Mercurial > repos > iuc > gemini_actionable_mutations

annotate gemini_actionable_mutations.xml @ 0:b6fb24500a86 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
author iuc
date Thu, 18 Feb 2016 08:54:38 -0500
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children 712aa8283200
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b6fb24500a86 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0">
b6fb24500a86 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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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>
b6fb24500a86 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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5 <token name="@BINARY@">actionable_mutations</token>
b6fb24500a86 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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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[
b6fb24500a86 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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12 gemini @BINARY@
b6fb24500a86 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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13 "${ infile }" | tr -s ' ' '\t'
b6fb24500a86 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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14 > "${ outfile }"
b6fb24500a86 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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15 ]]>
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16 </command>
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17 <inputs>
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18 <expand macro="infile" />
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19 </inputs>
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20 <outputs>
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21 <data name="outfile" format="tabular" />
b6fb24500a86 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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22 </outputs>
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23 <tests>
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24 <test>
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25 <!-- Like in set_somatic this example is nonsensical because otherwise
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26 the testdata would be too big.-->
b6fb24500a86 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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27 <param name="infile" value="gemini_comphets_input.db" ftype="gemini.sqlite" />
b6fb24500a86 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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28 <output name="outfile" file="gemini_actionable_mutations_result.tabular" />
b6fb24500a86 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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29 </test>
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30 </tests>
b6fb24500a86 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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31 <help><![CDATA[
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32 **What it does**
b6fb24500a86 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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33
b6fb24500a86 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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34 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
b6fb24500a86 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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35
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36 ]]></help>
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37 <expand macro="citations"/>
b6fb24500a86 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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38 </tool>