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annotate defuse_results_to_vcf.xml @ 11:b22f8634ff84 draft

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planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
author jjohnson
date Sun, 17 Jan 2016 14:11:06 -0500
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b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
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1 <?xml version="1.0"?>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
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2 <tool id="defuse_results_to_vcf" name="Defuse Results to VCF" version="0.6.1">
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3 <description>generate a VCF from a DeFuse Results file</description>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
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4 <requirements>
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5 <requirement type="package" version="0.6.1">defuse</requirement>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
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6 </requirements>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
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7 <command interpreter="python">defuse_results_to_vcf.py --input $defuse_results --reference ${defuse_results.metadata.dbkey} --output $vcf
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8 </command>
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9 <inputs>
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10 <param name="defuse_results" type="data" format="defuse.results.tsv" label="Defuse Results file"/>
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11 </inputs>
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12 <stdio>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
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13 <exit_code range="1:" level="fatal" description="Error" />
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
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14 </stdio>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
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15 <outputs>
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16 <data name="vcf" metadata_source="defuse_results" format="vcf"/>
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17 </outputs>
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18 <tests>
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19 <test>
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20 <param name="defuse_results" value="mm10_results.filtered.tsv" ftype="defuse.results.tsv" dbkey="mm10"/>
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21 <output name="vcf" file="mm10_results.filtered.vcf"/>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
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22 </test>
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23 </tests>
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24 <help>
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25 **Defuse Results to VCF**
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27 Generates a VCF_ Variant Call Format file from a DeFuse_ results.tsv file.
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29 This program relies on the header line of the results.tsv to determine which columns to use for genrating the VCF file.
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30
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31 .. _VCF: http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41
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32 .. _DeFuse: http://sourceforge.net/apps/mediawiki/defuse
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33 </help>
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34 </tool>