Mercurial > repos > mheinzl > variant_analyzer2

comparison mut2read.xml @ 11:84a1a3f70407 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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
comparison
equal deleted inserted replaced
10:e18c5293aac7 11:84a1a3f70407
1 <?xml version="1.0" encoding="UTF-8"?> 1 <?xml version="1.0" encoding="UTF-8"?>
2 <tool id="mut2read" name="DCS mutations to tags/reads:" version="2.0.0" profile="19.01"> 2 <tool id="mut2read" name="DCS mutations to tags/reads:" version="2.0.1" profile="19.01">
3 <description>Extracts all tags that carry a mutation in the duplex consensus sequence (DCS)</description> 3 <description>Extracts all tags that carry a mutation in the duplex consensus sequence (DCS)</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 '$__tool_directory__/mut2read.py' 11 python '$__tool_directory__/mut2read.py'
17 --mutFile '$file1' 12 --mutFile '$file1'
30 <data name="output_fastq" format="fastq" label="${tool.name} on ${on_string}: FASTQ"/> 25 <data name="output_fastq" format="fastq" label="${tool.name} on ${on_string}: FASTQ"/>
31 <data name="output_json" format="json" label="${tool.name} on ${on_string}: JSON"/> 26 <data name="output_json" format="json" label="${tool.name} on ${on_string}: JSON"/>
32 </outputs> 27 </outputs>
33 <tests> 28 <tests>
34 <test> 29 <test>
35 <param name="file1" value="FreeBayes_test.vcf" lines_diff="2"/> 30 <param name="file1" value="FreeBayes_test.vcf"/>
36 <param name="file2" value="DCS_test.bam"/> 31 <param name="file2" value="DCS_test.bam"/>
37 <param name="file3" value="Aligned_Families_test.tabular"/> 32 <param name="file3" value="Aligned_Families_test.tabular"/>
38 <output name="output_fastq" file="Interesting_Reads_test.fastq" lines_diff="136"/> 33 <output name="output_fastq" file="Interesting_Reads_test.fastq"/>
39 <output name="output_json" file="tag_count_dict_test.json" lines_diff="2"/> 34 <output name="output_json" file="tag_count_dict_test.json" lines_diff="2"/>
40 </test> 35 </test>
41 </tests> 36 </tests>
42 <help> <![CDATA[ 37 <help> <![CDATA[
43 **What it does** 38 **What it does**