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comparison 7_smp_matrix.xml @ 62:d497922d6caa

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planemo upload
author jpayne
date Fri, 28 Jun 2024 00:26:24 -0400
parents 2af5e948dd5c
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61:2af5e948dd5c 62:d497922d6caa
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 <container type="docker">quay.io/staphb/cfsan-snp-pipeline</container>
5 <requirement type="package" version="1.9">bcftools</requirement> 5 <!-- <requirement type="package" version="1.9">bcftools</requirement>
6 <requirement type="package" version="1.0.8">bzip2</requirement> 6 <requirement type="package" version="1.0.8">bzip2</requirement>
7 <requirement type="package" version="2.2.1">snp-pipeline</requirement> 7 <requirement type="package" version="2.2.1">snp-pipeline</requirement>
8 <requirement type="package" version="0.2.6">tabix</requirement> 8 <requirement type="package" version="0.2.6">tabix</requirement> -->
9 <!-- <requirement type="package" version="3.6.8">python</requirement> --> 9 <!-- <requirement type="package" version="3.6.8">python</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 python $__tool_directory__/snp-wind.py ./ -p "consensus.fasta" 13 python $__tool_directory__/snp-wind.py ./ -p "consensus.fasta"