Mercurial > repos > jjohnson > defuse8
annotate defuse_results_to_vcf.xml @ 1:e0a835a2f74a draft default tip
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 1a82c0609363fe0541e6dbdd46308a67f30ca9e1-dirty
author | jjohnson |
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date | Mon, 20 May 2019 15:30:06 -0400 |
parents | 63f23d5db27c |
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63f23d5db27c
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
jjohnson
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1 <?xml version="1.0"?> |
63f23d5db27c
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
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2 <tool id="defuse_results_to_vcf" name="Defuse Results to VCF" version="@DEFUSE_VERSION@.2"> |
63f23d5db27c
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
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3 <description>generate a VCF from a DeFuse Results file</description> |
63f23d5db27c
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
jjohnson
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4 <macros> |
63f23d5db27c
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
jjohnson
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5 <import>macros.xml</import> |
63f23d5db27c
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
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6 </macros> |
63f23d5db27c
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
jjohnson
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7 <command detect_errors="default"><![CDATA[ |
63f23d5db27c
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
jjohnson
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8 $__tool_directory__/defuse_results_to_vcf.py --input $defuse_results --reference ${defuse_results.metadata.dbkey} --output $vcf |
63f23d5db27c
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
jjohnson
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9 ]]></command> |
63f23d5db27c
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
jjohnson
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10 <inputs> |
63f23d5db27c
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
jjohnson
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11 <param name="defuse_results" type="data" format="defuse.results.tsv" label="Defuse Results file"/> |
63f23d5db27c
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
jjohnson
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12 </inputs> |
63f23d5db27c
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
jjohnson
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13 <outputs> |
63f23d5db27c
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
jjohnson
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14 <data name="vcf" metadata_source="defuse_results" format="vcf"/> |
63f23d5db27c
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
jjohnson
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15 </outputs> |
63f23d5db27c
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
jjohnson
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16 <tests> |
63f23d5db27c
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
jjohnson
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17 <test> |
63f23d5db27c
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
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18 <param name="defuse_results" value="mm10_results.filtered.tsv" ftype="defuse.results.tsv" dbkey="mm10"/> |
63f23d5db27c
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
jjohnson
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19 <output name="vcf" file="mm10_results.filtered.vcf"/> |
63f23d5db27c
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
jjohnson
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20 </test> |
63f23d5db27c
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
jjohnson
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21 </tests> |
63f23d5db27c
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
jjohnson
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22 <help> |
63f23d5db27c
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
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23 **Defuse Results to VCF** |
63f23d5db27c
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
jjohnson
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24 |
63f23d5db27c
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
jjohnson
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25 Generates a VCF_ Variant Call Format file from a DeFuse_ results.tsv file. |
63f23d5db27c
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
jjohnson
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26 |
63f23d5db27c
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
jjohnson
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27 This program relies on the header line of the results.tsv to determine which columns to use for genrating the VCF file. |
63f23d5db27c
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
jjohnson
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28 |
63f23d5db27c
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
jjohnson
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29 .. _VCF: http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41 |
63f23d5db27c
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
jjohnson
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30 .. _DeFuse: http://sourceforge.net/apps/mediawiki/defuse |
63f23d5db27c
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
jjohnson
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31 </help> |
63f23d5db27c
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
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32 </tool> |