Mercurial > repos > iuc > variant_analyzer

comparison mut2sscs.xml @ 0:5441e79a30f2 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
author iuc
date Wed, 20 Nov 2019 22:47:11 +0000
parents
children 833d9e71b864
comparison
equal deleted inserted replaced
-1:000000000000 0:5441e79a30f2
1 <?xml version="1.0" encoding="UTF-8"?>
2 <tool id="mut2sscs" name="DCS mutations to SSCS stats:" version="1.0.0" 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>
4 <macros>
5 <import>va_macros.xml</import>
6 </macros>
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 </requirements>
12 <command><![CDATA[
13 ln -s '$file2' bam_input.bam &&
14 ln -s '${file2.metadata.bam_index}' bam_input.bam.bai &&
15 python '$__tool_directory__/mut2sscs.py'
16 --mutFile '$file1'
17 --bamFile bam_input.bam
18 --outputJson '$output_json'
19 ]]>
20 </command>
21 <inputs>
22 <param name="file1" type="data" format="tabular" label="DCS Mutation File" optional="false" help="TABULAR file with DCS mutations. See Help section below for a detailed explanation."/>
23 <param name="file2" type="data" format="bam" label="SSCS BAM File" optional="false" help="BAM file with aligned SSCS reads."/>
24 </inputs>
25 <outputs>
26 <data name="output_json" format="json" label="${tool.name} on ${on_string}: JSON"/>
27 </outputs>
28 <tests>
29 <test>
30 <param name="file1" value="DCS_Mutations_test_data_VA.tabular"/>
31 <param name="file2" value="SSCS_test_data_VA.bam"/>
32 <output name="output_json" file="SSCS_counts_test_data_VA.json" lines_diff="2"/>
33 </test>
34 </tests>
35 <help> <![CDATA[
36 **What it does**
37
38 Takes a tabular file with DCS mutations and a BAM file of aligned SSCS reads
39 as input and writes statistics about tags of reads that carry a mutation in the
40 SSCS at the same position a mutation is called in the DCS to a user specified output file..
41
42 **Input**
43
44 **Dataset 1:** Tabular file with duplex consesus sequence (DCS) mutations as
45 generated by the **Variant Annotator** tool.
46
47 **Dataset 2:** BAM file of aligned single stranded consensus sequence (SSCS)
48 reads. This file can be obtained by the tool `Map with BWA-MEM
49 <https://arxiv.org/abs/1303.3997>`_.
50
51 **Dataset 3:** Tabular file with reads as produced by the
52 **Du Novo: Align families** tool of the `Du Novo Analysis Pipeline
53 <https://doi.org/10.1186/s13059-016-1039-4>`_
54
55 **Output**
56
57 The output is a json file containing dictonaries with stats of tags that carry a mutation in the SSCS
58 at the same position a mutation is called in the DCS.
59
60 ]]>
61 </help>
62 <expand macro="citation" />
63 </tool>