Mercurial > repos > iuc > variant_analyzer
comparison mut2read.xml @ 0:8d29173d49a9 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
author | iuc |
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date | Wed, 20 Nov 2019 17:47:35 -0500 |
parents | |
children | 3556001ff2db |
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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> |