Mercurial > repos > iuc > vardict_java

diff vardict.xml @ 2:6733325083d3 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict commit c247c47e1bc869c9094997f5052ce31367e10b1e"
author iuc
date Tue, 16 Nov 2021 19:05:24 +0000
parents e31b6f4d89ad
children 04c9c72b2648
line wrap: on
line diff
--- a/vardict.xml	Fri Sep 11 21:06:52 2020 +0000
+++ b/vardict.xml	Tue Nov 16 19:05:24 2021 +0000
@@ -5,8 +5,8 @@
     </macros>
     <requirements>
         <requirement type="package" version="@TOOL_VERSION@">vardict-java</requirement>
-        <requirement type="package" version="5.0.1">gawk</requirement>
-        <requirement type="package" version="1.10">samtools</requirement>
+        <requirement type="package" version="5.1.0">gawk</requirement>
+        <requirement type="package" version="1.14">samtools</requirement>
     </requirements>
     <expand macro="stdio" />
     <command detect_errors="exit_code"><![CDATA[
@@ -86,7 +86,7 @@
         <conditional name="select_mode">
             <param name="mode" type="select" label="Choose run mode">
                 <option value="single">Single sample mode</option>
-                <option value="paired" selected="True">Paired variant calling</option>
+                <option value="paired" selected="true">Paired variant calling</option>
             </param>
             <when value="single">
                 <expand macro="input_default" />
@@ -96,7 +96,7 @@
                 <expand macro="input_default" />
             </when>
         </conditional>
-        <section name="advancedsettings" title="Advanced Settings" expanded="False">
+        <section name="advancedsettings" title="Advanced Settings" expanded="false">
             <param argument="-f" type="float" min="0.0" max="1.0" value="0.01" label="Minimum variant allele fraction" />
             <param argument="-k" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Indicate whether to perform local realignment" />
             <param argument="-r" type="integer" min="0" value="2" label="Minimum number of reads supporting the variant" />
@@ -128,8 +128,8 @@
                 <param name="reference_source_selector" value="history"/>
                 <param name="ref_file" ftype="fasta" value="genome.fasta" />
             </conditional>
-            <output name="all_variants" file="all_variants_paired.vcf" />
-            <output name="passed_variants" file="passed_variants_paired.vcf" />
+            <output name="all_variants" compare="re_match_multiline" file="all_variants_paired.vcf" />
+            <output name="passed_variants" compare="re_match_multiline" file="passed_variants_paired.vcf" />
         </test>
         <test expect_num_outputs="2">
             <conditional name="select_mode">
@@ -141,8 +141,8 @@
                 <param name="reference_source_selector" value="cached"/>
                 <param name="ref_file" value="test_buildid"/>
             </conditional>
-            <output name="all_variants" file="all_variants_paired.vcf" />
-            <output name="passed_variants" file="passed_variants_paired.vcf" />
+            <output name="all_variants" compare="re_match_multiline" file="all_variants_paired.vcf" />
+            <output name="passed_variants" compare="re_match_multiline" file="passed_variants_paired.vcf" />
         </test>
         <test expect_num_outputs="2">
             <conditional name="select_mode">
@@ -153,8 +153,8 @@
                 <param name="reference_source_selector" value="cached"/>
                 <param name="ref_file" value="test_buildid"/>
             </conditional>
-            <output name="all_variants" file="all_variants_single.vcf" />
-            <output name="passed_variants" file="passed_variants_single.vcf" />
+            <output name="all_variants" compare="re_match_multiline" file="all_variants_single.vcf" />
+            <output name="passed_variants" compare="re_match_multiline" file="passed_variants_single.vcf" />
         </test>
     </tests>
     <help>