Mercurial > repos > iuc > bbtools_callvariants

diff callvariants.xml @ 6:51b4b41b7034 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit cd59ba2c349865259b92302a1d70e103b8a5e3cb
author iuc
date Tue, 27 Aug 2024 10:13:01 +0000
parents 4eef1fff762e
children 0df19a0b6eb9
line wrap: on
line diff
--- a/callvariants.xml	Tue May 30 09:00:32 2023 +0000
+++ b/callvariants.xml	Tue Aug 27 10:13:01 2024 +0000
@@ -3,6 +3,7 @@
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="bio.tools"/>
     <expand macro="requirements"/>
     <command detect_errors="exit_code"><![CDATA[
 #import os
@@ -38,7 +39,7 @@
     <inputs>
         <param name="input" type="data" format="bam" label="Bam file" help="Bam files produced by BBMap are recommended"/>
         <expand macro="reference_source_cond"/>
-        <param name="ploidy" type="integer" value="1" min="1" label="Ploidy" help="See help section below"/>
+        <param name="ploidy" type="integer" min="1" value="1" label="Ploidy" help="See help section below"/>
         <param name="output_format" type="select" label="Select output format">
             <option value="vcf" selected="true">vcf</option>
             <option value="gff">gff</option>
@@ -72,7 +73,7 @@
             <param name="output_variant_score_hist" value="yes"/>
             <param name="output_zygosity_hist" value="yes"/>
             <param name="output_quality_hist" value="yes"/>
-            <output name="output" file="cv_output.vcf" ftype="vcf" compare="contains"/>
+            <output name="output" file="cv_output.vcf" ftype="vcf" compare="diff" lines_diff="4"/>
             <output name="output_scorehist" file="cv_scorehist_output.tabular" ftype="tabular" compare="contains"/>
             <output name="output_zygosityhist" file="cv_zygosityhist_output.tabular" ftype="tabular" compare="contains"/>
             <output name="output_qualityhist" file="cv_qualityhist_output.tabular" ftype="tabular" compare="contains"/>
@@ -81,13 +82,13 @@
             <param name="input" value="cv_input.bam" ftype="bam"/>
             <param name="ploidy" value="2"/>
             <param name="output_format" value="gff"/>
-            <output name="output" file="cv_output.gff" ftype="gff" compare="contains"/>
+            <output name="output" file="cv_output.gff" ftype="gff" compare="contains" lines_diff="2"/>
         </test>
         <test expect_num_outputs="1">
             <param name="input" value="cv_input.bam" ftype="bam"/>
             <param name="ploidy" value="2"/>
             <param name="output_format" value="txt"/>
-            <output name="output" file="cv_output.txt" ftype="txt" compare="contains"/>
+            <output name="output" file="cv_output.txt" ftype="txt" compare="contains" lines_diff="2"/>
         </test>
     </tests>
     <help>
@@ -107,4 +108,3 @@
     </help>
     <expand macro="citations"/>
 </tool>
-