Mercurial > repos > devteam > vcftools_consensus

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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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79f5d34da277 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_consensus commit 5d67d705695dfee875bda85aa02ddf38924790a7
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1 <tool id="vcftools_consensus" name="Consensus" version="0.1.11">
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2 <description>Apply VCF variants to a fasta file to create consensus sequence</description>
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3
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4 <requirements>
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5 <requirement type="package" version="0.1.19">samtools</requirement>
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6 <requirement type="package" version="1.3.2">htslib</requirement>
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7 <requirement type="package" version="0.1.11">vcftools</requirement>
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8 </requirements>
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10 <stdio>
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11 <!--<regex match=".*" source="both" level="log" description="tool progress"/>-->
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12 <exit_code range="1:" level="fatal" />
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13 </stdio>
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15 <command>
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16 <![CDATA[
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17 ln -s '${variants}' variants.vcf &&
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18 vcf-sort variants.vcf | bgzip -c > variants.sorted.vcf.gz &&
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20 tabix -p vcf variants.sorted.vcf.gz &&
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22 #if $ref_genome_source.index_source == 'history':
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23 ln -s '${ref_genome_source.ref_file}' reference.fasta &&
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24 samtools faidx reference.fasta &&
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25 #end if
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26
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27 cat
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28 #if $ref_genome_source.index_source == 'builtin'
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29 '${ ref_genome_source.reference_genome.fields.path }'
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30 #else
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31 reference.fasta
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32 #end if
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33 | vcf-consensus variants.sorted.vcf.gz > '${output}'
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34 ]]>
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35 </command>
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36 <inputs>
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37 <conditional name="ref_genome_source">
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38 <param name="index_source" type="select" label="Reference genome source">
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39 <option value="builtin">Built-in genome</option>
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40 <option value="history">History</option>
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41 </param>
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42 <when value="builtin">
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43 <param name="reference_genome" type="select">
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44 <options from_data_table="fasta_indexes">
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45 <filter column="2" type="sort_by" />
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46 <validator message="No suitable reference genomes found" type="no_options" />
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47 </options>
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48 </param>
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49 </when>
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50 <when value="history">
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51 <param name="ref_file" type="data" format="fasta" label="Reference genome" />
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52 </when>
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53 </conditional>
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54 <param name="variants" label="Datasets containing Variants" type="data" format="vcf" />
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55 </inputs>
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56
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57 <outputs>
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58 <data name="output" format="fasta"/>
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59 </outputs>
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60
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61 <tests>
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62 <test>
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63 <param name="index_source" value="history" />
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64 <param ftype="fasta" name="ref_file" value="reference.fasta" />
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65 <param ftype="vcf" name="variants" value="sample1.vcf" />
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66 <output name="output" ftype="fasta" file="output1.fasta" />
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67 </test>
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68 </tests>
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69
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70 <help>
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71 Please see the VCFtools `documentation`__ for help and further information.
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72
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73 .. __: http://vcftools.sourceforge.net/docs.html
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74 </help>
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75 <citations>
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76 <citation type="doi">10.1093/bioinformatics/btr330</citation>
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77 </citations>
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78 </tool>