Add sam/bam/cram output options to nucmer

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" />

tools/mummer4/macros.xml

@@ -2,23 +2,24 @@
     <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">
         <citations>
             <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@">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="1.19.2">samtools</requirement>
             <yield />
         </requirements>
     </xml>
@@ -30,13 +31,13 @@
             <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>
-        <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 +55,7 @@
             <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>

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

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