Mercurial > repos > jpayne > snp_pipeline

comparison 6_merge_vcfs.xml @ 27:1044c9a132c5

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planemo upload commit 7f6183b769772449fbcee903686b8d5ec5b7439f-dirty
author jpayne
date Wed, 31 Jan 2018 13:24:56 -0500
parents 05f2f9e58b3f
children 1d77f9fb51f3
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26:05f2f9e58b3f 27:1044c9a132c5
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 export LD_LIBRARY_PATH="\$LD_LIBRARY_PATH:\$CONDA_DEFAULT/lib" && 11 export LD_LIBRARY_PATH="\$LD_LIBRARY_PATH:\$CONDA_DEFAULT_ENV/lib" &&
12 env && 12 env &&
13 ls -lah \$CONDA_DEFAULT && 13 ls -lah \$CONDA_DEFAULT_ENV &&
14 python $__tool_directory__/snp-wind.py ./ -p "consensus.vcf" 14 python $__tool_directory__/snp-wind.py ./ -p "consensus.vcf"
15 #for $vcf in $vcfs 15 #for $vcf in $vcfs
16 -n $vcf.element_identifier -f $vcf 16 -n $vcf.element_identifier -f $vcf
17 #end for 17 #end for
18 > ./file 18 > ./file