Mercurial > repos > jpayne > snp_pipeline

comparison 6_merge_vcfs.xml @ 20:baf9ccfae6f0

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planemo upload commit 7f6183b769772449fbcee903686b8d5ec5b7439f-dirty
author jpayne
date Wed, 31 Jan 2018 12:45:53 -0500
parents 4bb7e4a360bc
children 46b274d082a9
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19:4bb7e4a360bc 20:baf9ccfae6f0
6 <requirement type="package" version="1.0.1">snp-pipeline</requirement> 6 <requirement type="package" version="1.0.1">snp-pipeline</requirement>
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 &&
12 which bcftools &&
13 which bunzip &&
14 which snp-pipeline &&
15 which python &&
16 ldconfig -p | grep "libbz2.so*" &&
11 python $__tool_directory__/snp-wind.py ./ -p "consensus.vcf" 17 python $__tool_directory__/snp-wind.py ./ -p "consensus.vcf"
12 #for $vcf in $vcfs 18 #for $vcf in $vcfs
13 -n $vcf.element_identifier -f $vcf 19 -n $vcf.element_identifier -f $vcf
14 #end for 20 #end for
15 > ./file 21 > ./file