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author jjohnson
date Thu, 19 Oct 2017 10:05:54 -0400
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2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results
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1 <?xml version="1.0"?>
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2 <tool id="defuse_results_to_vcf" name="Defuse Results to VCF" version="0.6.1">
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results
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3 <description>generate a VCF from a DeFuse Results file</description>
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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7 <requirements>
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8 <expand macro="defuse_requirement" />
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9 </requirements>
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10 <command><![CDATA[
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11 python '$__tool_directory__/defuse_results_to_vcf.py --input $defuse_results --reference ${defuse_results.metadata.dbkey} --output $vcf
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12 ]]>
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13 </command>
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results
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14 <inputs>
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15 <param name="defuse_results" type="data" format="defuse.results.tsv" label="Defuse Results file"/>
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results
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16 </inputs>
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results
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17 <stdio>
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results
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18 <exit_code range="1:" level="fatal" description="Error" />
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results
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19 </stdio>
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20 <outputs>
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21 <data name="vcf" metadata_source="defuse_results" format="vcf"/>
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2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results
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22 </outputs>
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results
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23 <tests>
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results
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24 <test>
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25 <param name="defuse_results" value="mm10_results.filtered.tsv" ftype="defuse.results.tsv" dbkey="mm10"/>
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26 <output name="vcf" file="mm10_results.filtered.vcf"/>
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27 </test>
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results
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28 </tests>
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results
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29 <help>
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30 **Defuse Results to VCF**
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2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results
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32 Generates a VCF_ Variant Call Format file from a DeFuse_ results.tsv file.
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results
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34 This program relies on the header line of the results.tsv to determine which columns to use for genrating the VCF file.
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results
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2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results
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36 .. _VCF: http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results
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37 .. _DeFuse: http://sourceforge.net/apps/mediawiki/defuse
2ecf82136986 Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results
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38 </help>
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39 </tool>