Mercurial > repos > iuc > irissv
comparison irissv.xml @ 1:1d4f065fa0ef draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit e3ffd8ae7c25536658ff3ee76389f0c2a9894b4c"
author | iuc |
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date | Mon, 17 May 2021 17:29:39 +0000 |
parents | 30fc9f2bcbe4 |
children | b4b6b660293a |
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0:30fc9f2bcbe4 | 1:1d4f065fa0ef |
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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> |