Mercurial > repos > iuc > gemini_actionable_mutations

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit f7bdf08922aaf4119aefe7041e754a69cf64aebd
author iuc
date Wed, 13 Jul 2022 15:35:54 +0000
parents 643a9ad97f08
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643a9ad97f08 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@">
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2 <description>Retrieve genes with actionable somatic mutations via COSMIC and DGIdb</description>
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3 <expand macro="bio_tools"/>
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4 <macros>
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5 <import>gemini_macros.xml</import>
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6 <token name="@BINARY@">actionable_mutations</token>
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7 </macros>
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8 <expand macro="requirements" />
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9 <expand macro="stdio" />
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10 <expand macro="version_command" />
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11 <command>
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12 <![CDATA[
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13 gemini @BINARY@
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14 '$infile' | tr -s ' ' '\t'
643a9ad97f08 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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15 > '$outfile'
0
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16 ]]>
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17 </command>
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18 <inputs>
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19 <expand macro="infile" />
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20 </inputs>
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21 <outputs>
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22 <data name="outfile" format="tabular" />
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23 </outputs>
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24 <tests>
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25 <test>
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26 <!-- Like in set_somatic this example is nonsensical because otherwise
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27 the testdata would be too big.-->
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28 <param name="infile" value="gemini_load_result1.db" ftype="gemini.sqlite" />
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29 <output name="outfile" file="gemini_actionable_mutations_result.tabular" />
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30 </test>
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31 </tests>
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32 <help><![CDATA[
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33 **What it does**
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34
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35 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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36
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37 ]]></help>
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38 <expand macro="citations"/>
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39 </tool>