Mercurial > repos > jpayne > snp_pipeline

comparison 6_merge_vcfs.xml @ 9:41bd2a5793ee

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planemo upload commit 7f6183b769772449fbcee903686b8d5ec5b7439f-dirty
author jpayne
date Tue, 30 Jan 2018 15:55:32 -0500
parents 360e1c2bf24d
children 25b858c2f21d
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8:360e1c2bf24d 9:41bd2a5793ee
2 <description>into a multi-sample VCF with consensus SNPs</description> 2 <description>into a multi-sample VCF with consensus SNPs</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.3.1">bcftools</requirement> 4 <requirement type="package" version="1.3.1">bcftools</requirement>
5 <requirement type="package" version="1.0.1">snp-pipeline</requirement> 5 <requirement type="package" version="1.0.1">snp-pipeline</requirement>
6 <requirement type="package">tabix</requirement> 6 <requirement type="package">tabix</requirement>
7 <requirement type="package" version="3.5">python</requirement> 7 <requirement type="package" version="3.4">python</requirement>
8 </requirements> 8 </requirements>
9 <command detect_errors="exit_code"><![CDATA[ 9 <command detect_errors="exit_code"><![CDATA[
10 $__tool_directory__/snp-wind.py ./ -p "consensus.vcf" 10 python $__tool_directory__/snp-wind.py ./ -p "consensus.vcf"
11 #for $vcf in $vcfs 11 #for $vcf in $vcfs
12 -n $vcf.element_identifier -f $vcf 12 -n $vcf.element_identifier -f $vcf
13 #end for 13 #end for
14 > ./file 14 > ./file
15 && cat ./file 15 && cat ./file