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comparison snippy.xml @ 7:e32aac2299fb draft

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"planemo upload commit 401528f2dba371d4ca2491aaa83e0b2bfe36f81a"
author iuc
date Fri, 15 Nov 2019 08:19:05 -0500
parents 0aa87d97847f
children 32f2211eeec3
comparison
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6:4df82423ba61 7:e32aac2299fb
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 -czf out.tgz ${dir_name} 57 tar -cf - ${dir_name} | gzip > out.tgz
58 #if "outcon" in str($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