diff gemini_fusions.xml @ 0:8295781a3c27 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gemini_fusions.xml	Thu Feb 18 08:53:02 2016 -0500
@@ -0,0 +1,69 @@
+<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0">
+    <description>Identify somatic fusion genes from a GEMINI database</description>
+    <macros>
+        <import>gemini_macros.xml</import>
+        <token name="@BINARY@">fusions</token>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="stdio" />
+    <expand macro="version_command" />
+    <command>
+<![CDATA[
+
+        gemini @BINARY@
+
+        #if $annotation_databases:
+            --annotation-dir "${ annotation_databases.fields.path }"
+        #end if
+
+        $in_cosmic_census
+        
+        #if float($min_quality) >= 0:
+            --min-qual $min_quality
+        #end if
+
+        #if str($evidence_type):
+            --evidence_type $evidence_type
+        #end if 
+        
+        "${ infile }" | tr -s ' ' '\t'
+        > "${ outfile }" 
+]]>
+    </command>
+    <inputs>
+
+        <expand macro="infile" />
+        <expand macro="annotation_dir" />
+
+        <param argument="--in_cosmic_census" type="boolean" truevalue="--in_cosmic_census" falsevalue="" checked="False" label="One or both genes in fusion is in COSMIC cancer census" />
+
+        <param name="min_quality" type="float" value="-1" label="The min variant quality (VCF QUAL)" help="default: -1 (not set) (--min_qual)"/>
+
+        <param argument="--evidence_type" type="select" label="The supporting evidence types for the variant" >
+            <option value="" selected="True">select one (optional)</option>
+            <option value="PE">PE</option>
+            <option value="SR">SR</option>
+            <option value="PE,SR">PE,SR</option>
+        </param>
+
+    </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. The resulting output should be empty.-->
+            <param name="infile" value="gemini_amend_input.db" ftype="gemini.sqlite" />
+            <output name="outfile" file="gemini_fusions_result.tabular" />
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+**What it does**
+
+Identifies somatic fusion genes from a GEMINI database.
+]]>
+    </help>
+    <expand macro="citations"/>
+</tool>