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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_consensus commit 5d67d705695dfee875bda85aa02ddf38924790a7
author devteam
date Fri, 25 Nov 2016 07:30:19 -0500
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1 <tool id="vcftools_consensus" name="Consensus" version="0.1.11">
2 <description>Apply VCF variants to a fasta file to create consensus sequence</description>
3
4 <requirements>
5 <requirement type="package" version="0.1.19">samtools</requirement>
6 <requirement type="package" version="1.3.2">htslib</requirement>
7 <requirement type="package" version="0.1.11">vcftools</requirement>
8 </requirements>
9
10 <stdio>
11 <!--<regex match=".*" source="both" level="log" description="tool progress"/>-->
12 <exit_code range="1:" level="fatal" />
13 </stdio>
14
15 <command>
16 <![CDATA[
17 ln -s '${variants}' variants.vcf &&
18 vcf-sort variants.vcf | bgzip -c > variants.sorted.vcf.gz &&
19
20 tabix -p vcf variants.sorted.vcf.gz &&
21
22 #if $ref_genome_source.index_source == 'history':
23 ln -s '${ref_genome_source.ref_file}' reference.fasta &&
24 samtools faidx reference.fasta &&
25 #end if
26
27 cat
28 #if $ref_genome_source.index_source == 'builtin'
29 '${ ref_genome_source.reference_genome.fields.path }'
30 #else
31 reference.fasta
32 #end if
33 | vcf-consensus variants.sorted.vcf.gz > '${output}'
34 ]]>
35 </command>
36 <inputs>
37 <conditional name="ref_genome_source">
38 <param name="index_source" type="select" label="Reference genome source">
39 <option value="builtin">Built-in genome</option>
40 <option value="history">History</option>
41 </param>
42 <when value="builtin">
43 <param name="reference_genome" type="select">
44 <options from_data_table="fasta_indexes">
45 <filter column="2" type="sort_by" />
46 <validator message="No suitable reference genomes found" type="no_options" />
47 </options>
48 </param>
49 </when>
50 <when value="history">
51 <param name="ref_file" type="data" format="fasta" label="Reference genome" />
52 </when>
53 </conditional>
54 <param name="variants" label="Datasets containing Variants" type="data" format="vcf" />
55 </inputs>
56
57 <outputs>
58 <data name="output" format="fasta"/>
59 </outputs>
60
61 <tests>
62 <test>
63 <param name="index_source" value="history" />
64 <param ftype="fasta" name="ref_file" value="reference.fasta" />
65 <param ftype="vcf" name="variants" value="sample1.vcf" />
66 <output name="output" ftype="fasta" file="output1.fasta" />
67 </test>
68 </tests>
69
70 <help>
71 Please see the VCFtools `documentation`__ for help and further information.
72
73 .. __: http://vcftools.sourceforge.net/docs.html
74 </help>
75 <citations>
76 <citation type="doi">10.1093/bioinformatics/btr330</citation>
77 </citations>
78 </tool>