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comparison mut2read.xml @ 0:5441e79a30f2 draft

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"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
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children 833d9e71b864
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1 <?xml version="1.0" encoding="UTF-8"?>
2 <tool id="mut2read" name="DCS mutations to tags/reads:" version="1.0.0" profile="19.01">
3 <description>Extracts all tags that carry a mutation in the duplex consensus sequence (DCS)</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 '$__tool_directory__/mut2read.py'
16 --mutFile '$file1'
17 --bamFile bam_input.bam
18 --familiesFile '$file3'
19 --outputFastq '$output_fastq'
20 --outputJson '$output_json'
21 ]]>
22 </command>
23 <inputs>
24 <param name="file1" type="data" format="tabular" label="DCS Mutation File" optional="false" help="TABULAR file with DCS mutations. See Help section below for a detailed explanation."/>
25 <param name="file2" type="data" format="bam" label="DCS BAM File" optional="false" help="BAM file with aligned DCS reads."/>
26 <param name="file3" type="data" format="tabular" label="Aligned Families File" optional="false" help="TABULAR file with aligned families."/>
27 </inputs>
28 <outputs>
29 <data name="output_fastq" format="fastq" label="${tool.name} on ${on_string}: FASTQ"/>
30 <data name="output_json" format="json" label="${tool.name} on ${on_string}: JSON"/>
31 </outputs>
32 <tests>
33 <test>
34 <param name="file1" value="DCS_Mutations_test_data_VA.tabular"/>
35 <param name="file2" value="DCS_test_data_VA.bam"/>
36 <param name="file3" value="Aligned_Families_test_data_VA.tabular"/>
37 <output name="output_fastq" file="Interesting_Reads_test_data_VA.fastq" lines_diff="136"/>
38 <output name="output_json" file="tag_count_dict_test_data_VA.json" lines_diff="2"/>
39 </test>
40 </tests>
41 <help> <![CDATA[
42 **What it does**
43
44 Takes a tabular file with mutations, a BAM file of aligned DCS reads, and a
45 tabular file with aligned families as input and prints all tags of reads that
46 carry a mutation to a user specified output file and creates a fastq file of
47 reads of tags with a mutation.
48
49 **Input**
50
51 **Dataset 1:** Tabular file with duplex consesus sequence (DCS) mutations as
52 generated by the **Variant Annotator** tool.
53
54 **Dataset 2:** BAM file of aligned DCS reads. This file can be obtained by the
55 tool `Map with BWA-MEM <https://arxiv.org/abs/1303.3997>`_.
56
57 **Dataset 3:** Tabular file with reads as produced by the
58 **Du Novo: Align families** tool of the `Du Novo Analysis Pipeline
59 <https://doi.org/10.1186/s13059-016-1039-4>`_
60
61 **Output**
62
63 The output is a json file containing dictonaries of the tags of reads containing mutations
64 in the DCS and a fastq file of all reads of these tags.
65
66 ]]>
67 </help>
68 <expand macro="citation" />
69 </tool>