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comparison snippy.xml @ 9:43791d945de1 draft

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"planemo upload commit 5b41fad964a75dcdc794e90342144c3eccea16d7"
author iuc
date Sun, 01 Dec 2019 18:05:33 +0000
parents eea223efd86e
children a3f95a688c47
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8:eea223efd86e 9:43791d945de1
1 <tool id="snippy" name="snippy" version="@VERSION@+galaxy0"> 1 <tool id="snippy" name="snippy" version="@VERSION@+galaxy1">
2 <description> 2 <description>
3 Snippy finds SNPs between a haploid reference genome and your NGS sequence reads. 3 Snippy finds SNPs between a haploid reference genome and your NGS sequence reads.
4 </description> 4 </description>
5 <macros> 5 <macros>
6 <import>macros.xml</import> 6 <import>macros.xml</import>
52 #elif str( $fastq_input.fastq_input_selector ) == "paired_iv" 52 #elif str( $fastq_input.fastq_input_selector ) == "paired_iv"
53 #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input_interleaved.element_identifier) 53 #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input_interleaved.element_identifier)
54 #end if 54 #end if
55 55
56 mkdir -p ${dir_name} && cp -r out/reference out/snps.tab out/snps.aligned.fa out/snps.vcf ${dir_name}/ && 56 mkdir -p ${dir_name} && cp -r out/reference out/snps.tab out/snps.aligned.fa out/snps.vcf ${dir_name}/ &&
57 tar -cf - ${dir_name} | gzip > out.tgz 57 tar -czf out.tgz ${dir_name}
58 #if "outcon" in str($outputs) and $adv.rename_cons 58 #if "outcon" in str($outputs) and $adv.rename_cons
59 && sed -i 's/>.*/>${dir_name}/' out/snps.consensus.fa 59 && sed -i 's/>.*/>${dir_name}/' out/snps.consensus.fa
60 #end if 60 #end if
61 61
62 62