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comparison 6_merge_vcfs.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 568eb62c7524
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49:ebfa7fd256aa 50:e90a783a4e8b
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 <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="1.6">htslib</requirement> 8 <requirement type="package" version="1.9">htslib</requirement>
9 <requirement type="package" version="3.7.3">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 ls -lah \$CONDA_DEFAULT_ENV/bin && 13 ls -lah \$CONDA_DEFAULT_ENV/bin &&
14 ls -lah \$CONDA_DEFAULT_ENV/lib && 14 ls -lah \$CONDA_DEFAULT_ENV/lib &&
34 <element name="sample2" value="samples/sample2/consensus.vcf" /> 34 <element name="sample2" value="samples/sample2/consensus.vcf" />
35 <element name="sample3" value="samples/sample3/consensus.vcf" /> 35 <element name="sample3" value="samples/sample3/consensus.vcf" />
36 <element name="sample4" value="samples/sample4/consensus.vcf" /> 36 <element name="sample4" value="samples/sample4/consensus.vcf" />
37 </collection> 37 </collection>
38 </param> 38 </param>
39 <output name="snpmav" value="snpma.vcf" lines_diff="2" /> 39 <output name="snpmav" value="snpma.vcf" lines_diff="4" />
40 </test> 40 </test>
41 </tests> 41 </tests>
42 <help><![CDATA[ 42 <help><![CDATA[
43 <a href="http://snp-pipeline.readthedocs.io/en/latest/index.html">http://snp-pipeline.readthedocs.io/en/latest/index.html</a> 43 <a href="http://snp-pipeline.readthedocs.io/en/latest/index.html">http://snp-pipeline.readthedocs.io/en/latest/index.html</a>
44 ]]></help> 44 ]]></help>