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comparison mut2sscs.xml @ 11:84a1a3f70407 draft

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planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8
author mheinzl
date Mon, 15 Feb 2021 21:53:24 +0000
parents 11a2a34f8a2b
children d21960b45a6b
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10:e18c5293aac7 11:84a1a3f70407
1 <?xml version="1.0" encoding="UTF-8"?> 1 <?xml version="1.0" encoding="UTF-8"?>
2 <tool id="mut2sscs" name="DCS mutations to SSCS stats:" version="2.0.0" profile="19.01"> 2 <tool id="mut2sscs" name="DCS mutations to SSCS stats:" version="2.0.1" profile="19.01">
3 <description>Extracts all tags from the single stranded consensus sequence (SSCS) bam file that carry a mutation at the same position a mutation is called in the duplex consensus sequence (DCS) and calculates their frequencies</description> 3 <description>Extracts all tags from the single stranded consensus sequence (SSCS) bam file that carry a mutation at the same position a mutation is called in the duplex consensus sequence (DCS) and calculates their frequencies</description>
4 <macros> 4 <macros>
5 <import>va_macros.xml</import> 5 <import>va_macros.xml</import>
6 </macros> 6 </macros>
7 <requirements> 7 <expand macro="requirements"/>
8 <requirement type="package" version="2.7">python</requirement>
9 <requirement type="package" version="1.4.0">matplotlib</requirement>
10 <requirement type="package" version="0.15">pysam</requirement>
11 <requirement type="package" version="0.11.6">cyvcf2</requirement>
12 </requirements>
13 <command><![CDATA[ 8 <command><![CDATA[
14 ln -s '$file2' bam_input.bam && 9 ln -s '$file2' bam_input.bam &&
15 ln -s '${file2.metadata.bam_index}' bam_input.bam.bai && 10 ln -s '${file2.metadata.bam_index}' bam_input.bam.bai &&
16 python '$__tool_directory__/mut2sscs.py' 11 python '$__tool_directory__/mut2sscs.py'
17 --mutFile '$file1' 12 --mutFile '$file1'