Mercurial > repos > iuc > gemini_actionable_mutations
view gemini_actionable_mutations.xml @ 1:9f0f5e984ae3 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 7867095d83e5d0e0f923de7e9720d59df0034817
author | iuc |
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date | Tue, 22 Mar 2016 21:41:45 -0400 |
parents | b6fb24500a86 |
children | 712aa8283200 |
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<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0"> <description>Retrieve genes with actionable somatic mutations via COSMIC and DGIdb</description> <macros> <import>gemini_macros.xml</import> <token name="@BINARY@">actionable_mutations</token> </macros> <expand macro="requirements" /> <expand macro="stdio" /> <expand macro="version_command" /> <command> <![CDATA[ gemini @BINARY@ "${ infile }" | tr -s ' ' '\t' > "${ outfile }" ]]> </command> <inputs> <expand macro="infile" /> </inputs> <outputs> <data name="outfile" format="tabular" /> </outputs> <tests> <test> <!-- Like in set_somatic this example is nonsensical because otherwise the testdata would be too big.--> <param name="infile" value="gemini_comphets_input.db" ftype="gemini.sqlite" /> <output name="outfile" file="gemini_actionable_mutations_result.tabular" /> </test> </tests> <help><![CDATA[ **What it does** 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 ]]></help> <expand macro="citations"/> </tool>