diff gemini_actionable_mutations.xml @ 0:cf9516ee3910 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gemini_actionable_mutations.xml	Tue Feb 16 05:53:59 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>