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comparison mut2sscs.xml @ 6:11a2a34f8a2b draft

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planemo upload for repository https://github.com/gpovysil/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8
author mheinzl
date Mon, 18 Jan 2021 09:49:15 +0000
parents 9d74f30275c6
children 84a1a3f70407
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5:d9cbf833624e 6:11a2a34f8a2b
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="1.0.1" profile="19.01"> 2 <tool id="mut2sscs" name="DCS mutations to SSCS stats:" version="2.0.0" 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'
13 --bamFile bam_input.bam 18 --bamFile bam_input.bam
14 --outputJson '$output_json' 19 --outputJson '$output_json'
15 ]]> 20 ]]>
16 </command> 21 </command>
17 <inputs> 22 <inputs>
18 <param name="file1" type="data" format="tabular" label="DCS Mutation File" optional="false" help="TABULAR file with DCS mutations. See Help section below for a detailed explanation."/> 23 <param name="file1" type="data" format="vcf" label="DCS Mutation File" optional="false" help="VCF file with DCS mutations. See Help section below for a detailed explanation."/>
19 <param name="file2" type="data" format="bam" label="SSCS BAM File" optional="false" help="BAM file with aligned SSCS reads."/> 24 <param name="file2" type="data" format="bam" label="SSCS BAM File" optional="false" help="BAM file with aligned SSCS reads."/>
20 </inputs> 25 </inputs>
21 <outputs> 26 <outputs>
22 <data name="output_json" format="json" label="${tool.name} on ${on_string}: JSON"/> 27 <data name="output_json" format="json" label="${tool.name} on ${on_string}: JSON"/>
23 </outputs> 28 </outputs>
24 <tests> 29 <tests>
25 <test> 30 <test>
26 <param name="file1" value="DCS_Mutations_test_data_VA.tabular"/> 31 <param name="file1" value="FreeBayes_test.vcf"/>
27 <param name="file2" value="SSCS_test_data_VA.bam"/> 32 <param name="file2" value="SSCS_test.bam"/>
28 <output name="output_json" file="SSCS_counts_test_data_VA.json" lines_diff="2"/> 33 <output name="output_json" file="SSCS_counts_test.json" lines_diff="2"/>
29 </test> 34 </test>
30 </tests> 35 </tests>
31 <help> <![CDATA[ 36 <help> <![CDATA[
32 **What it does** 37 **What it does**
33 38
34 Takes a tabular file with DCS mutations and a BAM file of aligned SSCS reads 39 Takes a VCF file with DCS mutations and a BAM file of aligned SSCS reads
35 as input and writes statistics about tags of reads that carry a mutation in the 40 as input and writes statistics about tags of reads that carry a mutation in the
36 SSCS at the same position a mutation is called in the DCS to a user specified output file.. 41 SSCS at the same position a mutation is called in the DCS to a user specified output file..
37 42
38 **Input** 43 **Input**
39 44
40 **Dataset 1:** Tabular file with duplex consesus sequence (DCS) mutations as 45 **Dataset 1:** VCF file with duplex consesus sequence (DCS) mutations. E.g.
41 generated by the **Variant Annotator** tool. 46 generated by the `FreeBayes variant caller <https://arxiv.org/abs/1207.3907>`_.
42 47
43 **Dataset 2:** BAM file of aligned single stranded consensus sequence (SSCS) 48 **Dataset 2:** BAM file of aligned single stranded consensus sequence (SSCS)
44 reads. This file can be obtained by the tool `Map with BWA-MEM 49 reads. This file can be obtained by the tool `Map with BWA-MEM
45 <https://arxiv.org/abs/1303.3997>`_. 50 <https://arxiv.org/abs/1303.3997>`_.
46
47 **Dataset 3:** Tabular file with reads as produced by the
48 **Du Novo: Align families** tool of the `Du Novo Analysis Pipeline
49 <https://doi.org/10.1186/s13059-016-1039-4>`_
50 51
51 **Output** 52 **Output**
52 53
53 The output is a json file containing dictonaries with stats of tags that carry a mutation in the SSCS 54 The output is a json file containing dictonaries with stats of tags that carry a mutation in the SSCS
54 at the same position a mutation is called in the DCS. 55 at the same position a mutation is called in the DCS.