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comparison read2mut.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="read2mut" name="Call specific mutations in reads:" version="1.0.0" profile="19.01">
3 <description>Looks for reads with mutation at known positions and calculates frequencies and stats.</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 <requirement type="package" version="1.1.0">xlsxwriter</requirement>
12 </requirements>
13 <command><![CDATA[
14 ln -s '$file2' bam_input.bam &&
15 ln -s '${file2.metadata.bam_index}' bam_input.bam.bai &&
16 python '$__tool_directory__/read2mut.py'
17 --mutFile '$file1'
18 --bamFile bam_input.bam
19 --inputJson '$file3'
20 --sscsJson '$file4'
21 --thresh '$thresh'
22 --phred '$phred'
23 --trim '$trim'
24 --outputFile '$output_xlsx'
25 ]]>
26 </command>
27 <inputs>
28 <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."/>
29 <param name="file2" type="data" format="bam" label="BAM File of raw reads" optional="false" help="BAM file with aligned raw reads of selected tags."/>
30 <param name="file3" type="data" format="json" label="JSON File with DCS tag stats" optional="false" help="JSON file generated by DCS mutations to tags/reads"/>
31 <param name="file4" type="data" format="json" label="JSON File with SSCS tag stats" optional="false" help="JSON file generated by DCS mutations to SSCS stats."/>
32 <param name="thresh" type="integer" label="Tag count threshold" value="0" help="Integer threshold for displaying mutations. Only mutations occuring in DCS of less than thresh tags are displayed. Default of 0 displays all."/>
33 <param name="phred" type="integer" label="Phred quality score threshold" min="0" max="41" value="20" help="Integer threshold for Phred quality score. Only reads higher than this threshold are considered. Default = 20."/>
34 <param name="trim" type="integer" label="Trimming threshold" value="10" help="Integer threshold for assigning mutations at start and end of reads to lower tier. Default 10."/>
35 </inputs>
36 <outputs>
37 <data name="output_xlsx" format="xlsx" label="${tool.name} on ${on_string}: XLSX"/>
38 </outputs>
39 <tests>
40 <test>
41 <param name="file1" value="DCS_Mutations_test_data_VA.tabular"/>
42 <param name="file2" value="Interesting_Reads_test_data_VA.trim.bam"/>
43 <param name="file3" value="tag_count_dict_test_data_VA.json"/>
44 <param name="file4" value="SSCS_counts_test_data_VA.json"/>
45 <param name="thresh" value="0"/>
46 <param name="phred" value="20"/>
47 <param name="trim" value="10"/>
48 <output name="output_xlsx" file="mutant_reads_summary_short_trim_test_data_VA.xlsx" decompress="true" lines_diff="10"/>
49 </test>
50 </tests>
51 <help> <![CDATA[
52 **What it does**
53
54 Takes a tabular file with mutations, a BAM file of aligned raw reads, and JSON files
55 created by the tools **DCS mutations to tags/reads** and **DCS mutations to SSCS stats**
56 as input and calculates frequencies and stats for DCS mutations based on information
57 from the raw reads.
58
59 **Input**
60
61 **Dataset 1:** Tabular file with duplex consesus sequence (DCS) mutations as
62 generated by the **Variant Annotator** tool.
63
64 **Dataset 2:** BAM file of aligned raw reads. This file can be obtained by the
65 tool `Map with BWA-MEM <https://arxiv.org/abs/1303.3997>`_.
66
67 **Dataset 3:** JSON file generated by the **DCS mutations to tags/reads** tool
68 containing dictonaries of the tags of reads containing mutations
69 in the DCS.
70
71 **Dataset 4:** JSON file generated by the **DCS mutations to SSCS stats** tool
72 stats of tags that carry a mutation in the SSCS at the same position a mutation
73 is called in the DCS.
74
75 **Output**
76
77 The output is an XLSX file containing frequencies stats for DCS mutations based
78 on information from the raw reads. In addition to that a tier based
79 classification is provided based on the amout of support for a true variant call.
80
81 ]]>
82 </help>
83 <expand macro="citation" />
84 </tool>