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comparison mut2read.xml @ 2:18fcf8017300 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 12:54:49 +0000
parents 833d9e71b864
children
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1:833d9e71b864 2:18fcf8017300
1 <?xml version="1.0" encoding="UTF-8"?> 1 <?xml version="1.0" encoding="UTF-8"?>
2 <tool id="mut2read" name="DCS mutations to tags/reads:" version="1.0.1" profile="19.01"> 2 <tool id="mut2read" name="DCS mutations to tags/reads:" version="2.0.0" profile="19.01">
3 <description>Extracts all tags that carry a mutation in the duplex consensus sequence (DCS)</description> 3 <description>Extracts all tags that carry a mutation in the duplex consensus sequence (DCS)</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"/>
15 --outputFastq '$output_fastq' 15 --outputFastq '$output_fastq'
16 --outputJson '$output_json' 16 --outputJson '$output_json'
17 ]]> 17 ]]>
18 </command> 18 </command>
19 <inputs> 19 <inputs>
20 <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."/> 20 <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."/>
21 <param name="file2" type="data" format="bam" label="DCS BAM File" optional="false" help="BAM file with aligned DCS reads."/> 21 <param name="file2" type="data" format="bam" label="DCS BAM File" optional="false" help="BAM file with aligned DCS reads."/>
22 <param name="file3" type="data" format="tabular" label="Aligned Families File" optional="false" help="TABULAR file with aligned families."/> 22 <param name="file3" type="data" format="tabular" label="Aligned Families File" optional="false" help="TABULAR file with aligned families."/>
23 </inputs> 23 </inputs>
24 <outputs> 24 <outputs>
25 <data name="output_fastq" format="fastq" label="${tool.name} on ${on_string}: FASTQ"/> 25 <data name="output_fastq" format="fastq" label="${tool.name} on ${on_string}: FASTQ"/>
26 <data name="output_json" format="json" label="${tool.name} on ${on_string}: JSON"/> 26 <data name="output_json" format="json" label="${tool.name} on ${on_string}: JSON"/>
27 </outputs> 27 </outputs>
28 <tests> 28 <tests>
29 <test> 29 <test>
30 <param name="file1" value="DCS_Mutations_test_data_VA.tabular"/> 30 <param name="file1" value="FreeBayes_test.vcf"/>
31 <param name="file2" value="DCS_test_data_VA.bam"/> 31 <param name="file2" value="DCS_test.bam"/>
32 <param name="file3" value="Aligned_Families_test_data_VA.tabular"/> 32 <param name="file3" value="Aligned_Families_test.tabular"/>
33 <output name="output_fastq" file="Interesting_Reads_test_data_VA.fastq" lines_diff="136"/> 33 <output name="output_fastq" file="Interesting_Reads_test.fastq"/>
34 <output name="output_json" file="tag_count_dict_test_data_VA.json" lines_diff="2"/> 34 <output name="output_json" file="tag_count_dict_test.json" lines_diff="2"/>
35 </test> 35 </test>
36 </tests> 36 </tests>
37 <help> <![CDATA[ 37 <help> <![CDATA[
38 **What it does** 38 **What it does**
39 39
40 Takes a tabular file with mutations, a BAM file of aligned DCS reads, and a 40 Takes a VCF file with mutations, a BAM file of aligned DCS reads, and a
41 tabular file with aligned families as input and prints all tags of reads that 41 tabular file with aligned families as input and prints all tags of reads that
42 carry a mutation to a user specified output file and creates a fastq file of 42 carry a mutation to a user specified output file and creates a fastq file of
43 reads of tags with a mutation. 43 reads of tags with a mutation.
44 44
45 **Input** 45 **Input**
46 46
47 **Dataset 1:** Tabular file with duplex consesus sequence (DCS) mutations as 47 **Dataset 1:** VCF file with duplex consesus sequence (DCS) mutations. E.g.
48 generated by the **Variant Annotator** tool. 48 generated by the `FreeBayes variant caller <https://arxiv.org/abs/1207.3907>`_.
49 49
50 **Dataset 2:** BAM file of aligned DCS reads. This file can be obtained by the 50 **Dataset 2:** BAM file of aligned DCS reads. This file can be obtained by the
51 tool `Map with BWA-MEM <https://arxiv.org/abs/1303.3997>`_. 51 tool `Map with BWA-MEM <https://arxiv.org/abs/1303.3997>`_.
52 52
53 **Dataset 3:** Tabular file with reads as produced by the 53 **Dataset 3:** Tabular file with reads as produced by the