Mercurial > repos > mheinzl > variant_analyzer2
comparison mut2sscs.xml @ 43:d21960b45a6b draft
planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8
author | mheinzl |
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date | Tue, 02 Mar 2021 15:32:41 +0000 |
parents | 84a1a3f70407 |
children | 3691922baa08 |
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42:da224c392a54 | 43:d21960b45a6b |
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2 <tool id="mut2sscs" name="DCS mutations to SSCS stats:" version="2.0.1" 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 <expand macro="requirements"/> | 7 <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> | |
8 <command><![CDATA[ | 13 <command><![CDATA[ |
9 ln -s '$file2' bam_input.bam && | 14 ln -s '$file2' bam_input.bam && |
10 ln -s '${file2.metadata.bam_index}' bam_input.bam.bai && | 15 ln -s '${file2.metadata.bam_index}' bam_input.bam.bai && |
11 python '$__tool_directory__/mut2sscs.py' | 16 python '$__tool_directory__/mut2sscs.py' |
12 --mutFile '$file1' | 17 --mutFile '$file1' |