diff gemini_de_novo.xml @ 0:720cbfb4190d draft

Imported from capsule None

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gemini_de_novo.xml	Mon Aug 25 17:15:54 2014 -0400
@@ -0,0 +1,49 @@
+<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0">
+    <description>Identifying potential de novo mutations</description>
+    <expand macro="requirements" />
+    <expand macro="version_command" />
+    <macros>
+        <import>gemini_macros.xml</import>
+        <token name="@BINARY@">de_novo</token>
+    </macros>
+    <command>
+<![CDATA[
+        gemini @BINARY@
+
+            #if $report.report_selector != 'all':
+                --columns "${report.columns}"
+            #end if
+
+            #if $filter.filter_selector == 'yes':
+                --filter "${filter.filter}"
+            #end if
+            -d $d
+            "${ infile }"
+            > "${ outfile }"
+]]>
+    </command>
+    <expand macro="stdio" />
+    <inputs>
+        <param name="infile" type="data" format="sqlite" label="GEMINI database" />
+
+        <expand macro="column_filter" />
+        <expand macro="filter" />
+        <expand macro="min_sequence_depth" />
+    </inputs>
+    <outputs>
+        <data name="outfile" format="tabular" label="${tool.name} on ${on_string}" />
+    </outputs>
+    <tests>
+        <test>
+        </test>
+    </tests>
+    <help>
+**What it does**
+
+Assuming you have defined the familial relationships between samples when loading your VCF into GEMINI, 
+you can use this tool for identifying de novo (a.k.a spontaneous) mutations that arise in offspring.
+
+@CITATION@
+    </help>
+    <expand macro="citations"/>
+</tool>