Mercurial > repos > devteam > vcftools_consensus
comparison vcftools_consensus.xml @ 0:b5684d716c68 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_consensus commit caca2f9bbd012d710d7c9d16df5c4eb9237cd33c-dirty
| author | devteam |
|---|---|
| date | Fri, 04 Nov 2016 15:07:44 -0400 |
| parents | |
| children |
comparison
equal
deleted
inserted
replaced
| -1:000000000000 | 0:b5684d716c68 |
|---|---|
| 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> |