Mercurial > repos > iuc > gemini_actionable_mutations
diff gemini_actionable_mutations.xml @ 0:b6fb24500a86 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
author | iuc |
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date | Thu, 18 Feb 2016 08:54:38 -0500 |
parents | |
children | 712aa8283200 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/gemini_actionable_mutations.xml Thu Feb 18 08:54:38 2016 -0500 @@ -0,0 +1,38 @@ +<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>