comparison mut2read.xml @ 6:11a2a34f8a2b draft

planemo upload for repository https://github.com/gpovysil/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8
author mheinzl
date Mon, 18 Jan 2021 09:49:15 +0000
parents 9d74f30275c6
children 84a1a3f70407
comparison
equal deleted inserted replaced
5:d9cbf833624e 6:11a2a34f8a2b
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 <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="0.11.6">cyvcf2</requirement>
12 </requirements>
8 <command><![CDATA[ 13 <command><![CDATA[
9 ln -s '$file2' bam_input.bam && 14 ln -s '$file2' bam_input.bam &&
10 ln -s '${file2.metadata.bam_index}' bam_input.bam.bai && 15 ln -s '${file2.metadata.bam_index}' bam_input.bam.bai &&
11 python '$__tool_directory__/mut2read.py' 16 python '$__tool_directory__/mut2read.py'
12 --mutFile '$file1' 17 --mutFile '$file1'
15 --outputFastq '$output_fastq' 20 --outputFastq '$output_fastq'
16 --outputJson '$output_json' 21 --outputJson '$output_json'
17 ]]> 22 ]]>
18 </command> 23 </command>
19 <inputs> 24 <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."/> 25 <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."/> 26 <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."/> 27 <param name="file3" type="data" format="tabular" label="Aligned Families File" optional="false" help="TABULAR file with aligned families."/>
23 </inputs> 28 </inputs>
24 <outputs> 29 <outputs>
25 <data name="output_fastq" format="fastq" label="${tool.name} on ${on_string}: FASTQ"/> 30 <data name="output_fastq" format="fastq" label="${tool.name} on ${on_string}: FASTQ"/>
26 <data name="output_json" format="json" label="${tool.name} on ${on_string}: JSON"/> 31 <data name="output_json" format="json" label="${tool.name} on ${on_string}: JSON"/>
27 </outputs> 32 </outputs>
28 <tests> 33 <tests>
29 <test> 34 <test>
30 <param name="file1" value="DCS_Mutations_test_data_VA.tabular"/> 35 <param name="file1" value="FreeBayes_test.vcf" lines_diff="2"/>
31 <param name="file2" value="DCS_test_data_VA.bam"/> 36 <param name="file2" value="DCS_test.bam"/>
32 <param name="file3" value="Aligned_Families_test_data_VA.tabular"/> 37 <param name="file3" value="Aligned_Families_test.tabular"/>
33 <output name="output_fastq" file="Interesting_Reads_test_data_VA.fastq" lines_diff="136"/> 38 <output name="output_fastq" file="Interesting_Reads_test.fastq" lines_diff="136"/>
34 <output name="output_json" file="tag_count_dict_test_data_VA.json" lines_diff="2"/> 39 <output name="output_json" file="tag_count_dict_test.json" lines_diff="2"/>
35 </test> 40 </test>
36 </tests> 41 </tests>
37 <help> <![CDATA[ 42 <help> <![CDATA[
38 **What it does** 43 **What it does**
39 44
40 Takes a tabular file with mutations, a BAM file of aligned DCS reads, and a 45 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 46 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 47 carry a mutation to a user specified output file and creates a fastq file of
43 reads of tags with a mutation. 48 reads of tags with a mutation.
44 49
45 **Input** 50 **Input**
46 51
47 **Dataset 1:** Tabular file with duplex consesus sequence (DCS) mutations as 52 **Dataset 1:** VCF file with duplex consesus sequence (DCS) mutations. E.g.
48 generated by the **Variant Annotator** tool. 53 generated by the `FreeBayes variant caller <https://arxiv.org/abs/1207.3907>`_.
49 54
50 **Dataset 2:** BAM file of aligned DCS reads. This file can be obtained by the 55 **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>`_. 56 tool `Map with BWA-MEM <https://arxiv.org/abs/1303.3997>`_.
52 57
53 **Dataset 3:** Tabular file with reads as produced by the 58 **Dataset 3:** Tabular file with reads as produced by the