Mercurial > repos > iuc > gemini_actionable_mutations

annotate gemini_actionable_mutations.xml @ 1:4212dbb28643 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e4dce25c8dbeffca62c402f74ca733ddc7a6091b
author iuc
date Fri, 07 Dec 2018 12:46:52 -0500
parents cf9516ee3910
children 1a30b31af89a
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4212dbb28643 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e4dce25c8dbeffca62c402f74ca733ddc7a6091b
iuc
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1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.1">
0
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2 <description>Retrieve genes with actionable somatic mutations via COSMIC and DGIdb</description>
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3 <macros>
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4 <import>gemini_macros.xml</import>
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5 <token name="@BINARY@">actionable_mutations</token>
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6 </macros>
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7 <expand macro="requirements" />
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8 <expand macro="stdio" />
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9 <expand macro="version_command" />
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10 <command>
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11 <![CDATA[
1
4212dbb28643 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e4dce25c8dbeffca62c402f74ca733ddc7a6091b
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12 @PROVIDE_ANNO_DATA@
4212dbb28643 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e4dce25c8dbeffca62c402f74ca733ddc7a6091b
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13
0
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14 gemini @BINARY@
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15 "${ infile }" | tr -s ' ' '\t'
cf9516ee3910 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
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16 > "${ outfile }"
cf9516ee3910 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
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17 ]]>
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18 </command>
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19 <inputs>
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20 <expand macro="infile" />
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21 </inputs>
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22 <outputs>
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23 <data name="outfile" format="tabular" />
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24 </outputs>
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25 <tests>
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26 <test>
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27 <!-- Like in set_somatic this example is nonsensical because otherwise
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28 the testdata would be too big.-->
cf9516ee3910 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
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29 <param name="infile" value="gemini_comphets_input.db" ftype="gemini.sqlite" />
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30 <output name="outfile" file="gemini_actionable_mutations_result.tabular" />
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31 </test>
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32 </tests>
cf9516ee3910 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
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33 <help><![CDATA[
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34 **What it does**
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35
cf9516ee3910 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
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36 Retrieve genes with actionable somatic mutations via COSMIC and DGIdb. It checks for variants that have the somatic flag set (which can be done with GEMINI set_somatic) with high or medium impact severity. The results are then compared to entries in COSMIC and DGIdb
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37
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38 ]]></help>
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39 <expand macro="citations"/>
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40 </tool>