Mercurial > repos > jpayne > snp_pipeline

comparison 6_merge_vcfs.xml @ 51:568eb62c7524

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planemo upload commit 2107f35724b3f897c9414be40a9d14663cba9f4d-dirty
author jpayne
date Tue, 17 Sep 2019 11:06:59 -0400
parents e90a783a4e8b
children 0acc1975bbeb
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50:e90a783a4e8b 51:568eb62c7524
8 <requirement type="package" version="1.9">htslib</requirement> 8 <requirement type="package" version="1.9">htslib</requirement>
9 <requirement type="package" version="3.6.8">python</requirement> 9 <requirement type="package" version="3.6.8">python</requirement>
10 </requirements> 10 </requirements>
11 <command detect_errors="exit_code"><![CDATA[ 11 <command detect_errors="exit_code"><![CDATA[
12 export LD_LIBRARY_PATH="\$CONDA_DEFAULT_ENV/lib" && 12 export LD_LIBRARY_PATH="\$CONDA_DEFAULT_ENV/lib" &&
13 ls -lah \$CONDA_DEFAULT_ENV/bin &&
14 ls -lah \$CONDA_DEFAULT_ENV/lib &&
15 python $__tool_directory__/snp-wind.py ./ -p "consensus.vcf" 13 python $__tool_directory__/snp-wind.py ./ -p "consensus.vcf"
16 #for $vcf in $vcfs 14 #for $vcf in $vcfs
17 -n $vcf.element_identifier -f $vcf 15 -n $vcf.element_identifier -f $vcf
18 #end for 16 #end for
19 > ./file 17 > ./file