Mercurial > repos > jpayne > snp_pipeline

comparison 7_smp_matrix.xml @ 50:e90a783a4e8b

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planemo upload commit 2107f35724b3f897c9414be40a9d14663cba9f4d-dirty
author jpayne
date Thu, 09 May 2019 11:45:22 -0400
parents fc7a28de6aa0
children d53281e6edae
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49:ebfa7fd256aa 50:e90a783a4e8b
1 <tool id="snp_matrix" name="7. Create a SNP matrix" version="1.0.1" profile="16.10"> 1 <tool id="snp_matrix" name="7. Create a SNP matrix" version="1.0.1" profile="16.10">
2 <description>and associated distance metrics</description> 2 <description>and associated distance metrics</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.6">bcftools</requirement> 4 <requirement type="package" version="1.9">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="2.0.2">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="3.7.3">python</requirement> 8 <requirement type="package" version="3.6.8">python</requirement>
9 </requirements> 9 </requirements>
10 <command detect_errors="exit_code"><![CDATA[ 10 <command detect_errors="exit_code"><![CDATA[
11 export LD_LIBRARY_PATH="\$CONDA_DEFAULT_ENV/lib" && 11 export LD_LIBRARY_PATH="\$CONDA_DEFAULT_ENV/lib" &&
12 python $__tool_directory__/snp-wind.py ./ -p "consensus.fasta" 12 python $__tool_directory__/snp-wind.py ./ -p "consensus.fasta"
13 #for $fa in sorted($cons, key=lambda f: f.element_identifier) 13 #for $fa in sorted($cons, key=lambda f: f.element_identifier)