Mercurial > repos > mheinzl > variant_analyzer2
comparison mut2read.xml @ 6:11a2a34f8a2b draft
planemo upload for repository https://github.com/gpovysil/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8
author | mheinzl |
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date | Mon, 18 Jan 2021 09:49:15 +0000 |
parents | 9d74f30275c6 |
children | 84a1a3f70407 |
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5:d9cbf833624e | 6:11a2a34f8a2b |
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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 |