Mercurial > repos > sanbi-uwc > vcftools_consensus
annotate vcftools_consensus.xml @ 2:ee2618c3b7b7 draft default tip
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/vcftools_consensus commit e5b7cb72fdb6f033c01654aed287c0f0888a0bb0
| author | sanbi-uwc |
|---|---|
| date | Thu, 24 Nov 2016 08:13:19 -0500 |
| parents | 6bc49e31c33a |
| children |
| rev | line source |
|---|---|
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6bc49e31c33a
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/vcftools_consensus commit c6fec21756429f008c74be9a9d455748e44c5e6a
sanbi-uwc
parents:
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changeset
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1 <tool id="vcftools_consensus" name="Consensus" version="0.1.11"> |
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6bc49e31c33a
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/vcftools_consensus commit c6fec21756429f008c74be9a9d455748e44c5e6a
sanbi-uwc
parents:
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2 <description>Apply VCF variants to a fasta file to create consensus sequence</description> |
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6bc49e31c33a
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/vcftools_consensus commit c6fec21756429f008c74be9a9d455748e44c5e6a
sanbi-uwc
parents:
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3 |
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6bc49e31c33a
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/vcftools_consensus commit c6fec21756429f008c74be9a9d455748e44c5e6a
sanbi-uwc
parents:
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4 <requirements> |
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6bc49e31c33a
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/vcftools_consensus commit c6fec21756429f008c74be9a9d455748e44c5e6a
sanbi-uwc
parents:
diff
changeset
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5 <requirement type="package" version="0.1.19">samtools</requirement> |
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6bc49e31c33a
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/vcftools_consensus commit c6fec21756429f008c74be9a9d455748e44c5e6a
sanbi-uwc
parents:
diff
changeset
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6 <requirement type="package" version="1.3.2">htslib</requirement> |
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6bc49e31c33a
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/vcftools_consensus commit c6fec21756429f008c74be9a9d455748e44c5e6a
sanbi-uwc
parents:
diff
changeset
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7 <requirement type="package" version="0.1.11">vcftools</requirement> |
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6bc49e31c33a
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/vcftools_consensus commit c6fec21756429f008c74be9a9d455748e44c5e6a
sanbi-uwc
parents:
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8 </requirements> |
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6bc49e31c33a
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/vcftools_consensus commit c6fec21756429f008c74be9a9d455748e44c5e6a
sanbi-uwc
parents:
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9 |
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6bc49e31c33a
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/vcftools_consensus commit c6fec21756429f008c74be9a9d455748e44c5e6a
sanbi-uwc
parents:
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10 <stdio> |
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6bc49e31c33a
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/vcftools_consensus commit c6fec21756429f008c74be9a9d455748e44c5e6a
sanbi-uwc
parents:
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11 <!--<regex match=".*" source="both" level="log" description="tool progress"/>--> |
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6bc49e31c33a
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/vcftools_consensus commit c6fec21756429f008c74be9a9d455748e44c5e6a
sanbi-uwc
parents:
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12 <exit_code range="1:" level="fatal" /> |
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6bc49e31c33a
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/vcftools_consensus commit c6fec21756429f008c74be9a9d455748e44c5e6a
sanbi-uwc
parents:
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13 </stdio> |
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6bc49e31c33a
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/vcftools_consensus commit c6fec21756429f008c74be9a9d455748e44c5e6a
sanbi-uwc
parents:
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14 |
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6bc49e31c33a
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/vcftools_consensus commit c6fec21756429f008c74be9a9d455748e44c5e6a
sanbi-uwc
parents:
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15 <command> |
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6bc49e31c33a
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/vcftools_consensus commit c6fec21756429f008c74be9a9d455748e44c5e6a
sanbi-uwc
parents:
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16 <![CDATA[ |
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6bc49e31c33a
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/vcftools_consensus commit c6fec21756429f008c74be9a9d455748e44c5e6a
sanbi-uwc
parents:
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17 ln -s '${variants}' variants.vcf && |
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6bc49e31c33a
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/vcftools_consensus commit c6fec21756429f008c74be9a9d455748e44c5e6a
sanbi-uwc
parents:
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18 vcf-sort variants.vcf | bgzip -c > variants.sorted.vcf.gz && |
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6bc49e31c33a
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/vcftools_consensus commit c6fec21756429f008c74be9a9d455748e44c5e6a
sanbi-uwc
parents:
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19 |
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6bc49e31c33a
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/vcftools_consensus commit c6fec21756429f008c74be9a9d455748e44c5e6a
sanbi-uwc
parents:
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20 tabix -p vcf variants.sorted.vcf.gz && |
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6bc49e31c33a
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/vcftools_consensus commit c6fec21756429f008c74be9a9d455748e44c5e6a
sanbi-uwc
parents:
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21 |
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6bc49e31c33a
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/vcftools_consensus commit c6fec21756429f008c74be9a9d455748e44c5e6a
sanbi-uwc
parents:
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22 #if $ref_genome_source.index_source == 'history': |
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6bc49e31c33a
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/vcftools_consensus commit c6fec21756429f008c74be9a9d455748e44c5e6a
sanbi-uwc
parents:
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23 ln -s '${ref_genome_source.ref_file}' reference.fasta && |
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6bc49e31c33a
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/vcftools_consensus commit c6fec21756429f008c74be9a9d455748e44c5e6a
sanbi-uwc
parents:
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changeset
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24 samtools faidx reference.fasta && |
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6bc49e31c33a
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/vcftools_consensus commit c6fec21756429f008c74be9a9d455748e44c5e6a
sanbi-uwc
parents:
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25 #end if |
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6bc49e31c33a
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/vcftools_consensus commit c6fec21756429f008c74be9a9d455748e44c5e6a
sanbi-uwc
parents:
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26 |
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6bc49e31c33a
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/vcftools_consensus commit c6fec21756429f008c74be9a9d455748e44c5e6a
sanbi-uwc
parents:
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27 cat |
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6bc49e31c33a
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/vcftools_consensus commit c6fec21756429f008c74be9a9d455748e44c5e6a
sanbi-uwc
parents:
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28 #if $ref_genome_source.index_source == 'builtin' |
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6bc49e31c33a
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/vcftools_consensus commit c6fec21756429f008c74be9a9d455748e44c5e6a
sanbi-uwc
parents:
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29 '${ ref_genome_source.reference_genome.fields.path }' |
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6bc49e31c33a
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/vcftools_consensus commit c6fec21756429f008c74be9a9d455748e44c5e6a
sanbi-uwc
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30 #else |
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6bc49e31c33a
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/vcftools_consensus commit c6fec21756429f008c74be9a9d455748e44c5e6a
sanbi-uwc
parents:
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31 reference.fasta |
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6bc49e31c33a
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/vcftools_consensus commit c6fec21756429f008c74be9a9d455748e44c5e6a
sanbi-uwc
parents:
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32 #end if |
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6bc49e31c33a
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/vcftools_consensus commit c6fec21756429f008c74be9a9d455748e44c5e6a
sanbi-uwc
parents:
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33 | vcf-consensus variants.sorted.vcf.gz > '${output}' |
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6bc49e31c33a
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/vcftools_consensus commit c6fec21756429f008c74be9a9d455748e44c5e6a
sanbi-uwc
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34 ]]> |
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6bc49e31c33a
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/vcftools_consensus commit c6fec21756429f008c74be9a9d455748e44c5e6a
sanbi-uwc
parents:
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35 </command> |
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6bc49e31c33a
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/vcftools_consensus commit c6fec21756429f008c74be9a9d455748e44c5e6a
sanbi-uwc
parents:
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36 <inputs> |
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6bc49e31c33a
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/vcftools_consensus commit c6fec21756429f008c74be9a9d455748e44c5e6a
sanbi-uwc
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37 <conditional name="ref_genome_source"> |
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6bc49e31c33a
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/vcftools_consensus commit c6fec21756429f008c74be9a9d455748e44c5e6a
sanbi-uwc
parents:
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38 <param name="index_source" type="select" label="Reference genome source"> |
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6bc49e31c33a
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/vcftools_consensus commit c6fec21756429f008c74be9a9d455748e44c5e6a
sanbi-uwc
parents:
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39 <option value="builtin">Built-in genome</option> |
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6bc49e31c33a
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/vcftools_consensus commit c6fec21756429f008c74be9a9d455748e44c5e6a
sanbi-uwc
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40 <option value="history">History</option> |
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6bc49e31c33a
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/vcftools_consensus commit c6fec21756429f008c74be9a9d455748e44c5e6a
sanbi-uwc
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41 </param> |
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6bc49e31c33a
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/vcftools_consensus commit c6fec21756429f008c74be9a9d455748e44c5e6a
sanbi-uwc
parents:
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42 <when value="builtin"> |
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6bc49e31c33a
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/vcftools_consensus commit c6fec21756429f008c74be9a9d455748e44c5e6a
sanbi-uwc
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43 <param name="reference_genome" type="select"> |
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6bc49e31c33a
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/vcftools_consensus commit c6fec21756429f008c74be9a9d455748e44c5e6a
sanbi-uwc
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44 <options from_data_table="fasta_indexes"> |
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6bc49e31c33a
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/vcftools_consensus commit c6fec21756429f008c74be9a9d455748e44c5e6a
sanbi-uwc
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45 <filter column="2" type="sort_by" /> |
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6bc49e31c33a
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/vcftools_consensus commit c6fec21756429f008c74be9a9d455748e44c5e6a
sanbi-uwc
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46 <validator message="No suitable reference genomes found" type="no_options" /> |
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6bc49e31c33a
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/vcftools_consensus commit c6fec21756429f008c74be9a9d455748e44c5e6a
sanbi-uwc
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47 </options> |
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6bc49e31c33a
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/vcftools_consensus commit c6fec21756429f008c74be9a9d455748e44c5e6a
sanbi-uwc
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48 </param> |
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6bc49e31c33a
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/vcftools_consensus commit c6fec21756429f008c74be9a9d455748e44c5e6a
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49 </when> |
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6bc49e31c33a
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/vcftools_consensus commit c6fec21756429f008c74be9a9d455748e44c5e6a
sanbi-uwc
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50 <when value="history"> |
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6bc49e31c33a
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/vcftools_consensus commit c6fec21756429f008c74be9a9d455748e44c5e6a
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51 <param name="ref_file" type="data" format="fasta" label="Reference genome" /> |
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6bc49e31c33a
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/vcftools_consensus commit c6fec21756429f008c74be9a9d455748e44c5e6a
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52 </when> |
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6bc49e31c33a
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/vcftools_consensus commit c6fec21756429f008c74be9a9d455748e44c5e6a
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53 </conditional> |
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6bc49e31c33a
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/vcftools_consensus commit c6fec21756429f008c74be9a9d455748e44c5e6a
sanbi-uwc
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54 <param name="variants" label="Datasets containing Variants" type="data" format="vcf" /> |
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6bc49e31c33a
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/vcftools_consensus commit c6fec21756429f008c74be9a9d455748e44c5e6a
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55 </inputs> |
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6bc49e31c33a
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/vcftools_consensus commit c6fec21756429f008c74be9a9d455748e44c5e6a
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56 |
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6bc49e31c33a
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/vcftools_consensus commit c6fec21756429f008c74be9a9d455748e44c5e6a
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57 <outputs> |
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6bc49e31c33a
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/vcftools_consensus commit c6fec21756429f008c74be9a9d455748e44c5e6a
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58 <data name="output" format="fasta"/> |
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6bc49e31c33a
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/vcftools_consensus commit c6fec21756429f008c74be9a9d455748e44c5e6a
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59 </outputs> |
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6bc49e31c33a
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/vcftools_consensus commit c6fec21756429f008c74be9a9d455748e44c5e6a
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60 |
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6bc49e31c33a
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/vcftools_consensus commit c6fec21756429f008c74be9a9d455748e44c5e6a
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61 <tests> |
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6bc49e31c33a
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/vcftools_consensus commit c6fec21756429f008c74be9a9d455748e44c5e6a
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62 <test> |
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6bc49e31c33a
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/vcftools_consensus commit c6fec21756429f008c74be9a9d455748e44c5e6a
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63 <param name="index_source" value="history" /> |
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6bc49e31c33a
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/vcftools_consensus commit c6fec21756429f008c74be9a9d455748e44c5e6a
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64 <param ftype="fasta" name="ref_file" value="reference.fasta" /> |
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6bc49e31c33a
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/vcftools_consensus commit c6fec21756429f008c74be9a9d455748e44c5e6a
sanbi-uwc
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65 <param ftype="vcf" name="variants" value="sample1.vcf" /> |
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6bc49e31c33a
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/vcftools_consensus commit c6fec21756429f008c74be9a9d455748e44c5e6a
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66 <output name="output" ftype="fasta" file="output1.fasta" /> |
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6bc49e31c33a
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/vcftools_consensus commit c6fec21756429f008c74be9a9d455748e44c5e6a
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67 </test> |
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6bc49e31c33a
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/vcftools_consensus commit c6fec21756429f008c74be9a9d455748e44c5e6a
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68 </tests> |
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6bc49e31c33a
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/vcftools_consensus commit c6fec21756429f008c74be9a9d455748e44c5e6a
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69 |
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6bc49e31c33a
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/vcftools_consensus commit c6fec21756429f008c74be9a9d455748e44c5e6a
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70 <help> |
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6bc49e31c33a
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/vcftools_consensus commit c6fec21756429f008c74be9a9d455748e44c5e6a
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71 Please see the VCFtools `documentation`__ for help and further information. |
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6bc49e31c33a
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/vcftools_consensus commit c6fec21756429f008c74be9a9d455748e44c5e6a
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72 |
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6bc49e31c33a
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/vcftools_consensus commit c6fec21756429f008c74be9a9d455748e44c5e6a
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73 .. __: http://vcftools.sourceforge.net/docs.html |
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6bc49e31c33a
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/vcftools_consensus commit c6fec21756429f008c74be9a9d455748e44c5e6a
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74 </help> |
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6bc49e31c33a
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/vcftools_consensus commit c6fec21756429f008c74be9a9d455748e44c5e6a
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75 <citations> |
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6bc49e31c33a
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/vcftools_consensus commit c6fec21756429f008c74be9a9d455748e44c5e6a
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76 <citation type="doi">10.1093/bioinformatics/btr330</citation> |
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6bc49e31c33a
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/vcftools_consensus commit c6fec21756429f008c74be9a9d455748e44c5e6a
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77 </citations> |
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6bc49e31c33a
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/vcftools_consensus commit c6fec21756429f008c74be9a9d455748e44c5e6a
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78 </tool> |