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comparison irissv.xml @ 2:b4b6b660293a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 695cbdabe249ed4a72c5d2f345dda439f67a2637
author iuc
date Wed, 06 Jul 2022 07:07:21 +0000
parents 1d4f065fa0ef
children 3242dbeea69c
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1:1d4f065fa0ef 2:b4b6b660293a
1 <?xml version="1.0"?> 1 <tool id="irissv" name="Iris" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@">
2 <tool id="irissv" name="Iris" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
3 <description>Refine insertion sequences</description> 2 <description>Refine insertion sequences</description>
4 <macros> 3 <macros>
5 <import>macros.xml</import> 4 <import>macros.xml</import>
6 </macros> 5 </macros>
7 6
8 <expand macro="requirements"/> 7 <expand macro="requirements"/>
9 <expand macro="version_command"/> 8 <expand macro="version_command"/>
10 9
11 <command detect_errors="exit_code"><![CDATA[ 10 <command detect_errors="aggressive"><![CDATA[
12 @REF_FASTA@ 11 @REF_FASTA@
12
13 ln -s '$in_bam' reads.bam &&
14 ln -s '$in_bam.metadata.bam_index' 'reads.bam.bai' &&
13 15
14 iris 16 iris
15 genome_in=reference 17 genome_in=reference
16 vcf_in='${in_vcf}' 18 vcf_in='${in_vcf}'
17 reads_in='${in_bam}' 19 reads_in='reads.bam'
18 vcf_out='${out_vcf}' 20 vcf_out='${out_vcf}'
19 threads=\${GALAXY_SLOTS:-4} 21 threads=\${GALAXY_SLOTS:-4}
20 padding_before='${padding_before}' 22 padding_before='${padding_before}'
21 padding_after='${padding_after}' 23 padding_after='${padding_after}'
22 genome_buffer='${genome_buffer}' 24 genome_buffer='${genome_buffer}'