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changeset 16:a2feedafda6f draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit be1c2e9e056710ef8b1110a121dc38c6e06dbbee"
author iuc
date Mon, 21 Feb 2022 09:53:05 +0000
parents c3da1614f96d
children fcd4f3bf844e
files freebayes.xml leftalign.xml macros.xml
diffstat 3 files changed, 10 insertions(+), 5 deletions(-) [+]
line wrap: on
line diff
--- a/freebayes.xml	Fri Dec 03 22:27:08 2021 +0000
+++ b/freebayes.xml	Mon Feb 21 09:53:05 2022 +0000
@@ -1,4 +1,4 @@
-<tool id="freebayes" name="FreeBayes" version="@TOOL_VERSION@+galaxy1">
+<tool id="freebayes" name="FreeBayes" version="@TOOL_VERSION@+galaxy0">
     <description>bayesian genetic variant detector</description>
     <xrefs>
         <xref type="bio.tools">freebayes</xref>
@@ -8,8 +8,9 @@
     </macros>
     <expand macro="requirements">
         <requirement type="package" version="5.1.0">gawk</requirement>
-        <requirement type="package" version="20211022">parallel</requirement>
+        <requirement type="package" version="20211222">parallel</requirement>
     </expand>
+    <expand macro="version_command" />
     <command detect_errors="exit_code"><![CDATA[
     ##set up input files
 
@@ -696,7 +697,7 @@
             <param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta"/>
             <param name="input_bams" ftype="cram" value="freebayes-phix174.cram"/>
             <param name="options_type_selector" value="simple"/>
-            <output name="output_vcf" file="freebayes-phix174-test1.vcf" lines_diff="4" />
+            <output name="output_vcf" file="freebayes-phix174-test1.vcf" lines_diff="6" />
         </test>
     </tests>
     <help><![CDATA[
--- a/leftalign.xml	Fri Dec 03 22:27:08 2021 +0000
+++ b/leftalign.xml	Mon Feb 21 09:53:05 2022 +0000
@@ -8,6 +8,7 @@
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements" />
+    <expand macro="version_command" />
     <command detect_errors="exit_code"><![CDATA[
         ##set up input files
         #set $reference_fasta_filename = "localref.fa"
--- a/macros.xml	Fri Dec 03 22:27:08 2021 +0000
+++ b/macros.xml	Mon Feb 21 09:53:05 2022 +0000
@@ -1,12 +1,15 @@
 <macros>
-    <token name="@TOOL_VERSION@">1.3.5</token>
+    <token name="@TOOL_VERSION@">1.3.6</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">freebayes</requirement>
-            <requirement type="package" version="1.12">samtools</requirement>
+            <requirement type="package" version="1.14">samtools</requirement>
             <yield />
         </requirements>
     </xml>
+    <xml name="version_command">
+        <version_command>freebayes --version | cut -d v -f 3</version_command>
+    </xml>
     <xml name="citations">
         <citations>
             <citation type="bibtex">