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comparison 7_smp_matrix.xml @ 58:d53281e6edae

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planemo upload
author jpayne
date Mon, 17 Jun 2024 02:57:10 -0400
parents e90a783a4e8b
children 49d672730d3e
comparison
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57:d3095ad12f24 58:d53281e6edae
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 <container type="docker">quay.io/biocontainers/mulled-v2-d2e223d7ac457e81243657cd7ae8336bd1c16e8e:81b350b3fbf165cbf5db53022037a2657a660701-0</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="3.6.8">python</requirement> 9 <!-- <requirement type="package" version="3.6.8">python</requirement> -->
9 </requirements> 10 </requirements>
10 <command detect_errors="exit_code"><![CDATA[ 11 <command detect_errors="exit_code"><![CDATA[
11 export LD_LIBRARY_PATH="\$CONDA_DEFAULT_ENV/lib" && 12 export LD_LIBRARY_PATH="\$CONDA_DEFAULT_ENV/lib" &&
12 python $__tool_directory__/snp-wind.py ./ -p "consensus.fasta" 13 python $__tool_directory__/snp-wind.py ./ -p "consensus.fasta"
13 #for $fa in sorted($cons, key=lambda f: f.element_identifier) 14 #for $fa in sorted($cons, key=lambda f: f.element_identifier)