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comparison 5_call_consensus.xml @ 49:ebfa7fd256aa

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planemo upload commit 2107f35724b3f897c9414be40a9d14663cba9f4d-dirty
author jpayne
date Wed, 08 May 2019 11:43:17 -0400
parents fc7a28de6aa0
children e90a783a4e8b
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48:fc7a28de6aa0 49:ebfa7fd256aa
7 <requirement type="package" version="3.7.3">python</requirement> 7 <requirement type="package" version="3.7.3">python</requirement>
8 </requirements> 8 </requirements>
9 <command detect_errors="exit_code"><![CDATA[ 9 <command detect_errors="exit_code"><![CDATA[
10 export LD_LIBRARY_PATH="\$CONDA_DEFAULT_ENV/lib" && 10 export LD_LIBRARY_PATH="\$CONDA_DEFAULT_ENV/lib" &&
11 #set $identifier = $call_pileup.name.split(' ')[0] 11 #set $identifier = $call_pileup.name.split(' ')[0]
12 python $__tool_directory__/snp-cache.py snp_consenus_calls 12 python3 $__tool_directory__/snp-cache.py snp_consenus_calls
13 "\$(md5sum $snps $calls $call_pileup | cut -c -32 | md5sum | cut -c -32)" 13 "\$(md5sum $snps $calls $call_pileup | cut -c -32 | md5sum | cut -c -32)"
14 -c " 14 -c "
15 mkdir ./$identifier/ 15 mkdir ./$identifier/
16 && cp $call_pileup ./$identifier/reads.all.pileup 16 && cp $call_pileup ./$identifier/reads.all.pileup
17 && cfsan_snp_pipeline call_consensus -v 4 -l $snps --vcfFileName "consensus.vcf" ./$identifier/reads.all.pileup 1>&2 && tar zcv ./consensus.vcf ./consensus.fasta 17 && cfsan_snp_pipeline call_consensus -v 4 -l $snps --vcfFileName "consensus.vcf" ./$identifier/reads.all.pileup 1>&2 && tar zcv ./consensus.vcf ./consensus.fasta