Mercurial > repos > jpayne > snp_pipeline

comparison 6_merge_vcfs.xml @ 22:54255ae587ec

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planemo upload commit 7f6183b769772449fbcee903686b8d5ec5b7439f-dirty
author jpayne
date Wed, 31 Jan 2018 12:57:26 -0500
parents 46b274d082a9
children 43113449a74f
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21:46b274d082a9 22:54255ae587ec
7 <requirement type="package">tabix</requirement> 7 <requirement type="package">tabix</requirement>
8 <requirement type="package" version="3.4">python3</requirement> 8 <requirement type="package" version="3.4">python3</requirement>
9 </requirements> 9 </requirements>
10 <command detect_errors="exit_code"><![CDATA[ 10 <command detect_errors="exit_code"><![CDATA[
11 env && 11 env &&
12 which bcftools &&
13 which snp-pipeline &&
14 which python &&
15 ldconfig -p | grep "libbz2.so*" && 12 ldconfig -p | grep "libbz2.so*" &&
16 python $__tool_directory__/snp-wind.py ./ -p "consensus.vcf" 13 python $__tool_directory__/snp-wind.py ./ -p "consensus.vcf"
17 #for $vcf in $vcfs 14 #for $vcf in $vcfs
18 -n $vcf.element_identifier -f $vcf 15 -n $vcf.element_identifier -f $vcf
19 #end for 16 #end for