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comparison 5_call_consensus.xml @ 9:41bd2a5793ee

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planemo upload commit 7f6183b769772449fbcee903686b8d5ec5b7439f-dirty
author jpayne
date Tue, 30 Jan 2018 15:55:32 -0500
parents 360e1c2bf24d
children 25b858c2f21d
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8:360e1c2bf24d 9:41bd2a5793ee
1 <tool id="call_consensus" name="5. Call consensus SNPs" version="1.0.1" profile="16.10"> 1 <tool id="call_consensus" name="5. Call consensus SNPs" version="1.0.1" profile="16.10">
2 <description>for a sample, or lookup cached consensus SNP calls</description> 2 <description>for a sample, or lookup cached consensus SNP calls</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.0.1">snp-pipeline</requirement> 4 <requirement type="package" version="1.0.1">snp-pipeline</requirement>
5 <requirement type="package" version="1.5.11">boto3</requirement> 5 <requirement type="package" version="1.5.11">boto3</requirement>
6 <requirement type="package" version="3.5">python</requirement> 6 <requirement type="package" version="3.4">python</requirement>
7 </requirements> 7 </requirements>
8 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
9 #set $identifier = $call_pileup.name.split(' ')[0] 9 #set $identifier = $call_pileup.name.split(' ')[0]
10 $__tool_directory__/snp-cache.py snp_consenus_calls 10 python $__tool_directory__/snp-cache.py snp_consenus_calls
11 "\$(md5sum $snps $calls $call_pileup | cut -c -32 | md5sum | cut -c -32)" 11 "\$(md5sum $snps $calls $call_pileup | cut -c -32 | md5sum | cut -c -32)"
12 -c " 12 -c "
13 mkdir ./$identifier/ 13 mkdir ./$identifier/
14 && cp $call_pileup ./$identifier/reads.all.pileup 14 && cp $call_pileup ./$identifier/reads.all.pileup
15 && cfsan_snp_pipeline call_consensus -v 4 -l $snps --vcfFileName "consensus.vcf" ./$identifier/reads.all.pileup 1>&2 && tar zcv ./consensus.vcf ./consensus.fasta 15 && cfsan_snp_pipeline call_consensus -v 4 -l $snps --vcfFileName "consensus.vcf" ./$identifier/reads.all.pileup 1>&2 && tar zcv ./consensus.vcf ./consensus.fasta