small updates

galaxyproject · Feb 25, 2024 · ec863ea · ec863ea
1 parent e1150a4
commit ec863ea
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Showing 4 changed files with 15 additions and 24 deletions.
diff --git a/tools/freebayes/freebayes.xml b/tools/freebayes/freebayes.xml
@@ -1,4 +1,4 @@
-<tool id="freebayes" name="FreeBayes" version="@TOOL_VERSION@+galaxy0">
+<tool id="freebayes" name="FreeBayes" version="@TOOL_VERSION@+galaxy0" profile="22.05">
     <description>bayesian genetic variant detector</description>
     <xrefs>
         <xref type="bio.tools">freebayes</xref>
@@ -8,7 +8,7 @@
     </macros>
     <expand macro="requirements">
         <requirement type="package" version="5.3.0">gawk</requirement>
-        <requirement type="package" version="20230922">parallel</requirement>
+        <requirement type="package" version="20240122">parallel</requirement>
     </expand>
     <expand macro="version_command" />
     <command detect_errors="exit_code"><![CDATA[
@@ -189,12 +189,12 @@
                 --min-supporting-allele-qsum ${options_type.input_filters.min_supporting_allele_qsum}
                 --min-supporting-mapping-qsum ${options_type.input_filters.min_supporting_mapping_qsum}
                 #if str( $options_type.input_filters.mismatch_filters.mismatch_filters_selector ) == "set":
-                --mismatch-base-quality-threshold ${options_type.input_filters.mismatch_filters.mismatch_base_quality_threshold}
-                  #if str($options_type.input_filters.mismatch_filters.read_mismatch_limit)
-                    --read-mismatch-limit ${options_type.input_filters.mismatch_filters.read_mismatch_limit}
-                  #end if
-                  --read-max-mismatch-fraction ${options_type.input_filters.mismatch_filters.read_max_mismatch_fraction}
-                  --read-snp-limit ${options_type.input_filters.mismatch_filters.read_snp_limit}
+                    --mismatch-base-quality-threshold ${options_type.input_filters.mismatch_filters.mismatch_base_quality_threshold}
+                    #if str($options_type.input_filters.mismatch_filters.read_mismatch_limit)
+                        --read-mismatch-limit ${options_type.input_filters.mismatch_filters.read_mismatch_limit}
+                    #end if
+                    --read-max-mismatch-fraction ${options_type.input_filters.mismatch_filters.read_max_mismatch_fraction}
+                    --read-snp-limit ${options_type.input_filters.mismatch_filters.read_snp_limit}
                 #end if
                 --read-indel-limit ${options_type.input_filters.read_indel_limit}
                 --min-alternate-fraction ${options_type.input_filters.min_alternate_fraction}

diff --git a/tools/freebayes/leftalign.xml b/tools/freebayes/leftalign.xml
@@ -1,12 +1,11 @@
-<?xml version="1.0"?>
-<tool id="bamleftalign" name="BamLeftAlign" version="@TOOL_VERSION@">
+<tool id="bamleftalign" name="BamLeftAlign" version="@TOOL_VERSION@" profile="22.05">
     <description> indels in BAM datasets</description>
-    <xrefs>
-        <xref type="bio.tools">freebayes</xref>
-    </xrefs>
     <macros>
         <import>macros.xml</import>
     </macros>
+    <xrefs>
+        <xref type="bio.tools">freebayes</xref>
+    </xrefs>
     <expand macro="requirements" />
     <expand macro="version_command" />
     <command detect_errors="exit_code"><![CDATA[
@@ -24,7 +23,7 @@
         bamleftalign
             --fasta-reference '${reference_fasta_filename}'
             -c
-            --max-iterations "${iterations}"
+            --max-iterations '${iterations}'
             > '${output_bam}'
     ]]></command>
     <inputs>

diff --git a/tools/freebayes/macros.xml b/tools/freebayes/macros.xml
@@ -3,7 +3,7 @@
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">freebayes</requirement>
-            <requirement type="package" version="1.18">samtools</requirement>
+            <requirement type="package" version="1.19.2">samtools</requirement>
             <yield />
         </requirements>
     </xml>
@@ -12,15 +12,7 @@
     </xml>
     <xml name="citations">
         <citations>
-            <citation type="bibtex">
-                @misc{1207.3907,
-                    Author = {Erik Garrison},
-                    Title = {Haplotype-based variant detection from short-read sequencing},
-                    Year = {2012},
-                    Eprint = {arXiv:1207.3907},
-                    url = {http://arxiv.org/abs/1207.3907}
-                }
-            </citation>
+            <citation type="doi">10.48550/arXiv.1207.3907</citation>
             <yield />
         </citations>
     </xml>

diff --git a/tools/freebayes/test-data/left-align-output.bam b/tools/freebayes/test-data/left-align-output.bam