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comparison irissv.xml @ 1:1d4f065fa0ef draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit e3ffd8ae7c25536658ff3ee76389f0c2a9894b4c"
author iuc
date Mon, 17 May 2021 17:29:39 +0000
parents 30fc9f2bcbe4
children b4b6b660293a
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0:30fc9f2bcbe4 1:1d4f065fa0ef
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="irissv" name="Iris" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> 2 <tool id="irissv" name="Iris" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
3 <description>Refine insertion sequences</description> 3 <description>Refine insertion sequences</description>
4 <macros> 4 <macros>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
7 7
10 10
11 <command detect_errors="exit_code"><![CDATA[ 11 <command detect_errors="exit_code"><![CDATA[
12 @REF_FASTA@ 12 @REF_FASTA@
13 13
14 iris 14 iris
15 genome_in=reference.fa 15 genome_in=reference
16 vcf_in='${in_vcf}' 16 vcf_in='${in_vcf}'
17 reads_in='${in_bam}' 17 reads_in='${in_bam}'
18 vcf_out='${out_vcf}' 18 vcf_out='${out_vcf}'
19 threads=\${GALAXY_SLOTS:-4} 19 threads=\${GALAXY_SLOTS:-4}
20 padding_before='${padding_before}' 20 padding_before='${padding_before}'
72 <tests> 72 <tests>
73 <!-- #1 default --> 73 <!-- #1 default -->
74 <test expect_num_outputs="1"> 74 <test expect_num_outputs="1">
75 <conditional name="reference_source"> 75 <conditional name="reference_source">
76 <param name="reference_source_selector" value="history"/> 76 <param name="reference_source_selector" value="history"/>
77 <param name="ref_file" ftype="fasta" value="genome.fa"/> 77 <param name="ref_file" ftype="fasta.gz" value="genome.fa.gz"/>
78 </conditional> 78 </conditional>
79 <param name="in_vcf" value="sniffles.vcf"/> 79 <param name="in_vcf" value="sniffles.vcf"/>
80 <param name="in_bam" value="iris.bam"/> 80 <param name="in_bam" value="iris.bam"/>
81 <output name="out_vcf" file="test_out.vcf"/> 81 <output name="out_vcf" file="test_out.vcf"/>
82 </test> 82 </test>