Mercurial > repos > mheinzl > variant_analyzer2
comparison mut2read.xml @ 43:d21960b45a6b draft
planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8
author | mheinzl |
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date | Tue, 02 Mar 2021 15:32:41 +0000 |
parents | 84a1a3f70407 |
children | 3691922baa08 |
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42:da224c392a54 | 43:d21960b45a6b |
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2 <tool id="mut2read" name="DCS mutations to tags/reads:" version="2.0.1" profile="19.01"> | 2 <tool id="mut2read" name="DCS mutations to tags/reads:" version="2.0.1" 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' |
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="FreeBayes_test.vcf"/> | 35 <param name="file1" value="FreeBayes_test.vcf" lines_diff="2"/> |
31 <param name="file2" value="DCS_test.bam"/> | 36 <param name="file2" value="DCS_test.bam"/> |
32 <param name="file3" value="Aligned_Families_test.tabular"/> | 37 <param name="file3" value="Aligned_Families_test.tabular"/> |
33 <output name="output_fastq" file="Interesting_Reads_test.fastq"/> | 38 <output name="output_fastq" file="Interesting_Reads_test.fastq" lines_diff="136"/> |
34 <output name="output_json" file="tag_count_dict_test.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** |