Mercurial > repos > jpayne > snp_pipeline

comparison 6_merge_vcfs.xml @ 45:f58616a4b2f3

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planemo upload commit 2107f35724b3f897c9414be40a9d14663cba9f4d-dirty
author jpayne
date Tue, 07 May 2019 11:44:12 -0400
parents 69216317baa7
children d273453b30bb
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44:e7cac7790476 45:f58616a4b2f3
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.6">bcftools</requirement> 4 <requirement type="package" version="1.6">bcftools</requirement>
5 <requirement type="package" version="1.0.6">bzip2</requirement> 5 <requirement type="package" version="1.0.6">bzip2</requirement>
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" version="0.2.5">tabix</requirement> 7 <requirement type="package" version="0.2.5">tabix</requirement>
8 <!-- <requirement type="package" version="3.5">python</requirement> --> 8 <requirement type="package" version="3.6">python</requirement>
9 <requirement type="package" version="1.6">htslib</requirement> 9 <requirement type="package" version="1.6">htslib</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 env && 13 # env &&
14 ls -lah \$CONDA_DEFAULT_ENV/bin && 14 ls -lah \$CONDA_DEFAULT_ENV/bin &&
15 ls -lah \$CONDA_DEFAULT_ENV/lib && 15 ls -lah \$CONDA_DEFAULT_ENV/lib &&
16 python $__tool_directory__/snp-wind.py ./ -p "consensus.vcf" 16 python $__tool_directory__/snp-wind.py ./ -p "consensus.vcf"
17 #for $vcf in $vcfs 17 #for $vcf in $vcfs
18 -n $vcf.element_identifier -f $vcf 18 -n $vcf.element_identifier -f $vcf