Mercurial > repos > mheinzl > variant_analyzer2
comparison mut2read.xml @ 78:fdfe9a919ff7 draft
planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8-dirty
author | mheinzl |
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date | Fri, 22 Jul 2022 09:19:44 +0000 |
parents | 6ccff403db8a |
children | e46d5e377760 |
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77:1797e461d674 | 78:fdfe9a919ff7 |
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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="2.1.1" profile="19.01"> | 2 <tool id="mut2read" name="DCS mutations to tags/reads:" version="3.0.0" 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="vcf" label="DCS Mutation File" optional="false" help="VCF 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 the 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="FreeBayes_test.vcf" lines_diff="2"/> | 30 <param name="file1" value="FreeBayes_test.vcf"/> |
31 <param name="file2" value="DCS_test.bam"/> | 31 <param name="file2" value="DCS_test.bam"/> |
32 <param name="file3" value="Aligned_Families_test.tabular"/> | 32 <param name="file3" value="Aligned_Families_test.tabular"/> |
33 <output name="output_fastq" file="Interesting_Reads_test.fastq" lines_diff="136"/> | 33 <output name="output_fastq" file="Interesting_Reads_test.fastq"/> |
34 <output name="output_json" file="tag_count_dict_test.json" lines_diff="2"/> | 34 <output name="output_json" file="tag_count_dict_test.json"/> |
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 VCF 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 or have the reference allele 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 and the reference allele. |
44 | 44 |
45 **Input** | 45 **Input** |
46 | 46 |
47 **Dataset 1:** VCF file with duplex consesus sequence (DCS) mutations. E.g. | 47 **Dataset 1:** VCF file with duplex consensus sequence (DCS) mutations. E.g. |
48 generated by the `FreeBayes <https://arxiv.org/abs/1207.3907>`_ or `LoFreq <https://academic.oup.com/nar/article/40/22/11189/1152727>`_ variant caller. | 48 generated by the `FreeBayes <https://arxiv.org/abs/1207.3907>`_ or `LoFreq <https://academic.oup.com/nar/article/40/22/11189/1152727>`_ variant caller. |
49 | 49 |
50 | 50 |
51 **Dataset 2:** BAM file of aligned DCS reads. This file can be obtained by the | 51 **Dataset 2:** BAM file of aligned DCS reads. This file can be obtained by the |
52 tool `Map with BWA-MEM <https://arxiv.org/abs/1303.3997>`_. | 52 tool `Map with BWA-MEM <https://arxiv.org/abs/1303.3997>`_. |
55 **Du Novo: Align families** tool of the `Du Novo Analysis Pipeline | 55 **Du Novo: Align families** tool of the `Du Novo Analysis Pipeline |
56 <https://doi.org/10.1186/s13059-016-1039-4>`_ | 56 <https://doi.org/10.1186/s13059-016-1039-4>`_ |
57 | 57 |
58 **Output** | 58 **Output** |
59 | 59 |
60 The output is a json file containing dictonaries of the tags of reads containing mutations | 60 The output is a json file containing dictionaries of the tags of reads containing mutations |
61 in the DCS and a fastq file of all reads of these tags. | 61 in the DCS and a fastq file of all reads of these tags. |
62 | 62 |
63 ]]> | 63 ]]> |
64 </help> | 64 </help> |
65 <expand macro="citation" /> | 65 <expand macro="citation" /> |