Mercurial > repos > iuc > variant_analyzer

comparison read2mut.xml @ 2:3f1dbd2c59bf draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit f492e9717cb946f0eb5689cd7b6eb8067abf6468"
author iuc
date Tue, 10 Nov 2020 12:55:29 +0000
parents 3556001ff2db
children
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1:3556001ff2db 2:3f1dbd2c59bf
1 <?xml version="1.0" encoding="UTF-8"?> 1 <?xml version="1.0" encoding="UTF-8"?>
2 <tool id="read2mut" name="Call specific mutations in reads:" version="1.0.1" profile="19.01"> 2 <tool id="read2mut" name="Call specific mutations in reads:" version="2.0.0" profile="19.01">
3 <description>Looks for reads with mutation at known positions and calculates frequencies and stats.</description> 3 <description>Looks for reads with mutation at known positions and calculates frequencies and stats.</description>
4 <macros> 4 <macros>
5 <import>va_macros.xml</import> 5 <import>va_macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements"> 7 <expand macro="requirements">
16 --inputJson '$file3' 16 --inputJson '$file3'
17 --sscsJson '$file4' 17 --sscsJson '$file4'
18 --thresh '$thresh' 18 --thresh '$thresh'
19 --phred '$phred' 19 --phred '$phred'
20 --trim '$trim' 20 --trim '$trim'
21 $chimera_correction
21 --outputFile '$output_xlsx' 22 --outputFile '$output_xlsx'
22 ]]> 23 ]]>
23 </command> 24 </command>
24 <inputs> 25 <inputs>
25 <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."/> 26 <param name="file1" type="data" format="vcf" label="DCS Mutation File" optional="false" help="VCF file with DCS mutations. See Help section below for a detailed explanation."/>
26 <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."/> 27 <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."/>
27 <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"/> 28 <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"/>
28 <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."/> 29 <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."/>
29 <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."/> 30 <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."/>
30 <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."/> 31 <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."/>
31 <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."/> 32 <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."/>
33 <param name="chimera_correction" type="boolean" label="Apply chimera correction?" truevalue="--chimera_correction" falsevalue="" checked="False" help="Count chimeric variants and correct the variant frequencies."/>
32 </inputs> 34 </inputs>
33 <outputs> 35 <outputs>
34 <data name="output_xlsx" format="xlsx" label="${tool.name} on ${on_string}: XLSX"/> 36 <data name="output_xlsx" format="xlsx" label="${tool.name} on ${on_string}: XLSX"/>
35 </outputs> 37 </outputs>
36 <tests> 38 <tests>
37 <test> 39 <test>
38 <param name="file1" value="DCS_Mutations_test_data_VA.tabular"/> 40 <param name="file1" value="FreeBayes_test.vcf"/>
39 <param name="file2" value="Interesting_Reads_test_data_VA.trim.bam"/> 41 <param name="file2" value="Interesting_Reads_test.trim.bam"/>
40 <param name="file3" value="tag_count_dict_test_data_VA.json"/> 42 <param name="file3" value="tag_count_dict_test.json"/>
41 <param name="file4" value="SSCS_counts_test_data_VA.json"/> 43 <param name="file4" value="SSCS_counts_test.json"/>
42 <param name="thresh" value="0"/> 44 <param name="thresh" value="0"/>
43 <param name="phred" value="20"/> 45 <param name="phred" value="20"/>
44 <param name="trim" value="10"/> 46 <param name="trim" value="10"/>
45 <output name="output_xlsx" file="mutant_reads_summary_short_trim_test_data_VA.xlsx" decompress="true" lines_diff="10"/> 47 <param name="chimera_correction" value="True"/>
48 <output name="output_xlsx" file="Variant_Analyzer_test.xlsx" decompress="true" lines_diff="2"/>
46 </test> 49 </test>
47 </tests> 50 </tests>
48 <help> <![CDATA[ 51 <help> <![CDATA[
49 **What it does** 52 **What it does**
50 53
51 Takes a tabular file with mutations, a BAM file of aligned raw reads, and JSON files 54 Takes a VCF file with mutations, a BAM file of aligned raw reads, and JSON files
52 created by the tools **DCS mutations to tags/reads** and **DCS mutations to SSCS stats** 55 created by the tools **DCS mutations to tags/reads** and **DCS mutations to SSCS stats**
53 as input and calculates frequencies and stats for DCS mutations based on information 56 as input and calculates frequencies and stats for DCS mutations based on information
54 from the raw reads. 57 from the raw reads.
55 58
56 **Input** 59 **Input**
57 60
58 **Dataset 1:** Tabular file with duplex consesus sequence (DCS) mutations as 61 **Dataset 1:** VCF file with duplex consesus sequence (DCS) mutations. E.g.
59 generated by the **Variant Annotator** tool. 62 generated by the `FreeBayes variant caller <https://arxiv.org/abs/1207.3907>`_.
60 63
61 **Dataset 2:** BAM file of aligned raw reads. This file can be obtained by the 64 **Dataset 2:** BAM file of aligned raw reads. This file can be obtained by the
62 tool `Map with BWA-MEM <https://arxiv.org/abs/1303.3997>`_. 65 tool `Map with BWA-MEM <https://arxiv.org/abs/1303.3997>`_.
63 66
64 **Dataset 3:** JSON file generated by the **DCS mutations to tags/reads** tool 67 **Dataset 3:** JSON file generated by the **DCS mutations to tags/reads** tool