format="tabular" from_work_dir="out.delta" label="${tool.name} on ${on_string}: delta format">
+           <filter>out_format == "delta"</filter>
+        </data>
+        <data name="sam_output" format="sam" from_work_dir="out.sam" label="${tool.name} on ${on_string}: sam">
+           <filter>out_format != "delta"</filter>
+        </data>
         <data name="png_output" format="png" from_work_dir="out.png" label="${tool.name} on ${on_string}: plot" >
             <filter>mumplot['plot'] == 'yes'</filter>
         </data>
     </outputs>
     <tests>
-        <test>
+        <test expect_num_outputs="2">
             <param name="advanced" value="defaults" />
+            <param name="out_format" value="delta" />
             <param name="plot" value="yes" />
             <param name="seq_input" value="yes" />
             <param name="reference_sequence" ftype="fasta" value="human_aqp3.fasta"/>
@@ -143,6 +158,16 @@
             <output name="delta_output" ftype="tabular" compare="diff" lines_diff="2" value="nucmer.txt"/>
             <output name="png_output" ftype="png" compare="sim_size" value="plot.png" />
         </test>
+       <test expect_num_outputs="2">
+            <param name="advanced" value="defaults" />
+            <param name="out_format" value="--sam-short sam.out" />
+            <param name="plot" value="yes" />
+            <param name="seq_input" value="yes" />
+            <param name="reference_sequence" ftype="fasta" value="human_aqp3.fasta"/>
+            <param name="query_sequence" ftype="fasta" value="mouse_aqp3.fasta" />
+            <output name="png_output" ftype="png" compare="sim_size" value="plot.png" />
+           <output name="sam_output" ftype="sam" compare="sim_size" value="out.sam" />
+        </test>
     </tests>
     <help><![CDATA[
         nucmer is for the all-vs-all comparison of nucleotide sequences contained in multi-FastA data files. It is best used for highly similar sequence that may have large rearrangements. Common use cases are: comparing two unfinished shotgun sequencing assemblies, mapping an unfinished sequencing assembly to a finished genome, and comparing two fairly similar genomes that may have large rearrangements and duplications.
@@ -159,14 +184,14 @@
 
     --maxmatch        Use all anchor matches regardless of their uniqueness (false)
 
-    -b                Set the distance an alignment extension will attempt to extend poor scoring regions 
+    -b                Set the distance an alignment extension will attempt to extend poor scoring regions
                       before giving up (200)
 
     -c                Sets the minimum length of a cluster of matches (65)
 
     -D                Set the maximum diagonal difference between two adjacent anchors in a cluster (5)
 
-    -d                Set the maximum diagonal difference between two adjacent anchors in a cluster as a 
+    -d                Set the maximum diagonal difference between two adjacent anchors in a cluster as a
                       differential fraction of the gap length (0.12)
 
     --noextend        Do not perform cluster extension step (false)
@@ -181,7 +206,7 @@
 
     -L                Minimum length of an alignment, after clustering and extension (0)
 
-    --nooptimize      No alignment score optimization, i.e. if an alignment extension reaches the end of a 
+    --nooptimize      No alignment score optimization, i.e. if an alignment extension reaches the end of a
                       sequence, it will not backtrack to optimize the alignment score and instead terminate
                       the alignment at the end of the sequence (false)
 
@@ -198,16 +223,16 @@
 
     mummerplot
 
-    -b             Highlight alignments with breakpoints further than breaklen nucleotides from the nearest 
+    -b             Highlight alignments with breakpoints further than breaklen nucleotides from the nearest
                    sequence end
 
-    -color         Color plot lines with a percent similarity gradient or turn off all plot color (default 
-                   color by match dir) If the plot is very sparse, edit the .gp script to plot with 
+    -color         Color plot lines with a percent similarity gradient or turn off all plot color (default
+                   color by match dir) If the plot is very sparse, edit the .gp script to plot with
                    'linespoints' instead of 'lines'
 
     -c             Generate a reference coverage plot (default for .tiling)
 
-    --filter       Only display .delta alignments which represent the "best" hit to any particular spot on 
+    --filter       Only display .delta alignments which represent the "best" hit to any particular spot on
                    either sequence, i.e. a one-to-one mapping of reference and query subsequences
 
     --fat          Layout sequences using fattest alignment only
diff --git a/tools/mummer4/test-data/nucmer.txt b/tools/mummer4/test-data/nucmer.txt
index 2e6a1d3d45e..110abeb36b2 100644
--- a/tools/mummer4/test-data/nucmer.txt
+++ b/tools/mummer4/test-data/nucmer.txt
@@ -1,4 +1,4 @@
-reference.fa query.fa
+/tmp/tmpb5gyjkn2/files/c/d/c/dataset_cdcbdfb5-aa15-44c0-ad6f-c6cc0ca7ec0b.dat /tmp/tmpb5gyjkn2/files/6/7/e/dataset_67e08fb5-87b5-485b-8e09-8ab8a6fa3b42.dat
 NUCMER
 >NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 6480 5460
 74 223 43 194 19 19 0
diff --git a/tools/mummer4/test-data/plot.png b/tools/mummer4/test-data/plot.png
index 16f80abaf6db03379bb72e6cba2182b5352a3c6b..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 100644
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From 3878c4d7a200d7cba447d7ec41e38ce56a854d6a Mon Sep 17 00:00:00 2001
From: fubar2 <ross.lazarus@gmail.com>
Date: Fri, 15 Mar 2024 14:39:41 +1100
Subject: [PATCH 02/27] Much pfaffing about - mummer creates malformed sam
 headers!! These need to be replaced for any conversions

---
 tools/mummer4/macros.xml           |  10 +-
 tools/mummer4/nucmer.xml           | 174 +++++++++++++++++++----------
 tools/mummer4/test-data/nucmer.txt |   2 +-
 tools/mummer4/test-data/plot.png   | Bin 0 -> 6147 bytes
 4 files changed, 122 insertions(+), 64 deletions(-)

diff --git a/tools/mummer4/macros.xml b/tools/mummer4/macros.xml
index 611ef8d8d9c..c13ee1de7e9 100644
--- a/tools/mummer4/macros.xml
+++ b/tools/mummer4/macros.xml
@@ -2,7 +2,7 @@
     <token name="@MUMMER_GNUPLOT_MANUAL@"><![CDATA[&& gnuplot < out.gp]]></token>
     <xml name="bio_tools">
         <xrefs>
-            <xref type="bio.tools">mumer4</xref>
+            <xref type="bio.tools">mummer4</xref>
         </xrefs>
     </xml>
     <xml name="citation">
@@ -10,16 +10,14 @@
             <citation type="doi">10.1371/journal.pcbi.1005944</citation>
         </citations>
     </xml>
-    <xml name="gnuplot_requirement">
-        <requirement type="package" version="5.4.1">gnuplot</requirement>
-    </xml>
     <token name="@TOOL_VERSION@">4.0.0rc1</token>
-    <token name="@VERSION_SUFFIX@">2</token>
+    <token name="@VERSION_SUFFIX@">1</token>
     <token name="@PROFILE@">20.05</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">mummer4</requirement>
-            <yield />
+            <requirement type="package" version="5.4.8">gnuplot</requirement>
+            <requirement type="package" version="1.19.2">samtools</requirement>
         </requirements>
     </xml>
     <xml name="mumplot_input" >
diff --git a/tools/mummer4/nucmer.xml b/tools/mummer4/nucmer.xml
index 03f16403d75..805fff4d83a 100644
--- a/tools/mummer4/nucmer.xml
+++ b/tools/mummer4/nucmer.xml
@@ -5,7 +5,6 @@
     </macros>
     <expand macro="bio_tools"/>
     <expand macro="requirements">
-        <expand macro="gnuplot_requirement"/>
     </expand>
     <command detect_errors="exit_code">
         <![CDATA[
@@ -13,8 +12,12 @@
         ln -s $query_sequence query.fa &&
         nucmer
             $anchoring
-            #if $out_format != "delta":
-                  $out_format
+            #if $outform.out_format != "delta":
+                #if $outform.makeshort == "1":
+                    --sam-short=outsam.sam
+                #else:
+                    --sam-long=outsam.sam
+                #end if
             #end if
             -b '$breaklen'
             -c '$mincluster'
@@ -35,44 +38,110 @@
                 -M '$options.max_chunk'
             #end if
             'reference.fa' 'query.fa'
-            #if $mumplot.plot == 'yes' and $out_format == "delta":
+            #if $outform.out_format == "delta":
+               #if $mumplot.plot == 'yes' :
                 && mummerplot
-                    #if $mumplot.sequences.seq_input == 'yes':
+                    #if $outform.mumplot.sequences.seq_input == 'yes':
                         -R '$reference_sequence'
                         -Q '$query_sequence'
-                        $mumplot.sequences.layout
+                        $outform.mumplot.sequences.layout
                     #end if
-                    -b '$mumplot.breaklen'
-                    $mumplot.color
-                    $mumplot.coverage
-                    $mumplot.filter
-                    $mumplot.fat
-                    #if $mumplot.labels.IDs == 'yes':
-                        -IdR '$mumplot.labels.ref_id'
-                        -IdQ '$mumplot.labels.query_id'
+                    -b '$outform.mumplot.breaklen'
+                    $outform.mumplot.color
+                    $outform.mumplot.coverage
+                    $outform.mumplot.filter
+                    $outform.mumplot.fat
+                    #if $outform.mumplot.labels.IDs == 'yes':
+                        -IdR '$outform.mumplot.labels.ref_id'
+                        -IdQ '$outform.mumplot.labels.query_id'
                     #end if
-                    -s '$mumplot.size'
+                    -s '$outform.mumplot.size'
                     -terminal png
-                    -title '$mumplot.title'
-                    $mumplot.snp
-                    #if $mumplot.range.custom == 'yes':
-                        -x [$mumplot.range.min_x:$mumplot.range.max_x]
-                        -y [$mumplot.range.min_y:$mumplot.range.max_y]
+                    -title '$outform.mumplot.title'
+                    $outform.mumplot.snp
+                    #if $outform.mumplot.range.custom == 'yes':
+                        -x [$outform.mumplot.range.min_x:$outform.mumplot.range.max_x]
+                        -y [$outform.mumplot.range.min_y:$outform.mumplot.range.max_y]
                     #end if
                     'out.delta'
                     @MUMMER_GNUPLOT_MANUAL@
+                #end if
+            #else:
+                && tail  -n +3 outsam.sam > outsambody
+                && samtools dict reference.fa > outsamhead
+                && cat outsambody >> outsamhead
+                #if $outform.out_format in ['bam-short', 'bam-long']:
+                    && samtools view -b -o bam_out.bam outsamhead
+                    && samtools sort bam_out.bam -o outsam
+                    && samtools index outsam
+                #else if $outform.out_format in ['cram-short', 'cram-long']:
+                    && samtools view -C -o cram_out.cram  -T reference.fa  outsamhead && mv cram_out.cram outsam
+                    && samtools index outsam
+                #else
+                   && mv outsamhead outsam
+                #end if
             #end if
         ]]>
     </command>
     <inputs>
         <param name="reference_sequence" type="data" format="fasta" label="Reference Sequence" help="FastA or multi-FastA" />
         <param name="query_sequence" type="data" format="fasta" label="Query Sequence" help="FastA or multi-FastA" />
-        <param name="out_format" type="select" label="Output format" help="Default is delta format. Use sam-long or sam-short if downstream processing is needed in Galaxy">
-            <option value="delta">Use default</option>
-            <option value="--sam-short sam.out">Sam short format output</option>
-            <option value="--sam-long sam.out" >Sam long format output</option>
-        </param>
-        <param name="anchoring" type="select" label="Anchoring" help="Choose a match anchoring strategy">
+        <conditional name="outform">
+            <param name="out_format" type="select" label="Output format" help="Default is delta format. Use sam-long or sam-short if downstream processing is needed in Galaxy">
+            <option value="delta">Default Mummer delta format - allows plots</option>
+            <option value="sam-short">Sam short format</option>
+            <option value="sam-long" >Sam long format</option>
+            <option value="bam-short">Sam short as bam format</option>
+            <option value="bam-long" >Sam long as bam format</option>
+            <option value="cram-short">Sam short as cram format</option>
+            <option value="cram-long" >Sam long as cram format</option>
+            </param>
+            <when value="delta">
+                <param name="makeshort" type="hidden" value="False" />
+               <conditional name="mumplot" >
+                    <param name="plot" type="select" label="If output file is in delta (not sam) format, make a 2-D dotplot of the input sequences? (mummerplot)" >
+                        <option value="no">No plot</option>
+                        <option value="yes">Plot</option>
+                    </param>
+                    <when value="yes" >
+                        <expand macro="mumplot_input" >
+                            <conditional name="sequences" >
+                                <param name="seq_input" type="select" label="Plot an ordered set of reference/query sequences?" >
+                                    <option value="no">NO</option>
+                                    <option value="yes">YES</option>
+                                </param>
+                                <when value="yes">
+                                    <param name="reference_sequence" type="data" format="fasta" label="Reference Sequence" help="(-R)" />
+                                    <param name="query_sequence" type="data" format="fasta" multiple="True" label="Query Sequence(s)" help="(-Q)" />
+                                    <param type="boolean" argument="--layout" truevalue="--layout" falsevalue="" label="Layout" help="Layout a .delta multiplot in an intelligible fashion. (--layout)" />
+                                </when>
+                                <when value="no" />
+                            </conditional>
+                        </expand>
+                    </when>
+                    <when value="no" />
+                </conditional>
+            </when>
+            <when value="sam-short">
+                <param name="makeshort" type="hidden" value="1" />
+            </when>
+            <when value="sam-long">
+                <param name="makeshort" type="hidden" value="0" />
+            </when>
+            <when value="bam-short">
+                <param name="makeshort" type="hidden" value="1" />
+            </when>
+            <when value="bam-long">
+                <param name="shortsam" type="hidden" value="0" />
+            </when>
+            <when value="cram-short">
+                <param name="makeshort" type="hidden" value="1" />
+            </when>
+            <when value="cram-long">
+                <param name="makeshort" type="hidden" value="0" />
+            </when>
+        </conditional>
+         <param name="anchoring" type="select" label="Anchoring" help="Choose a match anchoring strategy">
             <option value="">Use default</option>
             <option value="--mum">Unique matches only (--mum)</option>
             <option value="--maxmatch">All matches (--maxmatch)</option>
@@ -112,39 +181,22 @@
             </when>
             <when value="defaults" />
         </conditional>
-        <conditional name="mumplot" >
-            <param name="plot" type="select" label="If output file is in delta (not sam) format, make a 2-D dotplot of the input sequences? (mummerplot)" >
-                <option value="yes">YES</option>
-                <option value="no">NO</option>
-            </param>
-            <when value="yes" >
-                <expand macro="mumplot_input" >
-                    <conditional name="sequences" >
-                        <param name="seq_input" type="select" label="Plot an ordered set of reference/query sequences?" >
-                            <option value="no">NO</option>
-                            <option value="yes">YES</option>
-                        </param>
-                        <when value="yes">
-                            <param name="reference_sequence" type="data" format="fasta" label="Reference Sequence" help="(-R)" />
-                            <param name="query_sequence" type="data" format="fasta" multiple="True" label="Query Sequence(s)" help="(-Q)" />
-                            <param type="boolean" argument="--layout" truevalue="--layout" falsevalue="" label="Layout" help="Layout a .delta multiplot in an intelligible fashion. (--layout)" />
-                        </when>
-                        <when value="no" />
-                    </conditional>
-                </expand>
-            </when>
-            <when value="no" />
-        </conditional>
     </inputs>
     <outputs>
         <data name="delta_output" format="tabular" from_work_dir="out.delta" label="${tool.name} on ${on_string}: delta format">
-           <filter>out_format == "delta"</filter>
+           <filter>outform["out_format"] == "delta"</filter>
         </data>
-        <data name="sam_output" format="sam" from_work_dir="out.sam" label="${tool.name} on ${on_string}: sam">
-           <filter>out_format != "delta"</filter>
+        <data name="sam_output" format="sam" from_work_dir="outsam"  label="${tool.name} on ${on_string}">
+           <filter>outform["out_format"] != "delta"</filter>
+           <change_format>
+                <when input="outform.out_format" value="bam-short" format="bam" />
+                <when input="outform.out_format" value="bam-long" format="bam" />
+                <when input="outform.out_format" value="cram-short" format="cram" />
+                <when input="outform.out_format" value="cram-long" format="cram" />
+           </change_format>
         </data>
         <data name="png_output" format="png" from_work_dir="out.png" label="${tool.name} on ${on_string}: plot" >
-            <filter>mumplot['plot'] == 'yes'</filter>
+            <filter>outform["out_format"] == "delta" and outform['mumplot']['plot'] == 'yes'</filter>
         </data>
     </outputs>
     <tests>
@@ -160,13 +212,21 @@
         </test>
        <test expect_num_outputs="2">
             <param name="advanced" value="defaults" />
-            <param name="out_format" value="--sam-short sam.out" />
-            <param name="plot" value="yes" />
+            <param name="out_format" value="bam_short" />
+            <param name="plot" value="no" />
             <param name="seq_input" value="yes" />
             <param name="reference_sequence" ftype="fasta" value="human_aqp3.fasta"/>
             <param name="query_sequence" ftype="fasta" value="mouse_aqp3.fasta" />
-            <output name="png_output" ftype="png" compare="sim_size" value="plot.png" />
-           <output name="sam_output" ftype="sam" compare="sim_size" value="out.sam" />
+           <output name="sam_output" ftype="bam" compare="sim_size" value="out.bam" />
+        </test>
+        <test expect_num_outputs="2">
+            <param name="advanced" value="defaults" />
+            <param name="out_format" value="cram_short" />
+            <param name="plot" value="no" />
+            <param name="seq_input" value="yes" />
+            <param name="reference_sequence" ftype="fasta" value="human_aqp3.fasta"/>
+            <param name="query_sequence" ftype="fasta" value="mouse_aqp3.fasta" />
+           <output name="sam_output" ftype="cram" compare="sim_size" value="out.cram" />
         </test>
     </tests>
     <help><![CDATA[
diff --git a/tools/mummer4/test-data/nucmer.txt b/tools/mummer4/test-data/nucmer.txt
index 110abeb36b2..a1e3a06be2c 100644
--- a/tools/mummer4/test-data/nucmer.txt
+++ b/tools/mummer4/test-data/nucmer.txt
@@ -1,4 +1,4 @@
-/tmp/tmpb5gyjkn2/files/c/d/c/dataset_cdcbdfb5-aa15-44c0-ad6f-c6cc0ca7ec0b.dat /tmp/tmpb5gyjkn2/files/6/7/e/dataset_67e08fb5-87b5-485b-8e09-8ab8a6fa3b42.dat
+/tmp/tmppews9qic/files/f/4/6/dataset_f46ded9e-52fb-4c4c-8e30-0e2765387c49.dat /tmp/tmppews9qic/files/2/5/1/dataset_25144f20-49a3-462c-9254-7c7a55cb192f.dat
 NUCMER
 >NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 6480 5460
 74 223 43 194 19 19 0
diff --git a/tools/mummer4/test-data/plot.png b/tools/mummer4/test-data/plot.png
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..16f80abaf6db03379bb72e6cba2182b5352a3c6b 100644
GIT binary patch
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z<M+nC9!xbap40Cxr;Wu9RJA-gWkdYqx!v?J0@b&JFoT)exyNH)8)$c@C1(;WPg;i9
zNSp5Zz@!Ez*_VqkQxC&Eo(BFjW>;&zX0`7D#)u<71QNUp4?<LLQ31XKd_3zRKAR?*
zKUIgokBNeY-k0)6@cc>#xTjDo7KkT%&_vxKyUbXJ<K<k7@d$^+l#~~I2d4gG;UkN7
z#5|rlGjiiVk0}CQo7x-d4qj<YRf56I5Y!QE(}5P(p_US&D`<SHvS^)H*a^18-dHpL
zn-=|oaI#M_Hyf*deR7C5&Ym2<&f~Q?MA0e{p8KG)DGP+&TqELlE=+WKukehm$C^%V
r<Kg+)Z?MI$$J?D2R<Q87ZALF*&x;sfW4a4;Obz&X`(rCMho=1-Llq@G

literal 0
HcmV?d00001


From 0097f343d6c72d8fb13fa9d0bd836d5cfef9acf4 Mon Sep 17 00:00:00 2001
From: fubar2 <ross.lazarus@gmail.com>
Date: Fri, 15 Mar 2024 15:05:20 +1100
Subject: [PATCH 03/27] conditional added to tests - passing now

---
 tools/mummer4/nucmer.xml           | 20 +++++++++++++-------
 tools/mummer4/test-data/nucmer.txt |  2 +-
 2 files changed, 14 insertions(+), 8 deletions(-)

diff --git a/tools/mummer4/nucmer.xml b/tools/mummer4/nucmer.xml
index 805fff4d83a..cd7174ac92b 100644
--- a/tools/mummer4/nucmer.xml
+++ b/tools/mummer4/nucmer.xml
@@ -202,7 +202,9 @@
     <tests>
         <test expect_num_outputs="2">
             <param name="advanced" value="defaults" />
-            <param name="out_format" value="delta" />
+            <conditional name="outform">
+                <param name="out_format" value="delta" />
+            </conditional>
             <param name="plot" value="yes" />
             <param name="seq_input" value="yes" />
             <param name="reference_sequence" ftype="fasta" value="human_aqp3.fasta"/>
@@ -210,19 +212,23 @@
             <output name="delta_output" ftype="tabular" compare="diff" lines_diff="2" value="nucmer.txt"/>
             <output name="png_output" ftype="png" compare="sim_size" value="plot.png" />
         </test>
-       <test expect_num_outputs="2">
+       <test expect_num_outputs="1">
             <param name="advanced" value="defaults" />
-            <param name="out_format" value="bam_short" />
-            <param name="plot" value="no" />
+            <param name="makeshort" value="1" />
+            <conditional name="outform">
+                <param name="out_format" value="bam-short" />
+            </conditional>
             <param name="seq_input" value="yes" />
             <param name="reference_sequence" ftype="fasta" value="human_aqp3.fasta"/>
             <param name="query_sequence" ftype="fasta" value="mouse_aqp3.fasta" />
            <output name="sam_output" ftype="bam" compare="sim_size" value="out.bam" />
         </test>
-        <test expect_num_outputs="2">
+        <test expect_num_outputs="1">
             <param name="advanced" value="defaults" />
-            <param name="out_format" value="cram_short" />
-            <param name="plot" value="no" />
+            <param name="makeshort" value="0" />
+            <conditional name="outform">
+                <param name="out_format" value="cram-long" />
+            </conditional>
             <param name="seq_input" value="yes" />
             <param name="reference_sequence" ftype="fasta" value="human_aqp3.fasta"/>
             <param name="query_sequence" ftype="fasta" value="mouse_aqp3.fasta" />
diff --git a/tools/mummer4/test-data/nucmer.txt b/tools/mummer4/test-data/nucmer.txt
index a1e3a06be2c..eae530ab476 100644
--- a/tools/mummer4/test-data/nucmer.txt
+++ b/tools/mummer4/test-data/nucmer.txt
@@ -1,4 +1,4 @@
-/tmp/tmppews9qic/files/f/4/6/dataset_f46ded9e-52fb-4c4c-8e30-0e2765387c49.dat /tmp/tmppews9qic/files/2/5/1/dataset_25144f20-49a3-462c-9254-7c7a55cb192f.dat
+/tmp/tmptxadxefw/files/e/6/5/dataset_e65143c6-5d0d-4b39-a3bb-803a153e03c1.dat /tmp/tmptxadxefw/files/a/d/5/dataset_ad5ab542-3f9f-4286-9025-94e9a55c878e.dat
 NUCMER
 >NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 6480 5460
 74 223 43 194 19 19 0

From 7e8a1eff8bdb08184c0c398d5fd4a898dc9a44b9 Mon Sep 17 00:00:00 2001
From: fubar2 <ross.lazarus@gmail.com>
Date: Fri, 15 Mar 2024 15:10:03 +1100
Subject: [PATCH 04/27] bump version prefix - same mummer4 conda from 4 years
 ago :(

---
 tools/mummer4/macros.xml           | 2 +-
 tools/mummer4/test-data/nucmer.txt | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/tools/mummer4/macros.xml b/tools/mummer4/macros.xml
index c13ee1de7e9..b3505cf7396 100644
--- a/tools/mummer4/macros.xml
+++ b/tools/mummer4/macros.xml
@@ -11,7 +11,7 @@
         </citations>
     </xml>
     <token name="@TOOL_VERSION@">4.0.0rc1</token>
-    <token name="@VERSION_SUFFIX@">1</token>
+    <token name="@VERSION_SUFFIX@">3</token>
     <token name="@PROFILE@">20.05</token>
     <xml name="requirements">
         <requirements>
diff --git a/tools/mummer4/test-data/nucmer.txt b/tools/mummer4/test-data/nucmer.txt
index eae530ab476..790940e3c9f 100644
--- a/tools/mummer4/test-data/nucmer.txt
+++ b/tools/mummer4/test-data/nucmer.txt
@@ -1,4 +1,4 @@
-/tmp/tmptxadxefw/files/e/6/5/dataset_e65143c6-5d0d-4b39-a3bb-803a153e03c1.dat /tmp/tmptxadxefw/files/a/d/5/dataset_ad5ab542-3f9f-4286-9025-94e9a55c878e.dat
+/tmp/tmpc2brs3qy/files/6/4/a/dataset_64a5193b-2c86-4944-b9b2-57de4d931c91.dat /tmp/tmpc2brs3qy/files/4/0/3/dataset_40346e9e-472b-47a5-a06d-b658657af917.dat
 NUCMER
 >NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 6480 5460
 74 223 43 194 19 19 0

From ba002ad8192db965b5adfbea29bd92b75f8edb75 Mon Sep 17 00:00:00 2001
From: fubar2 <ross.lazarus@gmail.com>
Date: Fri, 15 Mar 2024 15:26:23 +1100
Subject: [PATCH 05/27] add all test data and fix old warts in other modules...

---
 tools/mummer4/dnadiff.xml          |   6 ++--
 tools/mummer4/mummer.xml           |  18 +++++------
 tools/mummer4/mummerplot.xml       |  12 ++++----
 tools/mummer4/test-data/1delta.txt |   2 +-
 tools/mummer4/test-data/delta.txt  |   2 +-
 tools/mummer4/test-data/mdelta.txt |   2 +-
 tools/mummer4/test-data/out.bam    | Bin 0 -> 479 bytes
 tools/mummer4/test-data/out.cram   | Bin 0 -> 2679 bytes
 tools/mummer4/test-data/out.sam    |   0
 tools/mummer4/test-data/report.txt |  48 ++++++++++++++---------------
 10 files changed, 45 insertions(+), 45 deletions(-)
 create mode 100644 tools/mummer4/test-data/out.bam
 create mode 100644 tools/mummer4/test-data/out.cram
 create mode 100644 tools/mummer4/test-data/out.sam

diff --git a/tools/mummer4/dnadiff.xml b/tools/mummer4/dnadiff.xml
index bb3413515e6..aa1422d24d2 100755
--- a/tools/mummer4/dnadiff.xml
+++ b/tools/mummer4/dnadiff.xml
@@ -12,7 +12,7 @@
         dnadiff
             'reference.fa' 'query.fa'
 
-        ]]>  
+        ]]>
     </command>
     <inputs>
         <param name="reference_sequence" type="data" format="fasta" label="Reference Sequence" help="FastA or multi-FastA" />
@@ -48,7 +48,7 @@
         <data name="snps" format="tabular" from_work_dir="out.snps" label="${tool.name} on ${on_string}: snps" >
             <filter> report_only == 'no' </filter>
             <actions>
-            	<action name="column_names" type="metadata" default="[P1], [REF SUB], [QUERY SUB], [P2], [BUFF], [DIST], [LEN REF], [LEN QUERY], [REF FRAME], [QUERY FRAME], [REF TAG], [QUERY TAG]" />
+                <action name="column_names" type="metadata" default="[P1], [REF SUB], [QUERY SUB], [P2], [BUFF], [DIST], [LEN REF], [LEN QUERY], [REF FRAME], [QUERY FRAME], [REF TAG], [QUERY TAG]" />
             </actions>
         </data>
         <data name="rdiff" format="tabular" from_work_dir="out.rdiff" label="${tool.name} on ${on_string}: rdiff" >
@@ -65,7 +65,7 @@
         </data>
     </outputs>
     <tests>
-        <test>
+        <test  expect_num_outputs="9">
             <param name="reference_sequence" ftype="fasta" value="human_aqp3.fasta" />
             <param name="query_sequence" ftype="fasta" value="mouse_aqp3.fasta"/>
             <param name="report_only" value="no" />
diff --git a/tools/mummer4/mummer.xml b/tools/mummer4/mummer.xml
index 9c284d9c84b..4fa2baef911 100755
--- a/tools/mummer4/mummer.xml
+++ b/tools/mummer4/mummer.xml
@@ -9,7 +9,7 @@
     </expand>
     <command detect_errors="exit_code">
         <![CDATA[
-        mummer 
+        mummer
             $anchoring
             -l '$min'
             $direction
@@ -87,9 +87,9 @@
                     <option value="0">No</option>
                     <option value="1">Yes</option>
                 </param>
-                <param name="skip" type="integer" argument="-skip" value="10" label="Sparsify"
+                <param  type="integer" argument="-skip" value="10" label="Sparsify"
                     help="Sparsify the MEM-finding algorithm even more, performing jumps of skip*k [auto (l-10)/k]. (-skip)" />
-                <param name="kmer" type="integer" argument="-kmer" value="1" label="kmer Table"
+                <param  type="integer" argument="-kmer" value="1" label="kmer Table"
                     help="Use kmer table containing sa-intervals (speeds up searching first k characters) in the index and during search. (-kmer)" />
             </when>
             <when value="defaults" />
@@ -112,7 +112,7 @@
         </data>
     </outputs>
     <tests>
-        <test>
+        <test  expect_num_outputs="2">
             <param name="reference_sequence" ftype="fasta" value="human_aqp3.fasta" />
             <param name="query_sequence" ftype="fasta" value="mouse_aqp3.fasta" />
             <param name="options|advanced" value="defaults" />
@@ -128,7 +128,7 @@
 
     mummer
 
-    -mumreference    Compute maximal matches that are unique in the reference- sequence but not 
+    -mumreference    Compute maximal matches that are unique in the reference- sequence but not
                      necessarily in the query-sequence (default)
 
     -maxmatch        Compute all maximal matches regardless of their uniqueness
@@ -154,16 +154,16 @@
 
     mummerplot
 
-    -b             Highlight alignments with breakpoints further than breaklen nucleotides from the nearest 
+    -b             Highlight alignments with breakpoints further than breaklen nucleotides from the nearest
                    sequence end
 
-    -color         Color plot lines with a percent similarity gradient or turn off all plot color (default 
-                   color by match dir) If the plot is very sparse, edit the .gp script to plot with 
+    -color         Color plot lines with a percent similarity gradient or turn off all plot color (default
+                   color by match dir) If the plot is very sparse, edit the .gp script to plot with
                    'linespoints' instead of 'lines'
 
     -c             Generate a reference coverage plot (default for .tiling)
 
-    --filter       Only display .delta alignments which represent the "best" hit to any particular spot on 
+    --filter       Only display .delta alignments which represent the "best" hit to any particular spot on
                    either sequence, i.e. a one-to-one mapping of reference and query subsequences
 
     --fat          Layout sequences using fattest alignment only
diff --git a/tools/mummer4/mummerplot.xml b/tools/mummer4/mummerplot.xml
index 3a0b516abee..4340e1b8d2b 100755
--- a/tools/mummer4/mummerplot.xml
+++ b/tools/mummer4/mummerplot.xml
@@ -49,7 +49,7 @@
                     <option value="yes">YES</option>
                 </param>
                 <when value="yes">
-                    <param name="layout" type="boolean" argument="--layout" truevalue="--layout" falsevalue="" label="Layout" help="Layout a .delta multiplot in an intelligible fashion. (--layout)" />
+                    <param  type="boolean" argument="--layout" truevalue="--layout" falsevalue="" label="Layout" help="Layout a .delta multiplot in an intelligible fashion. (--layout)" />
                 </when>
                 <when value="no" />
             </conditional>
@@ -75,7 +75,7 @@
         <data name="output_png" format="png" from_work_dir="out.png" label="${tool.name} on ${on_string}: plot" />
     </outputs>
     <tests>
-        <test>
+        <test  expect_num_outputs="5">
             <param name="delta" value="nucmer.txt" ftype="tabular" />
             <param name="reference_sequence" ftype="fasta" value="human_aqp3.fasta" />
             <param name="query_sequence" ftype="fasta" value="mouse_aqp3.fasta" />
@@ -99,16 +99,16 @@ Mummerplot is a perl script that generates gnuplot scripts and data collections
 **Options:**::
 
 
-    -b             Highlight alignments with breakpoints further than breaklen nucleotides from the nearest 
+    -b             Highlight alignments with breakpoints further than breaklen nucleotides from the nearest
                    sequence end
 
-    -color         Color plot lines with a percent similarity gradient or turn off all plot color (default 
-                   color by match dir) If the plot is very sparse, edit the .gp script to plot with 
+    -color         Color plot lines with a percent similarity gradient or turn off all plot color (default
+                   color by match dir) If the plot is very sparse, edit the .gp script to plot with
                    'linespoints' instead of 'lines'
 
     -c             Generate a reference coverage plot (default for .tiling)
 
-    --filter       Only display .delta alignments which represent the "best" hit to any particular spot on 
+    --filter       Only display .delta alignments which represent the "best" hit to any particular spot on
                    either sequence, i.e. a one-to-one mapping of reference and query subsequences
 
     --fat          Layout sequences using fattest alignment only
diff --git a/tools/mummer4/test-data/1delta.txt b/tools/mummer4/test-data/1delta.txt
index b146c49d5bf..9e84f82ea55 100644
--- a/tools/mummer4/test-data/1delta.txt
+++ b/tools/mummer4/test-data/1delta.txt
@@ -1,4 +1,4 @@
-/tmp/tmpm1aw7z9b/files/6/1/9/dataset_619c747c-cdb5-4d85-adda-e0ec5f7fa2fe.dat /tmp/tmpm1aw7z9b/files/f/e/c/dataset_fec4ecfe-55bb-4ff9-86e1-292952d00dd1.dat
+/tmp/tmpmprg208i/files/f/1/b/dataset_f1b7734e-9d42-4c7c-9775-5f18da934854.dat /tmp/tmpmprg208i/files/6/f/5/dataset_6f561e62-f409-4d5b-9469-6080685d3666.dat
 NUCMER
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 74 223 43 194 19 19 0
diff --git a/tools/mummer4/test-data/delta.txt b/tools/mummer4/test-data/delta.txt
index b146c49d5bf..9e84f82ea55 100644
--- a/tools/mummer4/test-data/delta.txt
+++ b/tools/mummer4/test-data/delta.txt
@@ -1,4 +1,4 @@
-/tmp/tmpm1aw7z9b/files/6/1/9/dataset_619c747c-cdb5-4d85-adda-e0ec5f7fa2fe.dat /tmp/tmpm1aw7z9b/files/f/e/c/dataset_fec4ecfe-55bb-4ff9-86e1-292952d00dd1.dat
+/tmp/tmpmprg208i/files/f/1/b/dataset_f1b7734e-9d42-4c7c-9775-5f18da934854.dat /tmp/tmpmprg208i/files/6/f/5/dataset_6f561e62-f409-4d5b-9469-6080685d3666.dat
 NUCMER
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diff --git a/tools/mummer4/test-data/mdelta.txt b/tools/mummer4/test-data/mdelta.txt
index b146c49d5bf..9e84f82ea55 100644
--- a/tools/mummer4/test-data/mdelta.txt
+++ b/tools/mummer4/test-data/mdelta.txt
@@ -1,4 +1,4 @@
-/tmp/tmpm1aw7z9b/files/6/1/9/dataset_619c747c-cdb5-4d85-adda-e0ec5f7fa2fe.dat /tmp/tmpm1aw7z9b/files/f/e/c/dataset_fec4ecfe-55bb-4ff9-86e1-292952d00dd1.dat
+/tmp/tmpmprg208i/files/f/1/b/dataset_f1b7734e-9d42-4c7c-9775-5f18da934854.dat /tmp/tmpmprg208i/files/6/f/5/dataset_6f561e62-f409-4d5b-9469-6080685d3666.dat
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diff --git a/tools/mummer4/test-data/out.bam b/tools/mummer4/test-data/out.bam
new file mode 100644
index 0000000000000000000000000000000000000000..b8d1959c8fe26856219fd6876a419d9cf40e742c
GIT binary patch
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literal 0
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zL3&|$rnq}nsa~uhRz;zG@=lHN<mqXNr1p*NNT1zoudXcNtEdM9eLt-qsJukSb4;ur
z7BR$g^aB84;BYt_2!ffJ;*J0$34@W%$xA8fW)LK$MgSC8aRinERB;eYV^5d{o|Bf@
zW!5^Z6Zn03?(`_=Atw9)u?aEy%iDkS>`u1=kURus9Z!_y9fJ9T(BVL&T%+{=#{kpY
zo(5_1nhrJ+bZhRvS;lus?;CR|#~+#7jqIuUl!9tFW$ckoh0&=_M|X=}Z6Tk29&30q
zx4LPdKG*4EDIfQ`J@TvVi;um*)^Z!>=Ss)vCk<(j6I0qA>!KZO!iHO`^itd|loKY$
zXB#lZqEDH}2b)RRH&@P(m64hKEG9Sch;;-D|DMw`X12IPdLRIA8M9>pJNw~N0|b`6
HLF>N&#IHFv

literal 0
HcmV?d00001

diff --git a/tools/mummer4/test-data/out.sam b/tools/mummer4/test-data/out.sam
new file mode 100644
index 00000000000..e69de29bb2d
diff --git a/tools/mummer4/test-data/report.txt b/tools/mummer4/test-data/report.txt
index 784a47d1141..94f7aadc383 100644
--- a/tools/mummer4/test-data/report.txt
+++ b/tools/mummer4/test-data/report.txt
@@ -1,4 +1,4 @@
-/tmp/tmpm1aw7z9b/files/6/1/9/dataset_619c747c-cdb5-4d85-adda-e0ec5f7fa2fe.dat /tmp/tmpm1aw7z9b/files/f/e/c/dataset_fec4ecfe-55bb-4ff9-86e1-292952d00dd1.dat
+/tmp/tmpmprg208i/files/f/1/b/dataset_f1b7734e-9d42-4c7c-9775-5f18da934854.dat /tmp/tmpmprg208i/files/6/f/5/dataset_6f561e62-f409-4d5b-9469-6080685d3666.dat
 NUCMER
 
                                [REF]                [QRY]
@@ -39,49 +39,49 @@ TandemInsAvg                  0.0000               0.0000
 
 [SNPs]
 TotalSNPs                         78                   78
+AT                        2(2.5641%)           2(2.5641%)
+AC                        6(7.6923%)           5(6.4103%)
+AG                        2(2.5641%)           5(6.4103%)
+TA                        2(2.5641%)           2(2.5641%)
 TG                        2(2.5641%)           5(6.4103%)
 TC                       9(11.5385%)         28(35.8974%)
-TA                        2(2.5641%)           2(2.5641%)
-GC                        6(7.6923%)           6(7.6923%)
-GA                        5(6.4103%)           2(2.5641%)
-GT                        5(6.4103%)           2(2.5641%)
 CT                      28(35.8974%)          9(11.5385%)
 CA                        5(6.4103%)           6(7.6923%)
 CG                        6(7.6923%)           6(7.6923%)
-AT                        2(2.5641%)           2(2.5641%)
-AG                        2(2.5641%)           5(6.4103%)
-AC                        6(7.6923%)           5(6.4103%)
+GT                        5(6.4103%)           2(2.5641%)
+GA                        5(6.4103%)           2(2.5641%)
+GC                        6(7.6923%)           6(7.6923%)
 
 TotalGSNPs                         1                    1
-TA                        0(0.0000%)           0(0.0000%)
-TG                        0(0.0000%)           0(0.0000%)
-TC                        0(0.0000%)           0(0.0000%)
-AG                        0(0.0000%)           0(0.0000%)
-AC                       1(100.0000%)           0(0.0000%)
-AT                        0(0.0000%)           0(0.0000%)
-GC                        0(0.0000%)           0(0.0000%)
-GA                        0(0.0000%)           0(0.0000%)
 GT                        0(0.0000%)           0(0.0000%)
-CT                        0(0.0000%)           0(0.0000%)
+GA                        0(0.0000%)           0(0.0000%)
+GC                        0(0.0000%)           0(0.0000%)
 CG                        0(0.0000%)           0(0.0000%)
+CT                        0(0.0000%)           0(0.0000%)
 CA                        0(0.0000%)          1(100.0000%)
+TC                        0(0.0000%)           0(0.0000%)
+TG                        0(0.0000%)           0(0.0000%)
+TA                        0(0.0000%)           0(0.0000%)
+AT                        0(0.0000%)           0(0.0000%)
+AG                        0(0.0000%)           0(0.0000%)
+AC                       1(100.0000%)           0(0.0000%)
 
 TotalIndels                       13                   13
+A.                       3(23.0769%)           0(0.0000%)
 T.                        0(0.0000%)          2(15.3846%)
-G.                       2(15.3846%)           1(7.6923%)
 C.                       5(38.4615%)           0(0.0000%)
-A.                       3(23.0769%)           0(0.0000%)
-.G                        1(7.6923%)          2(15.3846%)
-.C                        0(0.0000%)          5(38.4615%)
+G.                       2(15.3846%)           1(7.6923%)
 .A                        0(0.0000%)          3(23.0769%)
 .T                       2(15.3846%)           0(0.0000%)
+.C                        0(0.0000%)          5(38.4615%)
+.G                        1(7.6923%)          2(15.3846%)
 
 TotalGIndels                       0                    0
-T.                        0(0.0000%)           0(0.0000%)
-A.                        0(0.0000%)           0(0.0000%)
 G.                        0(0.0000%)           0(0.0000%)
 C.                        0(0.0000%)           0(0.0000%)
-.A                        0(0.0000%)           0(0.0000%)
+T.                        0(0.0000%)           0(0.0000%)
+A.                        0(0.0000%)           0(0.0000%)
 .C                        0(0.0000%)           0(0.0000%)
 .G                        0(0.0000%)           0(0.0000%)
+.A                        0(0.0000%)           0(0.0000%)
 .T                        0(0.0000%)           0(0.0000%)

From ef6345a4b18a184b504fdfefd316764f847c472e Mon Sep 17 00:00:00 2001
From: fubar2 <ross.lazarus@gmail.com>
Date: Fri, 15 Mar 2024 16:00:48 +1100
Subject: [PATCH 06/27] trying a mesa dependency for libGL

---
 tools/mummer4/macros.xml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/tools/mummer4/macros.xml b/tools/mummer4/macros.xml
index b3505cf7396..1cd81bf59fd 100644
--- a/tools/mummer4/macros.xml
+++ b/tools/mummer4/macros.xml
@@ -18,6 +18,7 @@
             <requirement type="package" version="@TOOL_VERSION@">mummer4</requirement>
             <requirement type="package" version="5.4.8">gnuplot</requirement>
             <requirement type="package" version="1.19.2">samtools</requirement>
+            <requirement type="package">mesa-libgl-devel-cos7-x86_64</requirement>
         </requirements>
     </xml>
     <xml name="mumplot_input" >

From 9a7630ce4ea6811dcc803898f9d1dab00a6bddef Mon Sep 17 00:00:00 2001
From: fubar2 <ross.lazarus@gmail.com>
Date: Fri, 15 Mar 2024 16:06:50 +1100
Subject: [PATCH 07/27] add version to libgl thingy

---
 tools/mummer4/macros.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/mummer4/macros.xml b/tools/mummer4/macros.xml
index 1cd81bf59fd..a458e4a1f32 100644
--- a/tools/mummer4/macros.xml
+++ b/tools/mummer4/macros.xml
@@ -18,7 +18,7 @@
             <requirement type="package" version="@TOOL_VERSION@">mummer4</requirement>
             <requirement type="package" version="5.4.8">gnuplot</requirement>
             <requirement type="package" version="1.19.2">samtools</requirement>
-            <requirement type="package">mesa-libgl-devel-cos7-x86_64</requirement>
+            <requirement type="package" version="18.3.4">mesa-libgl-devel-cos7-x86_64</requirement>
         </requirements>
     </xml>
     <xml name="mumplot_input" >

From 502f0f9f003d5e5065bc35951996956fb71ebd30 Mon Sep 17 00:00:00 2001
From: fubar2 <ross.lazarus@gmail.com>
Date: Fri, 15 Mar 2024 19:35:13 +1100
Subject: [PATCH 08/27] remove useless mesa test

---
 tools/mummer4/macros.xml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/tools/mummer4/macros.xml b/tools/mummer4/macros.xml
index a458e4a1f32..b3505cf7396 100644
--- a/tools/mummer4/macros.xml
+++ b/tools/mummer4/macros.xml
@@ -18,7 +18,6 @@
             <requirement type="package" version="@TOOL_VERSION@">mummer4</requirement>
             <requirement type="package" version="5.4.8">gnuplot</requirement>
             <requirement type="package" version="1.19.2">samtools</requirement>
-            <requirement type="package" version="18.3.4">mesa-libgl-devel-cos7-x86_64</requirement>
         </requirements>
     </xml>
     <xml name="mumplot_input" >

From 1c0373f51f59d5faee0fbc5cc1f603b7b45d56de Mon Sep 17 00:00:00 2001
From: fubar2 <ross.lazarus@gmail.com>
Date: Fri, 15 Mar 2024 19:40:19 +1100
Subject: [PATCH 09/27] restore separate gnuplot macro

---
 tools/mummer4/macros.xml | 5 ++++-
 tools/mummer4/nucmer.xml | 1 +
 2 files changed, 5 insertions(+), 1 deletion(-)

diff --git a/tools/mummer4/macros.xml b/tools/mummer4/macros.xml
index b3505cf7396..60e658c2885 100644
--- a/tools/mummer4/macros.xml
+++ b/tools/mummer4/macros.xml
@@ -13,11 +13,14 @@
     <token name="@TOOL_VERSION@">4.0.0rc1</token>
     <token name="@VERSION_SUFFIX@">3</token>
     <token name="@PROFILE@">20.05</token>
+    <xml name="gnuplot_requirement">
+        <requirement type="package" version="5.4.8">gnuplot</requirement>
+    </xml>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">mummer4</requirement>
-            <requirement type="package" version="5.4.8">gnuplot</requirement>
             <requirement type="package" version="1.19.2">samtools</requirement>
+            <yield />
         </requirements>
     </xml>
     <xml name="mumplot_input" >
diff --git a/tools/mummer4/nucmer.xml b/tools/mummer4/nucmer.xml
index cd7174ac92b..66dcbe202f2 100644
--- a/tools/mummer4/nucmer.xml
+++ b/tools/mummer4/nucmer.xml
@@ -5,6 +5,7 @@
     </macros>
     <expand macro="bio_tools"/>
     <expand macro="requirements">
+        <expand macro="gnuplot_requirement"/>
     </expand>
     <command detect_errors="exit_code">
         <![CDATA[

From 11f984cc643a24c3b61a9b6cb859c2c9a92304e2 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= <bjoern@gruenings.eu>
Date: Fri, 15 Mar 2024 10:52:29 +0100
Subject: [PATCH 10/27] fix spelling

---
 tools/mummer4/macros.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/mummer4/macros.xml b/tools/mummer4/macros.xml
index 60e658c2885..d03a61523b4 100644
--- a/tools/mummer4/macros.xml
+++ b/tools/mummer4/macros.xml
@@ -31,7 +31,7 @@
             <option value="">Color</option>
             <option value="-color">No color (-color)</option>
         </param>
-        <param name="coverage" type="select" label="Coverage Plot" help="Generate a reference coverage plot (default for .tiling) or the defualt dotplot." >
+        <param name="coverage" type="select" label="Coverage Plot" help="Generate a reference coverage plot (default for .tiling) or the default dotplot." >
             <option value="">Dotplot</option>
             <option value="-c">Coverage Plot (-c)</option>
         </param>

From e80a86bd0319860a418e9fe04fd5791bbca5f229 Mon Sep 17 00:00:00 2001
From: fubar2 <ross.lazarus@gmail.com>
Date: Fri, 15 Mar 2024 21:30:30 +1100
Subject: [PATCH 11/27] update test outs

---
 tools/mummer4/test-data/nucmer.txt |   2 +-
 tools/mummer4/test-data/out.bam    | Bin 479 -> 481 bytes
 tools/mummer4/test-data/out.cram   | Bin 2679 -> 2679 bytes
 3 files changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/mummer4/test-data/nucmer.txt b/tools/mummer4/test-data/nucmer.txt
index 790940e3c9f..009b49695b7 100644
--- a/tools/mummer4/test-data/nucmer.txt
+++ b/tools/mummer4/test-data/nucmer.txt
@@ -1,4 +1,4 @@
-/tmp/tmpc2brs3qy/files/6/4/a/dataset_64a5193b-2c86-4944-b9b2-57de4d931c91.dat /tmp/tmpc2brs3qy/files/4/0/3/dataset_40346e9e-472b-47a5-a06d-b658657af917.dat
+/tmp/tmp6b44nh5p/files/8/c/3/dataset_8c31c46f-d1a9-4049-849a-9512bcbf746a.dat /tmp/tmp6b44nh5p/files/c/8/8/dataset_c88946f4-1dea-4e89-8914-5beea5bf845e.dat
 NUCMER
 >NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 6480 5460
 74 223 43 194 19 19 0
diff --git a/tools/mummer4/test-data/out.bam b/tools/mummer4/test-data/out.bam
index b8d1959c8fe26856219fd6876a419d9cf40e742c..c9d238f1a4a68a3996920351566391263c8ba964 100644
GIT binary patch
delta 297
zcmV+^0oMNC1K|UIABzYC000000RIL6LPG)oApwPu-AcnS9L2NC>;=TTzCfC!`!`u~
zHFYqBtyYWPmZV8pWnIRa>FY}s{6g5pfy24@9nQJF+Du+12rX`x__@$LWw^T6O$bNV
z?M?L4MfHHILKmx=F$q$nT!Rvfa1Jwt*M$}^XLyrq*H{UExof53jca+v=dA=MGGoE>
zoJsujsM~JmHKjE6hf%@;?6>)Wj`=_vYN@2oL^JqUH&&`l%{*x=w*(-wL@_ZZ-bt4M
zfSKhYbtX<1<qF>|^<erK!fwE2@$Ek*ag}EHX8n~WubqEOh)qaHtm*4;im5ey5>9b2
v{ni`zmznY)U(~WZ*D!=*9PyvXpDoh~Lg)e^^#7x%yhP|7XlT03lN<rVvwM+5

delta 295
zcmV+?0oeZG1K$IGABzYC000000RIL6LPG)o9|47s%}T^D6ooU(%nOLSzCfDXPWqQs
z)qzo%snw#}k~9fcrbe5L;@e9V{6lbY;c^z=$2q4byT$ziq3V2%Z)*WD!|kQ$otyOV
zAcI*}?G<ioQExiNa-L@~2wrB40Pt0bx3$Q4!SF5>x>q@WPqocU=(U9e3Y&ACB~oz%
zDa-NAwXnn92uf)fALr{6HTl)kE1h#sEiEWeErawXbhd!P0J8+7GKAYg6J;zTiYu7q
zu;NLqWms0t24Ad&mt$~l?{QOq{qL2aj1zpe{Y<0h!MsF7MZ`r)j-5M%SjjPRhv4OS
tXQckkjNu0!wQ2q{csGR^|AG8&SuPMlM+l+67e&o6LT@gLD%6u60mHAoiwOV#

diff --git a/tools/mummer4/test-data/out.cram b/tools/mummer4/test-data/out.cram
index 7372e04dd0c1feb1a278a623a178a9dc3106aee9..7b1a3d68e029ac5a7f0d249b3a63c3e244f02a6c 100644
GIT binary patch
delta 252
zcmV<Y00aN`6!#R6L4QiaFaSp9Wr`1x7ig2zG+A<0*kB4XPOILQG(WCtn~|mt-(Du-
zcJaaCTzs7CtHq+eU4vI8Nr6H0Am?!kF*%#n%_C@(RGSuKPB|-xq=Mm`5PBoPR!K&e
z7~EIVnvT=TdM=2uo|I(iIkl|R9d)F_9K1Y9l!n7;tfO??S7-<H9=i4z;zvKewYHDW
zq!7Om#uy3o=TUUtMK>B(c%9X|4Y*s&Ne?N6&k5|*nSbkvC`z!}{#*FfyCck3Fb~i~
zJ+xs?#R*{k3@@)?nA4<(z0)@P0Y6zs9uNTl0Nc|O*Z=?kdwY{H0dkW-0SU9C0n`X#
CWp@Ms

delta 252
zcmV<Y00aN`6!#R6L4QueAOJ?^C5;ck3$#E-%iyZXmQ0h0)2g=(<wvWwC{UNZy_qq(
zi!V7j7hlfh#bVK1ZNQThq`;uP74sB*NY-Rcdk0!6<hH|@QC1g3P+sGl5W3`GCq+$H
z7~E9C=$_HaIL3)Kj+A8O7&UdNdTL398F;)GD2*Sd>9P-T`Dl4WufFdNKD-Unb7zKN
zb@JheFvf_ZUyp)yHrPqq!l|s;Z^89OL^USw-y_(|fBvZ_yePqX_h;ePU=J`~!`wq1
z)Y$ns6(@lC13bTmeoj%1FIJiC8&}E5k`Ms^0Fc=E1ONa4dwY{H0dkW-0SU9C0n`Xr
Cws|E0


From b9fec7852c5490384ab8d12d92b230ab97378095 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= <bjoern@gruenings.eu>
Date: Fri, 15 Mar 2024 11:31:39 +0100
Subject: [PATCH 12/27] updates

---
 tools/mummer4/nucmer.xml | 46 ++++++++++++++++++++--------------------
 1 file changed, 23 insertions(+), 23 deletions(-)

diff --git a/tools/mummer4/nucmer.xml b/tools/mummer4/nucmer.xml
index 66dcbe202f2..dfae2adde62 100644
--- a/tools/mummer4/nucmer.xml
+++ b/tools/mummer4/nucmer.xml
@@ -88,19 +88,19 @@
         <param name="reference_sequence" type="data" format="fasta" label="Reference Sequence" help="FastA or multi-FastA" />
         <param name="query_sequence" type="data" format="fasta" label="Query Sequence" help="FastA or multi-FastA" />
         <conditional name="outform">
-            <param name="out_format" type="select" label="Output format" help="Default is delta format. Use sam-long or sam-short if downstream processing is needed in Galaxy">
-            <option value="delta">Default Mummer delta format - allows plots</option>
-            <option value="sam-short">Sam short format</option>
-            <option value="sam-long" >Sam long format</option>
-            <option value="bam-short">Sam short as bam format</option>
-            <option value="bam-long" >Sam long as bam format</option>
-            <option value="cram-short">Sam short as cram format</option>
-            <option value="cram-long" >Sam long as cram format</option>
+            <param name="out_format" type="select" label="Output format" help="Default is delta format. Use sam-long or sam-short if downstream processing is needed">
+                <option value="delta">Default Mummer delta format - allows plots</option>
+                <option value="sam-short">Sam short format</option>
+                <option value="sam-long" >Sam long format</option>
+                <option value="bam-short">Sam short as bam format</option>
+                <option value="bam-long" >Sam long as bam format</option>
+                <option value="cram-short">Sam short as cram format</option>
+                <option value="cram-long" >Sam long as cram format</option>
             </param>
             <when value="delta">
                 <param name="makeshort" type="hidden" value="False" />
-               <conditional name="mumplot" >
-                    <param name="plot" type="select" label="If output file is in delta (not sam) format, make a 2-D dotplot of the input sequences? (mummerplot)" >
+                <conditional name="mumplot" >
+                    <param name="plot" type="select" label="If the output file is in delta (not sam) format, make a 2-D dotplot of the input sequences? (mummerplot)" >
                         <option value="no">No plot</option>
                         <option value="yes">Plot</option>
                     </param>
@@ -114,7 +114,7 @@
                                 <when value="yes">
                                     <param name="reference_sequence" type="data" format="fasta" label="Reference Sequence" help="(-R)" />
                                     <param name="query_sequence" type="data" format="fasta" multiple="True" label="Query Sequence(s)" help="(-Q)" />
-                                    <param type="boolean" argument="--layout" truevalue="--layout" falsevalue="" label="Layout" help="Layout a .delta multiplot in an intelligible fashion. (--layout)" />
+                                    <param argument="--layout" type="boolean" truevalue="--layout" falsevalue="" label="Layout" help="Layout a .delta multiplot in an intelligible fashion." />
                                 </when>
                                 <when value="no" />
                             </conditional>
@@ -142,32 +142,32 @@
                 <param name="makeshort" type="hidden" value="0" />
             </when>
         </conditional>
-         <param name="anchoring" type="select" label="Anchoring" help="Choose a match anchoring strategy">
+        <param name="anchoring" type="select" label="Anchoring" help="Choose a match anchoring strategy">
             <option value="">Use default</option>
             <option value="--mum">Unique matches only (--mum)</option>
             <option value="--maxmatch">All matches (--maxmatch)</option>
         </param>
 
         <param name="breaklen" type="integer" argument="-b" value="200" label="Break Length"
-            help="Set the distance an alignment extension will attempt to extend poor scoring regions before giving up. (-b)" />
-        <param name="mincluster" type="integer" argument="-c" value="65" label="Minumum Cluster Length" help="Sets the minimum length of a cluster of matches. (-c)" />
+            help="Set the distance an alignment extension will attempt to extend poor scoring regions before giving up." />
+        <param name="mincluster" type="integer" argument="-c" value="65" label="Minumum Cluster Length" help="Sets the minimum length of a cluster of matches." />
         <param name="diagdiff" type="integer" argument="-D" value="5" label="Maximum Diagonal Difference"
-            help="Set the maximum diagonal difference between two adjacent anchors in a cluster. (-D)" />
+            help="Set the maximum diagonal difference between two adjacent anchors in a cluster." />
         <param name="diagfactor" type="float" argument="-d" value="0.12" label="Maximum Diagonal Difference"
-            help="Set the maximum diagonal difference between two adjacent anchors in a cluster as a differential fraction of the gap length. (-d)" />
-        <param type="boolean" argument="--noextend" truevalue="--noextend" falsevalue="" label="No Extend" help="Do not perform cluster extension step. (--noextend)" />
+            help="Set the maximum diagonal difference between two adjacent anchors in a cluster as a differential fraction of the gap length." />
+        <param type="boolean" argument="--noextend" truevalue="--noextend" falsevalue="" label="No Extend" help="Do not perform cluster extension step." />
         <param name="direction" type="select" label="Direction" help="Choose a direction of Query Sequence to Use">
-            <option value="">Use foward and reverse sequences</option>
+            <option value="">Use forward and reverse sequences</option>
             <option value="-f">Use only forward sequence of query (-f)</option>
-            <option value="-r">Use only reverese sequence of query (-r)</option>
+            <option value="-r">Use only reverse sequence of query (-r)</option>
         </param>
-        <param name="maxgap" type="integer" argument="-g" value="90" label="Maximum Gap Distance" help="Set the maximum gap between two adjacent matches in a cluster. (-g)" />
-        <param name="minmatch" type="integer" argument="-l" value="20" label="Minimum Match Length" help="Set the minimum length of a single exact match. (-l)" />
-        <param name="minalign" type="integer" argument="-L" value="0" label="Minumum Alignment Length" help="Minimum length of an alignment, after clustering and extension. (-L)" />
+        <param name="maxgap" type="integer" argument="-g" value="90" label="Maximum Gap Distance" help="Set the maximum gap between two adjacent matches in a cluster." />
+        <param name="minmatch" type="integer" argument="-l" value="20" label="Minimum Match Length" help="Set the minimum length of a single exact match." />
+        <param name="minalign" type="integer" argument="-L" value="0" label="Minumum Alignment Length" help="Minimum length of an alignment, after clustering and extension." />
         <param type="boolean" argument="--nooptimize" truevalue="--nooptimize" falsevalue="" label="No Alignment Score Optimization"
             help="No alignment score optimization, i.e. if an alignment extension reaches the end of a sequence, it will not backtrack to optimize the alignment score and instead terminate the alignment at the end of the sequence. (--nooptimize)" />
         <param type="boolean" argument="--nosimplify" truevalue="--nosimplify" falsevalue="" label="Don't Simplify Alignments"
-            help="Don't simplify alignments by removing shadowed clusters. Use this option when aligning a sequence to itself to look for repeats. (--nosimplify)" />
+            help="Don't simplify alignments by removing shadowed clusters. Use this option when aligning a sequence to itself to look for repeats." />
         <conditional name="options">
             <param name="advanced" type="select" label="Additional options">
                 <option value="defaults">Use defaults</option>

From efc3033a96893c254e6b66688411cd2b7b984be6 Mon Sep 17 00:00:00 2001
From: fubar2 <ross.lazarus@gmail.com>
Date: Fri, 15 Mar 2024 21:35:29 +1100
Subject: [PATCH 13/27] remove bogus samtools index steps - thanks Bjoern

---
 tools/mummer4/nucmer.xml           |   2 --
 tools/mummer4/test-data/nucmer.txt |   2 +-
 tools/mummer4/test-data/out.bam    | Bin 481 -> 483 bytes
 tools/mummer4/test-data/out.cram   | Bin 2679 -> 2679 bytes
 4 files changed, 1 insertion(+), 3 deletions(-)

diff --git a/tools/mummer4/nucmer.xml b/tools/mummer4/nucmer.xml
index dfae2adde62..5a4a9458375 100644
--- a/tools/mummer4/nucmer.xml
+++ b/tools/mummer4/nucmer.xml
@@ -74,10 +74,8 @@
                 #if $outform.out_format in ['bam-short', 'bam-long']:
                     && samtools view -b -o bam_out.bam outsamhead
                     && samtools sort bam_out.bam -o outsam
-                    && samtools index outsam
                 #else if $outform.out_format in ['cram-short', 'cram-long']:
                     && samtools view -C -o cram_out.cram  -T reference.fa  outsamhead && mv cram_out.cram outsam
-                    && samtools index outsam
                 #else
                    && mv outsamhead outsam
                 #end if
diff --git a/tools/mummer4/test-data/nucmer.txt b/tools/mummer4/test-data/nucmer.txt
index 009b49695b7..20a93ba2acb 100644
--- a/tools/mummer4/test-data/nucmer.txt
+++ b/tools/mummer4/test-data/nucmer.txt
@@ -1,4 +1,4 @@
-/tmp/tmp6b44nh5p/files/8/c/3/dataset_8c31c46f-d1a9-4049-849a-9512bcbf746a.dat /tmp/tmp6b44nh5p/files/c/8/8/dataset_c88946f4-1dea-4e89-8914-5beea5bf845e.dat
+/tmp/tmpnkfvax_1/files/2/9/1/dataset_291257b3-0107-40ad-9408-31d1d8005698.dat /tmp/tmpnkfvax_1/files/0/d/8/dataset_0d81d37d-b366-4fb8-a93d-b176e429dd81.dat
 NUCMER
 >NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 6480 5460
 74 223 43 194 19 19 0
diff --git a/tools/mummer4/test-data/out.bam b/tools/mummer4/test-data/out.bam
index c9d238f1a4a68a3996920351566391263c8ba964..e11aef0202ecccf7fadad93a98c8b7fdfa90a8df 100644
GIT binary patch
delta 299
zcmV+`0o4BC1LFgKABzYC000000RIL6LPG)oBLRhwO-{ow6olQSdjZ5Q7jW#Cyu^uD
z1u7M!HUuizMs^*GKvSc}EgT;OB>sfNVx-Y5zR}G2*=q7QA!K$rr}veDSkU#g+IYXW
z-A;#gI$Ph+b)~9BBZNem$Dpvx1p~meq{~X>SO~hxl-(GAiJ5h>gpGBOK;b0XJkbVQ
z$b_VKx5{<fR&mZl|2%5<<c|8a0Y2sfH$3IYtqyu<Lt|1jX=w|VmtYt=m#_jw!JGk^
zU@ox8ve@b{oz)9^HCKb~gZJBk*43APp9E!`(2M0~8Xdd#C1NIGJ~Fy*{2|0f_mMw@
xLH7@>w!fJoG5ny`^?wb6--i+Zf&AVwoe)A!2qAwzO6pTW-T-nZhQ^Z~0mIyOj!6Ij

delta 297
zcmV+^0oMNG1K|UIABzYC000000RIL6LPG)oApwPu-AcnS9L2NC>;=TTzCfC!`!`u~
zHFYqBtyYWPmZV8pWnIRa>FY}s{6g5pfy24@9nQJF+Du+12rX`x__@$LWw^T6O$bNV
z?M?L4MfHHILKmx=F$q$nT!Rvfa1Jwt*M$}^XLyrq*H{UExof53jca+v=dA=MGGoE>
zoJsujsM~JmHKjE6hf%@;?6>)Wj`=_vYN@2oL^JqUH&&`l%{*x=w*(-wL@_ZZ-bt4M
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v{ni`zmznY)U(~WZ*D!=*9PyvXpDoh~Lg)e^^#7x%yhP|7XlT03lOO@ZxGRxN

diff --git a/tools/mummer4/test-data/out.cram b/tools/mummer4/test-data/out.cram
index 7b1a3d68e029ac5a7f0d249b3a63c3e244f02a6c..cfc5b4672e575fbbd7dadbf5dbbff7d9ef40b3b5 100644
GIT binary patch
delta 252
zcmV<Y00aN`6!#R6L4QueAOJ?^C5;ck3$#F`WpLGGOQy-hY1Lao`O!LC45gdCy_qq(
zi!V7j7hlfh#bVK1ufekvq`;uP6Z1HQn4Ha;_8zoS$c@67QC1g3P+sGl5PHSIR*IS~
zF}SUSH65ds^^6l^Jt@i3GivKnchr#zGw}2vP#Qi?8~6U8KWG&}Z=qAi5cmD~qHG_X
zNg;kAj4|Tq*Q4mXi*7Wo@H%UD8*sB0lO9qC?-SU`fBvZ_yePqH`)A>ycSo47U>=}}
zdQf3b#R*{k2+yx!nA4<(SEp_E4P*)uj}QR>0QDE5D*ylhdwY{H0dkW-0SU9C0n`Xt
CMRyqh

delta 252
zcmV<Y00aN`6!#R6L4QiaFaSp9Wr`1x7ig2zG+A<0*kB4XPOILQG(WCtn~|mt-(Du-
zcJaaCTzs7CtHq+eU4vI8Nr6H0Am?!kF*%#n%_C@(RGSuKPB|-xq=Mm`5PBoPR!K&e
z7~EIVnvT=TdM=2uo|I(iIkl|R9d)F_9K1Y9l!n7;tfO??S7-<H9=i4z;zvKewYHDW
zq!7Om#uy3o=TUUtMK>B(c%9X|4Y*s&Ne?N6&k5|*nSbkvC`z!}{#*FfyCck3Fb~i~
zJ+xs?#R*{k3@@)?nA4<(z0)@P0Y6zs9uNTl0Nc|O*Z=?kdwY{H0dkW-0SU9C0n`X#
CWp@Ms


From fb278738593bd13558b879c96166270130fb6d0b Mon Sep 17 00:00:00 2001
From: fubar2 <ross.lazarus@gmail.com>
Date: Fri, 15 Mar 2024 21:47:57 +1100
Subject: [PATCH 14/27] add note on long and short outputs

---
 tools/mummer4/nucmer.xml | 16 ++++++++++++++--
 1 file changed, 14 insertions(+), 2 deletions(-)

diff --git a/tools/mummer4/nucmer.xml b/tools/mummer4/nucmer.xml
index 5a4a9458375..6e83a0792f2 100644
--- a/tools/mummer4/nucmer.xml
+++ b/tools/mummer4/nucmer.xml
@@ -235,9 +235,12 @@
         </test>
     </tests>
     <help><![CDATA[
-        nucmer is for the all-vs-all comparison of nucleotide sequences contained in multi-FastA data files. It is best used for highly similar sequence that may have large rearrangements. Common use cases are: comparing two unfinished shotgun sequencing assemblies, mapping an unfinished sequencing assembly to a finished genome, and comparing two fairly similar genomes that may have large rearrangements and duplications.
+        nucmer is for the all-vs-all comparison of nucleotide sequences contained in multi-FastA data files. It is best used for highly similar sequence that may
+        have large rearrangements. Common use cases are: comparing two unfinished shotgun sequencing assemblies, mapping an unfinished sequencing assembly
+        to a finished genome, and comparing two fairly similar genomes that may have large rearrangements and duplications.
 
-        All output coordinates reference the forward strand of the involved sequence, regardless of the match direction. Also, nucmer now uses only matches that are unique in the reference sequence by default, use different Anchoring options to change this behavior.
+        All output coordinates reference the forward strand of the involved sequence, regardless of the match direction. Also, nucmer now uses only matches that
+        are unique in the reference sequence by default, use different Anchoring options to change this behavior.
 
 **Options:**::
 
@@ -245,6 +248,15 @@
 
     nucmer
 
+    --sam-short, --sam-long      The original output format of nucmer, the delta format, contains only the minimum information necessary to quickly recreate the alignment.
+    It contains the name of the matching sequences, the length of the match, number of errors and positions of indels. An important addition in MUMmer4 is option
+    to produce output in SAM format, one of the most widely used formats for alignments of NGS data.
+    This also allows the MUMmer4 output to be used in any of the numerous tools that require SAM files as input. Nucmer4 supports two different options for SAM format output.
+    With --sam-short, nucmer4 reports only the name of the matching sequence, length, and CIGAR string (which reports the indel positions).
+    With --sam-long, it additionally reports the MD string (which specifies the mismatching positions), the sequence and, if applicable,
+    the quality values of the matching sequence. The long format is more expensive to compute and it generates larger output files,
+    but this option allows nucmer4 to match the behavior of other aligners such as Bowtie2 or BWA.
+
     --mum             Use anchor matches that are unique in both the reference and query (false)
 
     --maxmatch        Use all anchor matches regardless of their uniqueness (false)

From 6d9b011d9259d4d65fa9c26ddfd1978aa0c8ffa5 Mon Sep 17 00:00:00 2001
From: Ross Lazarus <fubar2@users.noreply.github.com>
Date: Fri, 15 Mar 2024 22:19:58 +1100
Subject: [PATCH 15/27] Update tools/mummer4/nucmer.xml
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Björn Grüning <bjoern@gruenings.eu>
---
 tools/mummer4/nucmer.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/mummer4/nucmer.xml b/tools/mummer4/nucmer.xml
index 6e83a0792f2..4fffd48d244 100644
--- a/tools/mummer4/nucmer.xml
+++ b/tools/mummer4/nucmer.xml
@@ -220,7 +220,7 @@
             <param name="seq_input" value="yes" />
             <param name="reference_sequence" ftype="fasta" value="human_aqp3.fasta"/>
             <param name="query_sequence" ftype="fasta" value="mouse_aqp3.fasta" />
-           <output name="sam_output" ftype="bam" compare="sim_size" value="out.bam" />
+            <output name="sam_output" ftype="bam" value="out.bam" ftype="bam" />
         </test>
         <test expect_num_outputs="1">
             <param name="advanced" value="defaults" />

From 90d0187d24e37248b4d2db59b230302b5ec481b2 Mon Sep 17 00:00:00 2001
From: Ross Lazarus <fubar2@users.noreply.github.com>
Date: Fri, 15 Mar 2024 22:20:46 +1100
Subject: [PATCH 16/27] Update tools/mummer4/nucmer.xml
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Björn Grüning <bjoern@gruenings.eu>
---
 tools/mummer4/nucmer.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/mummer4/nucmer.xml b/tools/mummer4/nucmer.xml
index 4fffd48d244..94cd760057c 100644
--- a/tools/mummer4/nucmer.xml
+++ b/tools/mummer4/nucmer.xml
@@ -231,7 +231,7 @@
             <param name="seq_input" value="yes" />
             <param name="reference_sequence" ftype="fasta" value="human_aqp3.fasta"/>
             <param name="query_sequence" ftype="fasta" value="mouse_aqp3.fasta" />
-           <output name="sam_output" ftype="cram" compare="sim_size" value="out.cram" />
+            <output name="sam_output" ftype="cram" compare="sim_size" value="out.cram" />
         </test>
     </tests>
     <help><![CDATA[

From 43948e3c50ff96e1f1c37170a2ac4ed46dbd7b52 Mon Sep 17 00:00:00 2001
From: fubar2 <ross.lazarus@gmail.com>
Date: Fri, 15 Mar 2024 22:53:28 +1100
Subject: [PATCH 17/27] revert invalid xml

---
 tools/mummer4/nucmer.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/mummer4/nucmer.xml b/tools/mummer4/nucmer.xml
index 94cd760057c..b568c2d9b23 100644
--- a/tools/mummer4/nucmer.xml
+++ b/tools/mummer4/nucmer.xml
@@ -220,7 +220,7 @@
             <param name="seq_input" value="yes" />
             <param name="reference_sequence" ftype="fasta" value="human_aqp3.fasta"/>
             <param name="query_sequence" ftype="fasta" value="mouse_aqp3.fasta" />
-            <output name="sam_output" ftype="bam" value="out.bam" ftype="bam" />
+            <output name="sam_output" ftype="bam" compare="sim_size" value="out.bam" />
         </test>
         <test expect_num_outputs="1">
             <param name="advanced" value="defaults" />

From 08d67639084e9c62860f971625da8e463a8a6948 Mon Sep 17 00:00:00 2001
From: fubar2 <ross.lazarus@gmail.com>
Date: Fri, 15 Mar 2024 22:58:06 +1100
Subject: [PATCH 18/27] remove empty sam from test data and update tests
 again..

---
 tools/mummer4/test-data/nucmer.txt |   2 +-
 tools/mummer4/test-data/out.bam    | Bin 483 -> 481 bytes
 tools/mummer4/test-data/out.cram   | Bin 2679 -> 2679 bytes
 tools/mummer4/test-data/out.sam    |   0
 4 files changed, 1 insertion(+), 1 deletion(-)
 delete mode 100644 tools/mummer4/test-data/out.sam

diff --git a/tools/mummer4/test-data/nucmer.txt b/tools/mummer4/test-data/nucmer.txt
index 20a93ba2acb..26ff4372919 100644
--- a/tools/mummer4/test-data/nucmer.txt
+++ b/tools/mummer4/test-data/nucmer.txt
@@ -1,4 +1,4 @@
-/tmp/tmpnkfvax_1/files/2/9/1/dataset_291257b3-0107-40ad-9408-31d1d8005698.dat /tmp/tmpnkfvax_1/files/0/d/8/dataset_0d81d37d-b366-4fb8-a93d-b176e429dd81.dat
+/tmp/tmpnf8gcn5v/files/b/d/f/dataset_bdfc9456-0f15-4f5d-96ca-574b25b33e43.dat /tmp/tmpnf8gcn5v/files/d/4/6/dataset_d462e1f9-1691-4066-a872-6d0853ed89b6.dat
 NUCMER
 >NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 6480 5460
 74 223 43 194 19 19 0
diff --git a/tools/mummer4/test-data/out.bam b/tools/mummer4/test-data/out.bam
index e11aef0202ecccf7fadad93a98c8b7fdfa90a8df..a3dd132d77963084c6fc4380cd35a3aa85b3623a 100644
GIT binary patch
delta 297
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delta 299
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diff --git a/tools/mummer4/test-data/out.cram b/tools/mummer4/test-data/out.cram
index cfc5b4672e575fbbd7dadbf5dbbff7d9ef40b3b5..13eb027d39b4e1a9df95d184c23481d6b97ffe95 100644
GIT binary patch
delta 252
zcmV<Y00aN`6!#R6L4QiaFaSp9Wr`1x7ig2zv}tlx*kB4XPOILQG(WRy6G_tz-(Du7
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CgK+Nv

delta 252
zcmV<Y00aN`6!#R6L4QueAOJ?^C5;ck3$#F`WpLGGOQy-hY1Lao`O!LC45gdCy_qq(
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zdQf3b#R*{k2+yx!nA4<(SEp_E4P*)uj}QR>0QDE5D*ylhdwY{H0dkW-0SU9C0n`Xt
CMRyqh

diff --git a/tools/mummer4/test-data/out.sam b/tools/mummer4/test-data/out.sam
deleted file mode 100644
index e69de29bb2d..00000000000

From e0da3abd2829ee62eb9377f36c2751ff2dc20469 Mon Sep 17 00:00:00 2001
From: fubar2 <ross.lazarus@gmail.com>
Date: Fri, 15 Mar 2024 23:23:35 +1100
Subject: [PATCH 19/27] fix a silly strange form bug - misnamed hidden variable

---
 tools/mummer4/nucmer.xml           |   8 ++++----
 tools/mummer4/test-data/nucmer.txt |   2 +-
 tools/mummer4/test-data/out.bam    | Bin 481 -> 480 bytes
 tools/mummer4/test-data/out.cram   | Bin 2679 -> 2679 bytes
 4 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/tools/mummer4/nucmer.xml b/tools/mummer4/nucmer.xml
index b568c2d9b23..f9c0e896599 100644
--- a/tools/mummer4/nucmer.xml
+++ b/tools/mummer4/nucmer.xml
@@ -96,7 +96,7 @@
                 <option value="cram-long" >Sam long as cram format</option>
             </param>
             <when value="delta">
-                <param name="makeshort" type="hidden" value="False" />
+                <param name="makeshort" type="hidden" value="0" />
                 <conditional name="mumplot" >
                     <param name="plot" type="select" label="If the output file is in delta (not sam) format, make a 2-D dotplot of the input sequences? (mummerplot)" >
                         <option value="no">No plot</option>
@@ -131,7 +131,7 @@
                 <param name="makeshort" type="hidden" value="1" />
             </when>
             <when value="bam-long">
-                <param name="shortsam" type="hidden" value="0" />
+                <param name="makeshort" type="hidden" value="0" />
             </when>
             <when value="cram-short">
                 <param name="makeshort" type="hidden" value="1" />
@@ -213,8 +213,8 @@
         </test>
        <test expect_num_outputs="1">
             <param name="advanced" value="defaults" />
-            <param name="makeshort" value="1" />
             <conditional name="outform">
+                <param name="makeshort" value="1" />
                 <param name="out_format" value="bam-short" />
             </conditional>
             <param name="seq_input" value="yes" />
@@ -224,8 +224,8 @@
         </test>
         <test expect_num_outputs="1">
             <param name="advanced" value="defaults" />
-            <param name="makeshort" value="0" />
             <conditional name="outform">
+                <param name="makeshort" value="0" />
                 <param name="out_format" value="cram-long" />
             </conditional>
             <param name="seq_input" value="yes" />
diff --git a/tools/mummer4/test-data/nucmer.txt b/tools/mummer4/test-data/nucmer.txt
index 26ff4372919..d90adfc5990 100644
--- a/tools/mummer4/test-data/nucmer.txt
+++ b/tools/mummer4/test-data/nucmer.txt
@@ -1,4 +1,4 @@
-/tmp/tmpnf8gcn5v/files/b/d/f/dataset_bdfc9456-0f15-4f5d-96ca-574b25b33e43.dat /tmp/tmpnf8gcn5v/files/d/4/6/dataset_d462e1f9-1691-4066-a872-6d0853ed89b6.dat
+/tmp/tmp0utvulpx/files/4/6/e/dataset_46e8d66a-7e94-469f-8937-84d85194b6c3.dat /tmp/tmp0utvulpx/files/1/b/2/dataset_1b2e463c-4205-4945-bc0a-04862da609a6.dat
 NUCMER
 >NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 6480 5460
 74 223 43 194 19 19 0
diff --git a/tools/mummer4/test-data/out.bam b/tools/mummer4/test-data/out.bam
index a3dd132d77963084c6fc4380cd35a3aa85b3623a..8c331d89237a914c93321bbc72e88882cc215541 100644
GIT binary patch
delta 296
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uV{6=RW<q}-P|NbahRGkog8x8%Z;4g_fD-_~-;aXw6o5C7T3Ak#9s$D&RfY2a

delta 297
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v_Z+PM%go^*7qzZWHS}?x2K*=TXUlkm5IRE${r@Pc&k=eDxdqHolN|xWnf8%~

diff --git a/tools/mummer4/test-data/out.cram b/tools/mummer4/test-data/out.cram
index 13eb027d39b4e1a9df95d184c23481d6b97ffe95..14efc219e6dcb440abb05c550d275e71cf1c0730 100644
GIT binary patch
delta 252
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delta 252
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CgK+Nv


From 13c3d9f7202c466f3fb4a6cd4ceab167fb8809cd Mon Sep 17 00:00:00 2001
From: fubar2 <ross.lazarus@gmail.com>
Date: Sat, 16 Mar 2024 11:57:24 +1100
Subject: [PATCH 20/27] removed all short-sam output options added samtools
 calmd to fix broken MD and NM headers - thanks, mummer.

---
 tools/mummer4/nucmer.xml           |  77 +++++++++++------------------
 tools/mummer4/test-data/nucmer.txt |   2 +-
 tools/mummer4/test-data/out.bam    | Bin 480 -> 2368 bytes
 tools/mummer4/test-data/out.cram   | Bin 2679 -> 2528 bytes
 4 files changed, 30 insertions(+), 49 deletions(-)

diff --git a/tools/mummer4/nucmer.xml b/tools/mummer4/nucmer.xml
index f9c0e896599..9cdec9c476c 100644
--- a/tools/mummer4/nucmer.xml
+++ b/tools/mummer4/nucmer.xml
@@ -14,11 +14,7 @@
         nucmer
             $anchoring
             #if $outform.out_format != "delta":
-                #if $outform.makeshort == "1":
-                    --sam-short=outsam.sam
-                #else:
-                    --sam-long=outsam.sam
-                #end if
+                --sam-long=outsam.sam
             #end if
             -b '$breaklen'
             -c '$mincluster'
@@ -71,13 +67,14 @@
                 && tail  -n +3 outsam.sam > outsambody
                 && samtools dict reference.fa > outsamhead
                 && cat outsambody >> outsamhead
-                #if $outform.out_format in ['bam-short', 'bam-long']:
-                    && samtools view -b -o bam_out.bam outsamhead
-                    && samtools sort bam_out.bam -o outsam
-                #else if $outform.out_format in ['cram-short', 'cram-long']:
-                    && samtools view -C -o cram_out.cram  -T reference.fa  outsamhead && mv cram_out.cram outsam
+                && samtools calmd outsamhead reference.fa > outsamcalm
+                #if $outform.out_format == 'bam-long':
+                    && samtools view -b -o bam_out.bam outsamcalm
+                    && samtools sort -o outsam -O bam bam_out.bam
+                #else if $outform.out_format == 'cram-long':
+                    && samtools view -C -o outsam -T reference.fa outsamcalm
                 #else
-                   && mv outsamhead outsam
+                   && samtools sort -o outsam -O sam outsamcalm
                 #end if
             #end if
         ]]>
@@ -86,17 +83,13 @@
         <param name="reference_sequence" type="data" format="fasta" label="Reference Sequence" help="FastA or multi-FastA" />
         <param name="query_sequence" type="data" format="fasta" label="Query Sequence" help="FastA or multi-FastA" />
         <conditional name="outform">
-            <param name="out_format" type="select" label="Output format" help="Default is delta format. Use sam-long or sam-short if downstream processing is needed">
-                <option value="delta">Default Mummer delta format - allows plots</option>
-                <option value="sam-short">Sam short format</option>
-                <option value="sam-long" >Sam long format</option>
-                <option value="bam-short">Sam short as bam format</option>
-                <option value="bam-long" >Sam long as bam format</option>
-                <option value="cram-short">Sam short as cram format</option>
-                <option value="cram-long" >Sam long as cram format</option>
+            <param name="out_format" type="select" label="Output format" help="Select delta format if a plot is needed. Jbrowse is a good choice to view cram and bam tracks">
+                <option value="bam-long">bam format</option>
+                <option value="sam-long">sam format</option>
+                <option value="cram-long">cram format</option>
+                <option value="delta">Mummer delta format - allows plots</option>
             </param>
             <when value="delta">
-                <param name="makeshort" type="hidden" value="0" />
                 <conditional name="mumplot" >
                     <param name="plot" type="select" label="If the output file is in delta (not sam) format, make a 2-D dotplot of the input sequences? (mummerplot)" >
                         <option value="no">No plot</option>
@@ -121,24 +114,9 @@
                     <when value="no" />
                 </conditional>
             </when>
-            <when value="sam-short">
-                <param name="makeshort" type="hidden" value="1" />
-            </when>
-            <when value="sam-long">
-                <param name="makeshort" type="hidden" value="0" />
-            </when>
-            <when value="bam-short">
-                <param name="makeshort" type="hidden" value="1" />
-            </when>
-            <when value="bam-long">
-                <param name="makeshort" type="hidden" value="0" />
-            </when>
-            <when value="cram-short">
-                <param name="makeshort" type="hidden" value="1" />
-            </when>
-            <when value="cram-long">
-                <param name="makeshort" type="hidden" value="0" />
-            </when>
+            <when value="sam-long"/>
+            <when value="bam-long"/>
+            <when value="cram-long"/>
         </conditional>
         <param name="anchoring" type="select" label="Anchoring" help="Choose a match anchoring strategy">
             <option value="">Use default</option>
@@ -188,9 +166,7 @@
         <data name="sam_output" format="sam" from_work_dir="outsam"  label="${tool.name} on ${on_string}">
            <filter>outform["out_format"] != "delta"</filter>
            <change_format>
-                <when input="outform.out_format" value="bam-short" format="bam" />
                 <when input="outform.out_format" value="bam-long" format="bam" />
-                <when input="outform.out_format" value="cram-short" format="cram" />
                 <when input="outform.out_format" value="cram-long" format="cram" />
            </change_format>
         </data>
@@ -214,8 +190,7 @@
        <test expect_num_outputs="1">
             <param name="advanced" value="defaults" />
             <conditional name="outform">
-                <param name="makeshort" value="1" />
-                <param name="out_format" value="bam-short" />
+                <param name="out_format" value="bam-long" />
             </conditional>
             <param name="seq_input" value="yes" />
             <param name="reference_sequence" ftype="fasta" value="human_aqp3.fasta"/>
@@ -225,7 +200,6 @@
         <test expect_num_outputs="1">
             <param name="advanced" value="defaults" />
             <conditional name="outform">
-                <param name="makeshort" value="0" />
                 <param name="out_format" value="cram-long" />
             </conditional>
             <param name="seq_input" value="yes" />
@@ -233,6 +207,16 @@
             <param name="query_sequence" ftype="fasta" value="mouse_aqp3.fasta" />
             <output name="sam_output" ftype="cram" compare="sim_size" value="out.cram" />
         </test>
+        <test expect_num_outputs="1">
+            <param name="advanced" value="defaults" />
+            <conditional name="outform">
+                <param name="out_format" value="sam-long" />
+            </conditional>
+            <param name="seq_input" value="yes" />
+            <param name="reference_sequence" ftype="fasta" value="human_aqp3.fasta"/>
+            <param name="query_sequence" ftype="fasta" value="mouse_aqp3.fasta" />
+            <output name="sam_output" ftype="sam" compare="sim_size" value="out.sam" />
+        </test>
     </tests>
     <help><![CDATA[
         nucmer is for the all-vs-all comparison of nucleotide sequences contained in multi-FastA data files. It is best used for highly similar sequence that may
@@ -248,11 +232,8 @@
 
     nucmer
 
-    --sam-short, --sam-long      The original output format of nucmer, the delta format, contains only the minimum information necessary to quickly recreate the alignment.
-    It contains the name of the matching sequences, the length of the match, number of errors and positions of indels. An important addition in MUMmer4 is option
-    to produce output in SAM format, one of the most widely used formats for alignments of NGS data.
-    This also allows the MUMmer4 output to be used in any of the numerous tools that require SAM files as input. Nucmer4 supports two different options for SAM format output.
-    With --sam-short, nucmer4 reports only the name of the matching sequence, length, and CIGAR string (which reports the indel positions).
+    --sam-long      The original output format of nucmer, the delta format, contains only the minimum information necessary to quickly recreate the alignment.
+    It contains the name of the matching sequences, the length of the match, number of errors and positions of indels.
     With --sam-long, it additionally reports the MD string (which specifies the mismatching positions), the sequence and, if applicable,
     the quality values of the matching sequence. The long format is more expensive to compute and it generates larger output files,
     but this option allows nucmer4 to match the behavior of other aligners such as Bowtie2 or BWA.
diff --git a/tools/mummer4/test-data/nucmer.txt b/tools/mummer4/test-data/nucmer.txt
index d90adfc5990..dbd97540df7 100644
--- a/tools/mummer4/test-data/nucmer.txt
+++ b/tools/mummer4/test-data/nucmer.txt
@@ -1,4 +1,4 @@
-/tmp/tmp0utvulpx/files/4/6/e/dataset_46e8d66a-7e94-469f-8937-84d85194b6c3.dat /tmp/tmp0utvulpx/files/1/b/2/dataset_1b2e463c-4205-4945-bc0a-04862da609a6.dat
+/tmp/tmpf56vpwj6/files/a/c/c/dataset_acc56cef-a327-4edc-8327-229262f73b1e.dat /tmp/tmpf56vpwj6/files/1/9/3/dataset_19318e75-7522-408f-b67f-a11b1f9e80ef.dat
 NUCMER
 >NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 6480 5460
 74 223 43 194 19 19 0
diff --git a/tools/mummer4/test-data/out.bam b/tools/mummer4/test-data/out.bam
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zE!Ay{G#4vZZkwIGT38rWoSnA);Q>4=-+YYn=6Q-&_F0QjsAk3XeEiLAfNe18Hr8h7
zeo&$s0K<_q3(M&j-#_?A=DTmN_||{*>AJni_5S*N-Sz(d_0#qF<@4+3>wfL!!xrp^
z>;Cb2`m}ZY{^f1&>;3hvA71Y-PfxE;*VE6g4_~h9(wF;}OFvy7Uq5_#xm_Q(^uOry
z^?W_)?e+F@)8{YO)64Vq>3Y`puTM`eAFlh$)AJth<$l{+*Zs5JKfT^wo?q@CkG}v?
m)=J2*Bme*(iwFb&00000{{{d;LjnLB00RI3000000002v&wLL6

literal 480
zcmb2|=3rp}f&Xj_PR>jW3XH82&Uzg&U})KV{0r-m=y(O+pwE||gp?+VmSt~!u~o&l
zd+Ifv+a+H=F6H{CSRo<t>;tc{`19RYFLO2g$>Npg@)c%UEq%A5zTod>&fF>C+c#*H
zY+T7X(Wk2=YZ;5<lugF0+grtSlnah;&0dpor!?r|u~L(zk?J#rS8iOhbdE<w{qo&)
z8K%c9dVag6@ExzbvHy|ke1qdm+;4mgf~B+cT%KttYivHGc&xHr$J_eKiV)AmJBrS!
zoNLk0H~&zzR^6EGeLLs0qtol>yM#_Uboy<&l>F~+s%~a(cH7d{{FM>PK6c}LqS52z
z>^u2sPW1t&KkaWjDSxQxze8PqXBb0+FvEfS{Y{@l8q6m|Mfgo+WMGg-3!p^|Q~UPv
z9&!+A-ruamp;9-A(SgJ3!f8Q|1x{XvMVBNritrrb;yK9BGeI{(Sz2K3J6!?uZPNAY
zIExMxy?NyEJN{{L=rtv!op1c7r%yYz)1&+FIriDNd(Jc5V-q_t=YcPaboz>Ssh=*L
zj299xmiX!-)7};)_*O*j09OQaIJ4mg)g2l6Y8$rx;NH&nZOMQ3XTYdKccL@{GdM~?
F1OOl3#q0n8

diff --git a/tools/mummer4/test-data/out.cram b/tools/mummer4/test-data/out.cram
index 14efc219e6dcb440abb05c550d275e71cf1c0730..fc1fc27f4079b2b4677db060c8cbf22266ef092d 100644
GIT binary patch
delta 433
zcmew^@<6!WImpqMnIXTlq&P8`0R{9i!njOK42?{aBFn!5MH;?0rptG8K&1Y+_TBYs
zHehIdo?6+pk73KvOMP(@b55Gf>{xVf(k1y+zFkxDj%+tKcG)alUN~v;`$yL9cXh;$
z-j&)jwMj+dO8+B^`kr&_ix)4dV=C1=<=bqye2%Kig*gvr2vp5(&efENP5Ll_b8VEL
zac-sGlx-@i-ltclt;|`eDEaKc*T@AI<j-xCw3b~a>ui19Z1U&%cR$>FaZXxv&VMI~
z<SC11D(A2Hm=>V6(MW3*?~eHHz;6e4{^eNpY5o5_>Xnn4u6~>Dr22iYMcX?Gx1046
zD<9VHYl)Fq{c6_VD>FHdX-n*`WICoV&TVYBzhfWc9J6gF(t(~|{l29e=<|lghQ`T;
zj75_j82MGKgjwrfvjauFrcPsGm>w*^*l>&^VeWATMuvvn4ZDR{LR=UppJLo%$;e>+
z_TNheCI&4nh*~~gZXP~<K}jiT8Cf}bmH$A%KZW0x>4Uhn+xdp7<-)1YQhuBWnz#8F
L(<ipcfm~_;fnTlt

delta 576
zcmaDL{9UBpImpqMnIX9-F*iQHv_ucYV1R%sMks@UiHV`%+af{fDL|2i*Np=5-5e09
z|Gs^9{SGTIxII_x<v+;1#bIe`!POM+WhakhUcKG+Y4O#qIwEGZ)yBzJy7etB#pBOC
zJ(_eeX8pm<B1;Y|*ejeltG2%5T8eKqf0X8vWrt@3hKaib#66xPP<8ZRSl28)!yRi|
zF4``hTG%6;E2DYxl3~`Xps!aZaT$O3q7Wd%|NNmye`fs;hx~o-{p|MeU-nLKODO&F
zP&lzi(A{2+^>xmM$=h0kBRAh}n7wtzRf)a#&nKw=|FL`Chea%_->z>xesEsGKCPym
z?N%!`e%2IAZ}_SFr=GXAYqM1RTBDod^^<fr2mn32F7fX#pl_?ICp$8hO%7mWRnM}>
zzCH~U0$x+6F)>UJ7G!L=^25c3kAab);bg-}QI-%F7GIaB$+sD|=<_f>05VxwIYHDb
z3I9?CCI&q{h)#Y!ZXP~<K}jiT8Cf}b6_AR_>zPDZCY!A2+kArQ6I(qa3rMh`yWtEX
z$YoC*>|`<Iak;qD&urDEtM7b|Dg1Nf)TkGG_N(ILsu%5|J8T^jdRmyLw}fl|nsffU
z!2Z`ackFrg;hVMov!f}VDs>kQR($n8{`gd(xAGVFxCOVSTiHzB-rRm*yP0&TPsx>i
vE6m$tvzPeYx%EV9hwNO5{ZEZA?hc+f|Gj;PhCu%rpttAy@_(MZi&G5%rRnl6


From 961152f378128e3702eebff63a28720bb16ea092 Mon Sep 17 00:00:00 2001
From: fubar2 <ross.lazarus@gmail.com>
Date: Sat, 16 Mar 2024 12:49:08 +1100
Subject: [PATCH 21/27] add missing sam.out test file :(

---
 tools/mummer4/nucmer.xml           |   5 +++--
 tools/mummer4/test-data/nucmer.txt |   2 +-
 tools/mummer4/test-data/out.bam    | Bin 2368 -> 2377 bytes
 tools/mummer4/test-data/out.cram   | Bin 2528 -> 2561 bytes
 tools/mummer4/test-data/out.sam    |   6 ++++++
 5 files changed, 10 insertions(+), 3 deletions(-)
 create mode 100644 tools/mummer4/test-data/out.sam

diff --git a/tools/mummer4/nucmer.xml b/tools/mummer4/nucmer.xml
index 9cdec9c476c..556e67de953 100644
--- a/tools/mummer4/nucmer.xml
+++ b/tools/mummer4/nucmer.xml
@@ -67,14 +67,15 @@
                 && tail  -n +3 outsam.sam > outsambody
                 && samtools dict reference.fa > outsamhead
                 && cat outsambody >> outsamhead
-                && samtools calmd outsamhead reference.fa > outsamcalm
+                && samtools sort -o outsamheadsort outsamhead
+                && samtools calmd outsamheadsort reference.fa > outsamcalm
                 #if $outform.out_format == 'bam-long':
                     && samtools view -b -o bam_out.bam outsamcalm
                     && samtools sort -o outsam -O bam bam_out.bam
                 #else if $outform.out_format == 'cram-long':
                     && samtools view -C -o outsam -T reference.fa outsamcalm
                 #else
-                   && samtools sort -o outsam -O sam outsamcalm
+                   && mv outsamcalm outsam
                 #end if
             #end if
         ]]>
diff --git a/tools/mummer4/test-data/nucmer.txt b/tools/mummer4/test-data/nucmer.txt
index dbd97540df7..4d207057955 100644
--- a/tools/mummer4/test-data/nucmer.txt
+++ b/tools/mummer4/test-data/nucmer.txt
@@ -1,4 +1,4 @@
-/tmp/tmpf56vpwj6/files/a/c/c/dataset_acc56cef-a327-4edc-8327-229262f73b1e.dat /tmp/tmpf56vpwj6/files/1/9/3/dataset_19318e75-7522-408f-b67f-a11b1f9e80ef.dat
+/tmp/tmp885k3_3o/files/9/9/8/dataset_99883b3a-5339-4acd-82bb-7e6cc0cad9db.dat /tmp/tmp885k3_3o/files/c/b/a/dataset_cbaf4d80-a79c-4055-8ede-298a050d1575.dat
 NUCMER
 >NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 6480 5460
 74 223 43 194 19 19 0
diff --git a/tools/mummer4/test-data/out.bam b/tools/mummer4/test-data/out.bam
index 05aefec7b15a6f1266e07212f7e49582b35ef406..2424d37470d4c9d7c20474c9d3b10a73b542cc36 100644
GIT binary patch
delta 340
zcmV-a0jvJN63G&OABzYC000000RIL6LPG)oN&$`1+fKqT90u^}U3mfH-Ckfltvj?=
zs3d3tV@mXP>3WDnM$K0A_05P81&LlXX}^o_*MHONtNEEY2Vi_VflsBRh`{ASYVSL<
z+NfYh<K;bEma?4IgycNW5S3hHB&L)n0?taA@q)m4DvfS`a-JHO3#yHyj215ECS$7M
zmZl_!j}OwV)>dMSL;E_cqDWtoI`MeOd#o|T1RE7pZ$qsaVTtB0HksiuPYI2Ma5NST
zDO4t`OACdJ3Zro~g?AI#t2TJQ?qOB#_q&m(Kn&i@zS5}oU5H{I`EBS``)rljCHv!H
zC!#-EtLiUHL92CZ4*NUnY-cyxBBzc7c1l3>gz>hr?@`<ggEXqG{WhRRwV&v4fg>Y1
mX|R92R1_};>N__&0{~nA0Dk`<pt=O$1M68L@MHp`KmiC$-JQAs

delta 331
zcmV-R0kr<f62KCFABzYC000000RIL6LPG)oK>>x)O-{ow5Cvd&>0SV_%LQ!5i5(|i
z6{u8@+B8tXwz6Ye6eV?)xa~Q)5egvwD;6V--r{{4&E>^n^gIG!ay^9)rKC89tEH^H
z@62Yaf*ns*w{TU;a<-0R!9<3sWJMMuN?BUKc_}lN$8f=arKz=G+&EFt+Bllf+zDo~
zL}_Lzj|IHHlWx;kNeBt;ZWzb2!|wQ$ks<GiC5EKLsGxcq*4CsZ6<nY~rzv8JYm`&2
zP@x?anc)ddb8J)?PpTQbnaW<Z!TY9%Rr$HUo<s|rz^nO38r7<4P2~5XSM8%!ChDxS
zo!!<JJN2_d57TdrRrO!{VPlUG(h>5JR_)sF1J<g2=LY(hkem`QJz?~|3j^?08lmMt
dedWd@0Kgdl;P1zQ>KuR<<2DH*`~jm$0SMJmoM8X}

diff --git a/tools/mummer4/test-data/out.cram b/tools/mummer4/test-data/out.cram
index fc1fc27f4079b2b4677db060c8cbf22266ef092d..a1a5c44975a2805ee697c9fd6ea68af46b3a5577 100644
GIT binary patch
delta 333
zcmV-T0kZz!6M+<v8h@_=00000000000s;Vm7@kEdIRO9wfenGtABzY8000000RM%L
z-%f)t6vpRec?w>D{((ZFS0r09O(vqKx1_X1af6ytU3^I2$!u99Te9uqB<K7tzTbC#
zZ)UUnb^%@sP9O%=1DD2F)eXXFFRva!Rq$e2W6UT^AmKDiaDPAujWVz*ctTSQ?qjZG
z!)UBpmJz915|XrKR3)Kks3tLH;N^)U*MIINP2+V`M+SYErrsL6?uNHobyiDf><_{i
zqYNE5vbxn)4^qQcczL-5cMCp>-WjtQL0L@uzCX!e2<EGQ>W{`cKQO-ea--<qwNQI9
zou`?Q9Ho}!H8g`1n_ivfUuq4*a|TGxIKDf*^@I8Jh#x#3ISzQ&#rp%$+Vls}0RRB;
fA#FDR004lDfQ*wt0d|v60Tu+^^<KKOy8$H#mvD|S

delta 307
zcmV-30nGk^6yOt(8h?%f00000000000s;Vm0+LyG^#K3?fcJrCABzY8000000RM%K
z-A;or0EOped5XROw8henUXg6cG?|E^-jdQEWe&QOZp61YGeol+cX5)F@8Ua0-7FTx
z-5R`=f+QH!kK#Ct&IhBTqJ9E(DauWQF{hj*M9`e!m=JoKgMV!)7+qrUkO{3?PBU$J
zPL#GJB}>bxW~pqcAsOc2^;w|MAI`BEI~}GSLp#?tlk=b5@ZRXo8x@@YLKtI|qnRUb
ztnp@0Cb2Rqstvebi&6H$x%~*L@~{8ACwY>B)%KS{CHK9C?ifbde;BFZf4+oV7^~`<
z{nVKW#w!@Rc^(4BFBc0lKEH^*0h~6r$Y%in0ITnWivR!sfPsL4lTiVI1UeH1f3w^H
FB?$8Eh*tmr

diff --git a/tools/mummer4/test-data/out.sam b/tools/mummer4/test-data/out.sam
new file mode 100644
index 00000000000..69883d1bed4
--- /dev/null
+++ b/tools/mummer4/test-data/out.sam
@@ -0,0 +1,6 @@
+@HD	VN:1.0	SO:coordinate
+@SQ	SN:NG_007476.1:4960-11439	LN:6480	M5:dcb745df791cdf1218f74d62ab4e1507	UR:file:///tmp/tmp885k3_3o/files/8/f/5/dataset_8f5d35c8-47ee-4bac-87e6-449833607f46.dat
+@PG	ID:samtools	PN:samtools	VN:1.19.2	CL:samtools sort -o outsamheadsort outsamhead
+@PG	ID:samtools.1	PN:samtools	PP:samtools	VN:1.19.2	CL:samtools calmd outsamheadsort reference.fa
+NC_000070.6:c41098183-41092724	0	NG_007476.1:4960-11439	74	10	42S25M1I1M1I124M5266S	*	0	0	ACCGCTCTCGGTGCCTTGCGCTAGCTACTTTGCACTCGTACGCCGCCGGACCTCGCCGCTGCCTGCCTCGCGCCATGGGTCGACAGAAGGAGTTGATGAATCGTTGTGGGGAGATGCTTCACATCCGCTACCGGCTGCTTCGCCAGGCGCTGGCGGAGTGCCTGGGGACCCTCATCCTTGTGGTGAGTGCAGGGTAGTGAGCAGTCCTATCTATTTCAGGCCCCGTGGTCCCCAACTCCTTATTCACTCCAGGGACAGTTTTCCAGGCAGACACGACCAGTTCCCCAGCTCTGCTCCCGAGGCTTAACCCTCAGGGTCAAGCTGACCTCCAAAGCCTTCAACAGTCTTGACAGTTCTAACTCAACTTGTGACAGTGCTACTTACCCAAGAACAGCTCTGCTATTTTGCCTTTCCCCCTGGAGACAGAGACCAAGGCTGCGGAGGGTCACCCCTTAGTGTGGGACCTCCCACACGTTTCCTGGCTTCCCAACTTTCCCAGGGCTCCAACCTCAGGACACAGCAGAGAAAGGCAAATGGACACCCCTATTAAGTTATTTGGGTCTTGGGTGTCTGGCCCCTAATGAATAATTAAGCCTCAGAAAGTCCAAAAGTTGCAGTGAAGTGAGGGCGGATTACGGCAGGTAGGGGCAGAGGGCGCAGATTTCTTGGGCTGTAAGCAGCAAAATCGGAAGAACGGAGATTGTGGAAGGAAACAGAGCCTAACAGAACAGTGGGCGCGTCTAAATGTGTTGTGCACACGCTGTAGGAGTCCTTCGGATCCTGCGACCCAGATGCTTCCAGCGTCTTTGCTGGCCTTTTGATCCCCCCTCTGCCTCTCCTCTCAATGGCCCCTGGTGAACCCCCAGATCTCAGGCTTCTGCAGTTTTGCCCCGAGTTCTGGTTAACTTGGCGCACTTCTTGATCAGACAGACACTATGGCTTTCATTTCCTGTCCCAGTTACTCTGATTTTCAGCCACTGACTTGTTTTTCTGAGTCTCTTCTCAATTCCGGTGTCCCTTTTTGCAGTGGGGTGGGTTACTTGAGTTCCAGCAACAGCCTCAGTCTTGGGTAGTGCAGATCAGTCAACTGGCGAGGGAACATGGTGGGGCAGGCTACACATGGAGAAAGGGGGCCCAAATGTGCCTCTGACTTCATAGACTAGTGGCCTATCAGTTGTCCCCACTCCCTCCTGCCTCGGTGGTTCCCTGTTTCCTATCTTGATTTGTGAGTCTGGCCACCTGTTCGGTTGAGAGCAGCAAGAGGACAAGGGAGGGTGTCTTACAGTTTCAAAATGGGGCCCCCTCATCCCGTCCCAGTTCTCAGAGCCTATTCCTCTGTAAAAGAACAGTCAGTCCCCCCACTGAGTCCCAGGATCACTTGGCTTAGCCTAGACCACAAAAAGAGGGTTCTGGATTTGTGGTGAAGGCTTTCAGGCTCAGGTAGATGCGAGAGATCAGGTGTCAGGGAAAAGCTTGAGGAGAGGGGAGAGCAAGCCTAGTGGATCCCCTGATGACTGAGGGCCTGCTCGTGTCCCTGTGTTGGGGACTTGAGACCTCTGTGTCAGGATCCAGGTTGACTTTGGGGTGAGGAAAGCCCCCTTTTTTCTGAGGTATATAGTTGGGTGGTATATGGGGTGAGGGGCTGGCTAAGAACCTGCAGCTGGGTGAAAGTGCAGGATAAGGAAGAGGAAAGATTAGCCCCAAGGTGGTGGAACTGGCTTTGACAGCCTCCTCCTCCGGAGGCCCCTTGGCACGGAGCCAAGTCTGGGCCTCAGGCAAAGAGCTCAGGCCAGGGTCTGACTGGACATAGTGCCCGGGACGGCCACATGCCTCCACCCCTTGCTCTTACAATCTCTGACCTTTGCTCTCACCTGCCGGAACACCTTTGACCTACATCGCTGCCACTGGCCTCCCTGCCTCATCTTCCCGAGTGATAATAATCAGTGCTTAACAACCCAGCACCCAGGCTTGGACCCATTAGAGTTAATGAGGCACAGCTTGCTGCTGGCCAGCGTAGCACTTACTTGTTTGTGAGACCCCGGGTCTCCTTCGCCCTAGTCCTTGGCTGTTCTAGAACTCACTCTGTAGACCAGGCTGGTCTCTCTGCCTCGAGAGTGCAGGGATCAGGCCTGGCTCAGCATAGCACTGGTTCAGTTATGGAGAACTGAGAAAGGAGTCCCAGGGCCGGGCTGGAGGAGCGTGGAGGGCCACTAGAGACTTGAGGCAACAGCACTTAACAGTTGGTGGAGAGTATTCACACTTGAACATATGTCTGTCTGTCCCTGCCGATCCTGAGGCACCTTTTAGTCCCTCTATCCCAGGGTTAGAACAGATCTCACGGGACCTAGAGGGAAGAGCTGCTTAAAACCTTCTATTTAGGACTCTACAGATCAGAGTGGAAATCCTGGAGACAGCGGGCTGGAGAAGGAAGAGGAAAAGTGGCCTGGGGAGGGACCGGCAGGGACAGATGTGAACAGGGAGGCTATAATGAGGAACACGTGAGGACCAGATACGCAGACATTTCTCCATGCAGGAGTAGATTCAACTTCTCTTTTGATCTCTCTCCGTGGCCCCCACCTCCTCCACTATGACCTGGGCTTTGGAAGAGTCCAGGACGATGGGGTATTTCCTACCTCTGTGTGCCAAATCTGGAGGACGGGCAGAAACTGCTGTAGTGATAGCTCCCTTCTGTGCCCTTCCCGGATTCAAGAAAAACCAGTGGATGTCATTTAACCACCTGGGTCCCCAGTCATGTACCCATTACTGATTCCCCCCCATCCCCCCATGAGGCTCTGCACGTCTCCTCTTTCTGGGACTTAAGGAGGGATTTGGGTTATATCCCAGGAAGCACCTTCAGTGGTGTCAGGCATGTCTGATCTCAGTGGGACTTCACTTGCTTTGTTTTCCGACAGATGTTTGGCTGTGGCTCCGTGGCTCAGGTGGTGCTCAGCCGTGGCACCCATGGTGGCTTCCTCACCATCAACTTGGCTTTTGGCTTCGCTGTCACCCTTGGCATCTTGGTGGCTGGCCAGGTGTCTGGTAAGGCCTCAACCCCAGCTTCAGTTTTCAGCCCTCACCAGCATTTCCAACAAGTATCTGCCTAGAGAGCAGAGGGGGAGGAACAACTCCAACCAAGGACGCACACTAACAGCACCTCAGCTTTGGGCCCTTTGGAGGCAAGGGTGGAAGAGACTTCACAGAACCTTTGACTTTCACCTTGGAATCAAAGATCAGTCTGTGACATAGTCCAACTGCCATCCAGGCTAAGAAAACCTACCTACACCCCAGAAAGGAAGAGCCCAAGGTGGCAGGCTGTAACTAATGGATGCTATCTCCTCTTCGCAGGTGCCCACTTGAACCCCGCTGTGACCTTCGCAATGTGCTTCCTGGCACGAGAGCCCTGGATCAAGCTGCCCATCTATGCACTGGCACAGACACTGGGGGCCTTCTTGGGCGCTGGGATTGTTTTTGGGCTGTACTACGGTAAGCATTCCCCATCCCGCCCTCCCTTCTCCACACTTTCCCTCTTTAAGTACTTGTTGGCACCAAGCCCACTGATGACAACCGGGGCCTGCCCAGGCCCAGGGCCCGTGACTCATTCACGAACACTCAGGCCCAGGTTGGGGGCCTAGGGGAAAGAAACGAGTTGGGCAACAACAGAATCTCAGGTCCTCCACCCCGCCCCACCCCCTGAGCCTCTACAGTCATATGCTTACCCATGACCCCTGGCGGGGTGGGGAGGGCAGCTCTGAGAGGAGAGGCTCTGCCCTCACTCACAATGGCTCTAATCTGTCACCAGATGCAATCTGGGCCTTTGCCAACAATGAGCTTTTCGTCTCTGGCCCCAACGGCACAGCTGGAATCTTTGCCACCTATCCCTCTGGACACTTGGACATGGTCAATGGCTTCTTTGATCAGGTATGGACTAGGGACATGTGAAGTAAAGGTAGAGGGAGGAACAGTCTTGTTTTGGACAACGCTCCTTGATTGTAGCAGGATTTCTTCTCAGTTCGTGAGAACCCCAACCTCAGAACATGGTGGTGGCGTTGTCTTTTATAAAGCATGGCGCTTCCCAGTGAGTTCTTGGTTTTGCGATCATCCTAGAGTCAGGATGGTCTCTAGCGTGGAGGACTGGAGCGTGGGAGAAGGAGCTGGCCCTCACCGTGCTCTCTCCCCTCTCCCAGTTCATAGGCACAGCCGCCCTTATTGTGTGTGTACTGGCCATCGTTGACCCTTATAACAACCCTGTGCCCCGTGGCCTGGAGGCTTTCACTGTGGGCCTGGTGGTCCTGGTCATTGGAACCTCCATGGGCTTCAATTCTGGCTATGCCGTCAACCCTGCCCGTGACTTTGGACCTCGCCTCTTCACCGCCCTGGCTGGCTGGGGCTCAGAAGTCTTCACGTGAGTACAGTCCCCACTCCCCAGCTTGCCTCCCCTCTTCCTGCCGACCTGTCTCTGATTTCCGGTGTTCTCCCTCCAGGACTGGCCGGCACTGGTGGTGGGTACCCATTGTCTCCCCACTCCTGGGTTCCATCGCTGGTGTCTTCGTGTACCAGCTCATGATTGGTTGCCACCTGGAGCAGCCCCCACCCTCCACCGAGGAAGAGAATGTGAAGCTGGCCCACATGAAACACAAGGAGCAGATCTGAGTGGGCAGCAGCCCCCCTCCCCCACTGTGCACTCTCCTGAGTGTCCACTGACTGTGTGGGGACCAGTCCCCGAAAGCCCTTTGTGATGCCTCTCTCGGGCTAAACCGCTCCCTGTGTCCACCCCTGCTGGATGGGCCCTCCAGAATTTCTATGAACTCTGCCCATTAGGGCATTAGGTTCCCACCCACCTTTAAGCCAAGGTAGGATAGCAAATAAGATGGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAATGAATGTGTACATGTGTGCTGTTTTCTAAGCTGAATGATGCAAAGGCAAGGGACCAAGTTTTCAAAACAAACTGTAGCAGCTCAGGGGAAGGGAGCCCAGGGGAAGGGAGAAAGTGAGTCAGGAATGTGCCAGAGTGTGCATGCTTCAGGGACTCCTCCATGTGGAGGTGGACCCAGAAGTGAGTTTCTAAGTATGCGTGTGCCTACTGTTTTTTTTTTTTTTTTTGAAATGGACTTCTAGGCTTGGGGAGGGGGAAGGGATAAGAAGGGTGTAGCTCACATCTGGAGCTATGACCCTTGACTGGGGGCTGTGTAATATGTTTCTGTTATAAGATAGACATTGGGAGGGGCTGAAGTCCAGGTCGTAAGTTTCATAATTTGTTTTTTAAATATATAAATATATACATACATATATGTTACAGCCCTAGGAATAGGGGTGGGAAACTCCACTTTTTAAAAGGGGTTTCCTTTCTTTAATCCTCCAATCAACAATGTACTGTTGCCTTTTATATATAAAAAAGAATAAAACGTATACATGCTACAGG	*	NM:i:19	MD:Z:5C3A0G6C30C2G2T0C0C2C2C11C20C2A11C23G10G4
+NC_000070.6:c41098183-41092724	2048	NG_007476.1:4960-11439	5080	10	4147H31M1I239M5D2M2D20M1D11M1D19M1D188M802H	*	0	0	GGAGCTGGCCCTCACCGTGCTCTCTCCCCTCTCCCAGTTCATAGGCACAGCCGCCCTTATTGTGTGTGTACTGGCCATCGTTGACCCTTATAACAACCCTGTGCCCCGTGGCCTGGAGGCTTTCACTGTGGGCCTGGTGGTCCTGGTCATTGGAACCTCCATGGGCTTCAATTCTGGCTATGCCGTCAACCCTGCCCGTGACTTTGGACCTCGCCTCTTCACCGCCCTGGCTGGCTGGGGCTCAGAAGTCTTCACGTGAGTACAGTCCCCACTCCCCAGCTTGCCTCCCCTCTTCCTGCCGACCTGTCTCTGATTTCCGGTGTTCTCCCTCCAGGACTGGCCGGCACTGGTGGTGGGTACCCATTGTCTCCCCACTCCTGGGTTCCATCGCTGGTGTCTTCGTGTACCAGCTCATGATTGGTTGCCACCTGGAGCAGCCCCCACCCTCCACCGAGGAAGAGAATGTGAAGCTGGCCCACATGAAACACAAGGAGCAGATCTGAGTGGGCAG	*	NM:i:72	MD:Z:7C0A0G6C2T4C2A23T7C8G8T8C2C8C2C5A11C5C26C17C2C23G8C2C5T2T2A5T2G11T1C19C5^CCCAG2^CA7C6T5^G0C6C0C2^A4C4C1A0T0G0A4^C1G4C7C4A3T11G5C2G14C5T2G20G5C2C28A27T0G4G26

From 8ac9199bf3b5252a737914dfde2eab72501bad75 Mon Sep 17 00:00:00 2001
From: Ross Lazarus <fubar2@users.noreply.github.com>
Date: Sat, 16 Mar 2024 21:08:10 +1100
Subject: [PATCH 22/27] Update tools/mummer4/nucmer.xml
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Björn Grüning <bjoern@gruenings.eu>
---
 tools/mummer4/nucmer.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/mummer4/nucmer.xml b/tools/mummer4/nucmer.xml
index 556e67de953..fff870f1ad4 100644
--- a/tools/mummer4/nucmer.xml
+++ b/tools/mummer4/nucmer.xml
@@ -92,7 +92,7 @@
             </param>
             <when value="delta">
                 <conditional name="mumplot" >
-                    <param name="plot" type="select" label="If the output file is in delta (not sam) format, make a 2-D dotplot of the input sequences? (mummerplot)" >
+                    <param name="plot" type="select" label="Create a 2-D dotplot of the input sequences?" >
                         <option value="no">No plot</option>
                         <option value="yes">Plot</option>
                     </param>

From d589b9dec920c3776a5dfc4a469ca10cb485f302 Mon Sep 17 00:00:00 2001
From: fubar2 <ross.lazarus@gmail.com>
Date: Sat, 16 Mar 2024 21:15:26 +1100
Subject: [PATCH 23/27] remove sam output option

---
 tools/mummer4/nucmer.xml           |  17 +----------------
 tools/mummer4/test-data/nucmer.txt |   2 +-
 tools/mummer4/test-data/out.bam    | Bin 2377 -> 2377 bytes
 tools/mummer4/test-data/out.cram   | Bin 2561 -> 2559 bytes
 4 files changed, 2 insertions(+), 17 deletions(-)

diff --git a/tools/mummer4/nucmer.xml b/tools/mummer4/nucmer.xml
index 556e67de953..3df76c311de 100644
--- a/tools/mummer4/nucmer.xml
+++ b/tools/mummer4/nucmer.xml
@@ -74,8 +74,6 @@
                     && samtools sort -o outsam -O bam bam_out.bam
                 #else if $outform.out_format == 'cram-long':
                     && samtools view -C -o outsam -T reference.fa outsamcalm
-                #else
-                   && mv outsamcalm outsam
                 #end if
             #end if
         ]]>
@@ -86,7 +84,6 @@
         <conditional name="outform">
             <param name="out_format" type="select" label="Output format" help="Select delta format if a plot is needed. Jbrowse is a good choice to view cram and bam tracks">
                 <option value="bam-long">bam format</option>
-                <option value="sam-long">sam format</option>
                 <option value="cram-long">cram format</option>
                 <option value="delta">Mummer delta format - allows plots</option>
             </param>
@@ -115,7 +112,6 @@
                     <when value="no" />
                 </conditional>
             </when>
-            <when value="sam-long"/>
             <when value="bam-long"/>
             <when value="cram-long"/>
         </conditional>
@@ -164,10 +160,9 @@
         <data name="delta_output" format="tabular" from_work_dir="out.delta" label="${tool.name} on ${on_string}: delta format">
            <filter>outform["out_format"] == "delta"</filter>
         </data>
-        <data name="sam_output" format="sam" from_work_dir="outsam"  label="${tool.name} on ${on_string}">
+        <data name="sam_output" format="bam" from_work_dir="outsam"  label="${tool.name} on ${on_string}">
            <filter>outform["out_format"] != "delta"</filter>
            <change_format>
-                <when input="outform.out_format" value="bam-long" format="bam" />
                 <when input="outform.out_format" value="cram-long" format="cram" />
            </change_format>
         </data>
@@ -208,16 +203,6 @@
             <param name="query_sequence" ftype="fasta" value="mouse_aqp3.fasta" />
             <output name="sam_output" ftype="cram" compare="sim_size" value="out.cram" />
         </test>
-        <test expect_num_outputs="1">
-            <param name="advanced" value="defaults" />
-            <conditional name="outform">
-                <param name="out_format" value="sam-long" />
-            </conditional>
-            <param name="seq_input" value="yes" />
-            <param name="reference_sequence" ftype="fasta" value="human_aqp3.fasta"/>
-            <param name="query_sequence" ftype="fasta" value="mouse_aqp3.fasta" />
-            <output name="sam_output" ftype="sam" compare="sim_size" value="out.sam" />
-        </test>
     </tests>
     <help><![CDATA[
         nucmer is for the all-vs-all comparison of nucleotide sequences contained in multi-FastA data files. It is best used for highly similar sequence that may
diff --git a/tools/mummer4/test-data/nucmer.txt b/tools/mummer4/test-data/nucmer.txt
index 4d207057955..9d9ca0a1c53 100644
--- a/tools/mummer4/test-data/nucmer.txt
+++ b/tools/mummer4/test-data/nucmer.txt
@@ -1,4 +1,4 @@
-/tmp/tmp885k3_3o/files/9/9/8/dataset_99883b3a-5339-4acd-82bb-7e6cc0cad9db.dat /tmp/tmp885k3_3o/files/c/b/a/dataset_cbaf4d80-a79c-4055-8ede-298a050d1575.dat
+/tmp/tmp9c1vttkt/files/d/a/d/dataset_dad621f0-f707-414f-9100-3fea68df8a40.dat /tmp/tmp9c1vttkt/files/9/9/3/dataset_993c6a6c-b8c1-4d0f-8ddb-d66169de19cd.dat
 NUCMER
 >NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 6480 5460
 74 223 43 194 19 19 0
diff --git a/tools/mummer4/test-data/out.bam b/tools/mummer4/test-data/out.bam
index 2424d37470d4c9d7c20474c9d3b10a73b542cc36..827195cd2111941b49675e09b2cc34e28334445c 100644
GIT binary patch
delta 321
zcmV-H0lxmp63G&f6o21N!Y~vD@Zw#00ps0XVC_!n{`Cr#1WjN}iQba4wT(nZ4J-Ki
zX2ghsL@%1O-^KUqX?k-#?d2DQ4DUwtxlq6&I-jZ9xs6_~(VPBo{y^u2D#nW_N@bcb
zP%=-V5I_!cIw@2lvxrV(rRyq{v9@UrwYDH2v#HdHz)Bj3qkoh>Ju16g8O1sG&0Dwf
z8g|~ldfw$NM{c;_8a=kgFVKiM5}6KVig73b<1iC835AG3)W&828Pn+d!*WdTN2<lf
zJGW|SSseEJksxP+-cG*KpmiG`gf4Jf-(vG(Q16q&@wk)0kJhsMOQ><x=;Qv4v1Vh|
zwP6-d1aVGaa5cu*EzNrnR^1>KHVe1)tit9K?JjU)49*(jUoRDevyS@C^?QVnOG3!+
TAB2=wgnR%j$tB3MM*#u|7l5Gc

delta 321
zcmV-H0lxmp63G&f6o1=J!Y~{L@akQ80ps0XU_Grnv{$GkXaZwO^mgfbh(t!sR`m7F
zh!F*eUNmXHi|^Ne)9b7GnK%bvd^>?prKE_!<w9!jJG0uTU`ONSJzSQuoYsWoJkJo7
zTx2AslqUktN}2J3z<DZ-ZgQR)mkX+mql^|V=O$yS;g+T(hkuU`(yi83VvIxkI;^5d
zUy?fUc*uLKF~bBK6;y9Str=m7<}Nmw;W1AMjfHSD77Zy>Cag;fg^UWLaW#c^6WOaa
zc)#vpRqpq@k*Gin-pszzsP|onVjuZ!=vDh{mDwfx<6$SFKU%BmFF~tyYYzK6>uhH?
z+9Icp1a?Y5^fiR>wzBV0+zf*>s;&JtphmTy=x~7}BROfXf4x)`F9zy6H#!3VTmS%m
T{~(~c1mFYfSt9VWM*#u|Yp0qR

diff --git a/tools/mummer4/test-data/out.cram b/tools/mummer4/test-data/out.cram
index a1a5c44975a2805ee697c9fd6ea68af46b3a5577..7f2262fb97274ac27273dcc220f82d07e6d798f7 100644
GIT binary patch
delta 332
zcmV-S0ki&r6#o;D8h@<;00000000000s;Vm7oO=70RaF2feeAsABzY8000000RM%L
zK~BRk5Jk(<Jw+}M#}k~m_9{{<6{HdZ0k)B2I}qB$$T6)rBzHosDxy{@EJm7ni~s(7
zUri?2%>upT0x&`4y-?OV-S*O(X;wa<G8g%>B7{+vVi1(4B!2{;*Bq^Kk<uAKcZtxd
zW;D?a<Dhf{G0Yl9bsEc>8b}C3&yOPV-N$~og01&!AHCbU+F7@5``1dh&M0r)S40Sj
zcy#2EGmUYkR|Yq7niWfQyAXryytSJF75TUy`UA%?ny-FoFj(h<&<6I?53+kRQXj~8
zo@Zh>NiB;13^Ph@I(?r1S8E(!GGMsi*tTXDg!A!{AbdJ;9Pz%(^as1;$<xsR008+$
ekjnr70Dy~ti<40Shm&9d1OzycMkce|0VN3b!j5VH

delta 333
zcmV-T0kZ!86M+<v8h@_=00000000000s;Vm7@kEdIRO9wfenGtABzY8000000RM%L
z-%f)t6vpRec?w>D{((ZFS0r09O(vqKx1_X1af6ytU3^I2$!u99Te9uqB<K7tzTbC#
zZ)UUnb^%@sP9O%=1DD2F)eXXFFRva!Rq$e2W6UT^AmKDiaDPAujWVz*ctTSQ?qjZG
z!)UBpmJz915|XrKR3)Kks3tLH;N^)U*MIINP2+V`M+SYErrsL6?uNHobyiDf><_{i
zqYNE5vbxn)4^qQcczL-5cMCp>-WjtQL0L@uzCX!e2<EGQ>W{`cKQO-ea--<qwNQI9
zou`?Q9Ho}!H8g`1n_ivfUuq4*a|TGxIKDf*^@I8Jh#x#3ISzQ&#rp%$+Vls}0RRB;
fA#FDR004lDfQ*w-0fm!b0S5%#^<KKO+5sg9!ds4x


From 8c2b97d89da684bebab57907316aa7ce69385cf9 Mon Sep 17 00:00:00 2001
From: fubar2 <ross.lazarus@gmail.com>
Date: Sun, 17 Mar 2024 14:11:46 +1100
Subject: [PATCH 24/27] Noticed that cat and tail each take a long time when
 there are many GB to process, so removed one file copy operation by appending
 the tail output to the prepared head for the fixed sam to save 10 minutes in
 a 3 hour job on my test server...

---
 tools/mummer4/nucmer.xml           |   6 ++----
 tools/mummer4/test-data/nucmer.txt |   2 +-
 tools/mummer4/test-data/out.bam    | Bin 2377 -> 2356 bytes
 tools/mummer4/test-data/out.cram   | Bin 2559 -> 2561 bytes
 4 files changed, 3 insertions(+), 5 deletions(-)

diff --git a/tools/mummer4/nucmer.xml b/tools/mummer4/nucmer.xml
index e73e9699c34..50aebc58654 100644
--- a/tools/mummer4/nucmer.xml
+++ b/tools/mummer4/nucmer.xml
@@ -64,14 +64,12 @@
                     @MUMMER_GNUPLOT_MANUAL@
                 #end if
             #else:
-                && tail  -n +3 outsam.sam > outsambody
                 && samtools dict reference.fa > outsamhead
-                && cat outsambody >> outsamhead
+                && tail -n +3 outsam.sam >> outsamhead
                 && samtools sort -o outsamheadsort outsamhead
                 && samtools calmd outsamheadsort reference.fa > outsamcalm
                 #if $outform.out_format == 'bam-long':
-                    && samtools view -b -o bam_out.bam outsamcalm
-                    && samtools sort -o outsam -O bam bam_out.bam
+                    && samtools view -b -o outsam outsamcalm
                 #else if $outform.out_format == 'cram-long':
                     && samtools view -C -o outsam -T reference.fa outsamcalm
                 #end if
diff --git a/tools/mummer4/test-data/nucmer.txt b/tools/mummer4/test-data/nucmer.txt
index 9d9ca0a1c53..7ca0b635805 100644
--- a/tools/mummer4/test-data/nucmer.txt
+++ b/tools/mummer4/test-data/nucmer.txt
@@ -1,4 +1,4 @@
-/tmp/tmp9c1vttkt/files/d/a/d/dataset_dad621f0-f707-414f-9100-3fea68df8a40.dat /tmp/tmp9c1vttkt/files/9/9/3/dataset_993c6a6c-b8c1-4d0f-8ddb-d66169de19cd.dat
+/tmp/tmpy6gw75je/files/a/8/d/dataset_a8dfaa04-d4b3-4511-a077-0f1d1613de54.dat /tmp/tmpy6gw75je/files/2/f/e/dataset_2fe26f9b-5fd1-4dbe-86f6-7aac41156c5a.dat
 NUCMER
 >NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 6480 5460
 74 223 43 194 19 19 0
diff --git a/tools/mummer4/test-data/out.bam b/tools/mummer4/test-data/out.bam
index 827195cd2111941b49675e09b2cc34e28334445c..e99718bd46a75b8fcc848f75928b18c0e4bd5c8e 100644
GIT binary patch
delta 319
zcmV-F0l@yr60{P3ABzYC000000RIL6LPG)oH35Z@O-{ow5QW{PdjZ5Q7fAer6E|KJ
zs8o>J5U5~VP2w>WH8n~M6}RL_s1+ijP_Y=z%v-!qPw(P<KKK|AGQOJ7hr)=2)5VRc
zy>IPm0|AHQ#VuVFrkE}{*GgxJFe=Y@EQC7C>8voB8gV**PmQfBty1fBE^6z96eFjV
z%_LL`Manh3zcX&NM#C5j&C71yv&XGYpONkKj%kKWG7AAZ3`>o&#*9NObC9tD4sqr5
zD8@=U)KXhWd14_9$K{k>PfQ0*@P6IVvgq%9B#|eQUe3PNsPk=zVjua}&_VNrVE0P@
z9(pF?hih3j{zs@`-Pl9_79F;@sWEZziy)5?5^;p_w!&=`SACGLwPOzlgpd<L$ltw@
R@|2KIIvdF%`vId#0SK4Zk$eCE

delta 340
zcmV-a0jvJB63G&OABzYC000000RIL6LPG)oN&$`1-%i3X6bA6(U3mfH-CkhrPU-&j
z3Y7#+U`&bLlC!mqL`DrO`1)qVh=N2fnzY}=_v>kTb3N_l7laJ&M)bK*z#=-IsoJ@X
zUarxb{&4<4=Y=Z9izrHEnlMl@PofY&4stpvR3fv8PGhBi>nfG8wrLKvwjdz0snm(U
zN*aixls-KwyIdK?Irq(5xAGcx-oJX@<t;~UxZoN+w#F~eh&U3N4rPjQC;{Uz6E+Ej
zh(XlGW&jz}==;NROz%gk#l}0gYH3*<_WO|_XM)~NzS5v|8y|!&a9iJE^I}l%lf&`2
zlfjSHviwU+sBzWk<Nl4YW@Fa1VHQsWaZX@x#@H>*dk|LLAQd(XxAm;T<`eBMaAFM3
m8sc9s6@;^n`p)%xgpf-@$nPJ7lvjj&04&KR$YcVeGyw?h5u|qj

diff --git a/tools/mummer4/test-data/out.cram b/tools/mummer4/test-data/out.cram
index 7f2262fb97274ac27273dcc220f82d07e6d798f7..0b9d2fe0caecb7fa69ace0147a6fab9c08f30e28 100644
GIT binary patch
delta 333
zcmV-T0kZ!86M+<v8h@_=00000000000s;Vm7@kEdIRO9wfenGtABzY8000000RM%L
z-)@316vo|Uc?w>D{$YhmuShg;OB`ck+bt<=aX6t%=|+6Wz0;yG5>3>LlbrLr_<rB{
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ztQd_{%@QJ2O+qrQ8C7v8Dym6@8F+u?$hF_Q*~Y7ZMQe@LrYZ+xznX4Us>W*RjNKxP
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z@jTCj<RmrEZ!{UC*tF_A|5|GpUNS&(!SUPZ!4GERBYyC9;yB=47w;byFgz;J0RRBM
fhtA9Z004lDfQ*w-0fm!b0S5%#^<KKO+5sg9_a2xJ

delta 332
zcmV-S0ki&r6#o;D8h@<;00000000000s;Vm7oO=70RaF2feeAsABzY8000000RM%L
zK~BRk5Jk(<Jw+}M#}k~m_9{{<6{HdZ0k)B2I}qB$$T6)rBzHosDxy{@EJm7ni~s(7
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zW;D?a<Dhf{G0Yl9bsEc>8b}C3&yOPV-N$~og01&!AHCbU+F7@5``1dh&M0r)S40Sj
zcy#2EGmUYkR|Yq7niWfQyAXryytSJF75TUy`UA%?ny-FoFj(h<&<6I?53+kRQXj~8
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ekjnr70Dy~ti<40Shm&9d1OzycMkce|0VN3b!j5VH


From 3366f6b016120207275105dc42d35ed5c576f3bf Mon Sep 17 00:00:00 2001
From: fubar2 <ross.lazarus@gmail.com>
Date: Mon, 18 Mar 2024 16:29:55 +1100
Subject: [PATCH 25/27] Incorporating suggestions for samtools wrangling.

---
 tools/mummer4/nucmer.xml           |   7 +++----
 tools/mummer4/test-data/nucmer.txt |   2 +-
 tools/mummer4/test-data/out.bam    | Bin 2356 -> 2355 bytes
 tools/mummer4/test-data/out.cram   | Bin 2561 -> 2559 bytes
 4 files changed, 4 insertions(+), 5 deletions(-)

diff --git a/tools/mummer4/nucmer.xml b/tools/mummer4/nucmer.xml
index 50aebc58654..4131bb87971 100644
--- a/tools/mummer4/nucmer.xml
+++ b/tools/mummer4/nucmer.xml
@@ -66,12 +66,11 @@
             #else:
                 && samtools dict reference.fa > outsamhead
                 && tail -n +3 outsam.sam >> outsamhead
-                && samtools sort -o outsamheadsort outsamhead
-                && samtools calmd outsamheadsort reference.fa > outsamcalm
+                && samtools view -T reference.fa -u -x ^ outsamhead | samtools sort -@ \${GALAXY_SLOTS:-1} -u -T "\${TMPDIR:-.}" |
                 #if $outform.out_format == 'bam-long':
-                    && samtools view -b -o outsam outsamcalm
+                    samtools calmd -b --threads {GALAXY_SLOTS:-1} - reference.fa > outsam
                 #else if $outform.out_format == 'cram-long':
-                    && samtools view -C -o outsam -T reference.fa outsamcalm
+                    samtools view -C --reference reference.fa -o outsam -
                 #end if
             #end if
         ]]>
diff --git a/tools/mummer4/test-data/nucmer.txt b/tools/mummer4/test-data/nucmer.txt
index 7ca0b635805..e515076f29e 100644
--- a/tools/mummer4/test-data/nucmer.txt
+++ b/tools/mummer4/test-data/nucmer.txt
@@ -1,4 +1,4 @@
-/tmp/tmpy6gw75je/files/a/8/d/dataset_a8dfaa04-d4b3-4511-a077-0f1d1613de54.dat /tmp/tmpy6gw75je/files/2/f/e/dataset_2fe26f9b-5fd1-4dbe-86f6-7aac41156c5a.dat
+/tmp/tmpk0v09mol/files/2/f/7/dataset_2f771d7a-b9f1-4fc9-b1ea-d06b84d013a0.dat /tmp/tmpk0v09mol/files/d/1/b/dataset_d1bcd825-fbc8-415a-9896-a6af5fd5ebaa.dat
 NUCMER
 >NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 6480 5460
 74 223 43 194 19 19 0
diff --git a/tools/mummer4/test-data/out.bam b/tools/mummer4/test-data/out.bam
index e99718bd46a75b8fcc848f75928b18c0e4bd5c8e..cf2fb8bbbab03220cc8aaeb7b738cd6238fe1699 100644
GIT binary patch
delta 317
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P5`Zs`hu~ndG64bzy*8A)

delta 318
zcmV-E0m1&W60{P3ABzYC000000RIL6LPG)oH35Z@O-{ow5QW{PdjZ5Q7fAer6E|KJ
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Q@|2KIIvdF%voQez2<LB*VgLXD

diff --git a/tools/mummer4/test-data/out.cram b/tools/mummer4/test-data/out.cram
index 0b9d2fe0caecb7fa69ace0147a6fab9c08f30e28..c533ffaf3f27a3ab09283847aabf296ab5f8a696 100644
GIT binary patch
delta 332
zcmV-S0ki&r6#o;D8h@<;00000000000s;Vm7oO=70RaF2feeAsABzY8000000RM%L
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From ae1faadd805fc68b2a120b3d6959f18724ce8789 Mon Sep 17 00:00:00 2001
From: fubar2 <ross.lazarus@gmail.com>
Date: Mon, 18 Mar 2024 16:37:06 +1100
Subject: [PATCH 26/27] do not remove any headers - they've been repaired!

---
 tools/mummer4/nucmer.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/mummer4/nucmer.xml b/tools/mummer4/nucmer.xml
index 4131bb87971..0bb0669701d 100644
--- a/tools/mummer4/nucmer.xml
+++ b/tools/mummer4/nucmer.xml
@@ -66,7 +66,7 @@
             #else:
                 && samtools dict reference.fa > outsamhead
                 && tail -n +3 outsam.sam >> outsamhead
-                && samtools view -T reference.fa -u -x ^ outsamhead | samtools sort -@ \${GALAXY_SLOTS:-1} -u -T "\${TMPDIR:-.}" |
+                && samtools view -T reference.fa -u outsamhead | samtools sort -@ \${GALAXY_SLOTS:-1} -u -T "\${TMPDIR:-.}" |
                 #if $outform.out_format == 'bam-long':
                     samtools calmd -b --threads {GALAXY_SLOTS:-1} - reference.fa > outsam
                 #else if $outform.out_format == 'cram-long':

From 4a3953854916763fd5d4b3abf5fa6090081a0a85 Mon Sep 17 00:00:00 2001
From: fubar2 <ross.lazarus@gmail.com>
Date: Mon, 18 Mar 2024 20:39:40 +1100
Subject: [PATCH 27/27] remove redundant samtools view

---
 tools/mummer4/nucmer.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/mummer4/nucmer.xml b/tools/mummer4/nucmer.xml
index 0bb0669701d..97081d7ab0d 100644
--- a/tools/mummer4/nucmer.xml
+++ b/tools/mummer4/nucmer.xml
@@ -66,7 +66,7 @@
             #else:
                 && samtools dict reference.fa > outsamhead
                 && tail -n +3 outsam.sam >> outsamhead
-                && samtools view -T reference.fa -u outsamhead | samtools sort -@ \${GALAXY_SLOTS:-1} -u -T "\${TMPDIR:-.}" |
+                && samtools sort  -@ \${GALAXY_SLOTS:-1} -T "\${TMPDIR:-.}" outsamhead |
                 #if $outform.out_format == 'bam-long':
                     samtools calmd -b --threads {GALAXY_SLOTS:-1} - reference.fa > outsam
                 #else if $outform.out_format == 'cram-long':