Mercurial > repos > iuc > variant_analyzer

comparison read2mut.xml @ 1:833d9e71b864 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 60dc8db809909edf44d662683b1f392b9d5964bf"
author iuc
date Wed, 04 Dec 2019 21:20:55 +0000
parents 5441e79a30f2
children 18fcf8017300
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0:5441e79a30f2 1:833d9e71b864
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="1.0.0" profile="19.01"> 2 <tool id="read2mut" name="Call specific mutations in reads:" version="1.0.1" 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 </requirements> 9 </expand>
13 <command><![CDATA[ 10 <command><![CDATA[
14 ln -s '$file2' bam_input.bam && 11 ln -s '$file2' bam_input.bam &&
15 ln -s '${file2.metadata.bam_index}' bam_input.bam.bai && 12 ln -s '${file2.metadata.bam_index}' bam_input.bam.bai &&
16 python '$__tool_directory__/read2mut.py' 13 python '$__tool_directory__/read2mut.py'
17 --mutFile '$file1' 14 --mutFile '$file1'