Mercurial > repos > mheinzl > variant_analyzer2
comparison read2mut.xml @ 72:3691922baa08 draft
planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8
author | mheinzl |
---|---|
date | Fri, 19 Mar 2021 14:05:39 +0000 |
parents | f0fc93b7945c |
children | 3e3136368e0d |
comparison
equal
deleted
inserted
replaced
71:8664c0aa91c3 | 72:3691922baa08 |
---|---|
1 <?xml version="1.0" encoding="UTF-8"?> | 1 <?xml version="1.0" encoding="UTF-8"?> |
2 <tool id="read2mut" name="Call specific mutations in reads:" version="2.1.2" profile="17.01"> | 2 <tool id="read2mut" name="Call specific mutations in reads:" version="2.1.2" profile="19.01"> |
3 <description>Looks for reads with mutation at known positions and calculates frequencies and stats.</description> | 3 <description>Looks for reads with mutation at known positions and calculates frequencies and stats.</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="1.1.0">xlsxwriter</requirement> | 8 <requirement type="package" version="1.1.0">xlsxwriter</requirement> |
12 <requirement type="package" version="0.11.6">cyvcf2</requirement> | 9 </expand> |
13 </requirements> | 10 </requirements> |
14 <command><![CDATA[ | 11 <command><![CDATA[ |
15 ln -s '$file2' bam_input.bam && | 12 ln -s '$file2' bam_input.bam && |
16 ln -s '${file2.metadata.bam_index}' bam_input.bam.bai && | 13 ln -s '${file2.metadata.bam_index}' bam_input.bam.bai && |
17 python '$__tool_directory__/read2mut.py' | 14 python '$__tool_directory__/read2mut.py' |