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comparison mut2sscs.xml @ 0:e5953c54cfb5 draft

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planemo upload for repository https://github.com/gpovysil/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8
author mheinzl
date Sun, 04 Oct 2020 17:19:39 +0000
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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">
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>
5 <import>va_macros.xml</import>
6 </macros>
7 <expand macro="requirements"/>
8 <command><![CDATA[
9 ln -s '$file2' bam_input.bam &&
10 ln -s '${file2.metadata.bam_index}' bam_input.bam.bai &&
11 python '$__tool_directory__/mut2sscs.py'
12 --mutFile '$file1'
13 --bamFile bam_input.bam
14 --outputJson '$output_json'
15 ]]>
16 </command>
17 <inputs>
18 <param name="file1" type="data" format="tabular" label="DCS Mutation File" optional="false" help="TABULAR file with DCS mutations. See Help section below for a detailed explanation."/>
19 <param name="file2" type="data" format="bam" label="SSCS BAM File" optional="false" help="BAM file with aligned SSCS reads."/>
20 </inputs>
21 <outputs>
22 <data name="output_json" format="json" label="${tool.name} on ${on_string}: JSON"/>
23 </outputs>
24 <tests>
25 <test>
26 <param name="file1" value="DCS_Mutations_test_data_VA.tabular"/>
27 <param name="file2" value="SSCS_test_data_VA.bam"/>
28 <output name="output_json" file="SSCS_counts_test_data_VA.json" lines_diff="2"/>
29 </test>
30 </tests>
31 <help> <![CDATA[
32 **What it does**
33
34 Takes a tabular 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
36 SSCS at the same position a mutation is called in the DCS to a user specified output file..
37
38 **Input**
39
40 **Dataset 1:** Tabular file with duplex consesus sequence (DCS) mutations as
41 generated by the **Variant Annotator** tool.
42
43 **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
45 <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 **Output**
52
53 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
56 ]]>
57 </help>
58 <expand macro="citation" />
59 </tool>