Mercurial > repos > jpayne > snp_pipeline

comparison 6_merge_vcfs.xml @ 58:d53281e6edae

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planemo upload
author jpayne
date Mon, 17 Jun 2024 02:57:10 -0400
parents d3095ad12f24
children 49d672730d3e
comparison
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57:d3095ad12f24 58:d53281e6edae
1 <tool id="merge_vcfs" name="6. Merge VCFs" version="1.0.1" profile="16.10"> 1 <tool id="merge_vcfs" name="6. Merge VCFs" version="1.0.1" profile="16.10">
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 <container type="docker">quay.io/biocontainers/mulled-v2-72d480da2f80e0804df2fc75273988c6dba1648d:f354c444b518b0ada8e031aa2984346e2f5d8837-0</container>
4 <requirement type="package" version="1.9">bcftools</requirement> 5 <requirement type="package" version="1.9">bcftools</requirement>
5 <requirement type="package" version="1.0.6">bzip2</requirement> 6 <requirement type="package" version="1.0.8">bzip2</requirement>
6 <requirement type="package" version="2.0.2">snp-pipeline</requirement> 7 <requirement type="package" version="2.2.1">snp-pipeline</requirement>
7 <requirement type="package" version="0.2.5">tabix</requirement> 8 <requirement type="package" version="0.2.6">tabix</requirement>
8 <requirement type="package" version="1.9">htslib</requirement> 9 <requirement type="package" version="1.9">htslib</requirement>
9 <requirement type="package" version="3.6.8">python</requirement> 10 <!-- <requirement type="package" version="3.6.8">python</requirement> -->
10 </requirements> 11 </requirements>
11 <command detect_errors="exit_code"><![CDATA[ 12 <command detect_errors="exit_code"><![CDATA[
12 export LD_LIBRARY_PATH="\$CONDA_DEFAULT_ENV/lib" && 13 export LD_LIBRARY_PATH="\$CONDA_DEFAULT_ENV/lib" &&
13 python $__tool_directory__/snp-wind.py ./ -p "consensus.vcf" 14 python $__tool_directory__/snp-wind.py ./ -p "consensus.vcf"
14 #for $vcf in $vcfs 15 #for $vcf in $vcfs