diff findDMR/findDMR.xml @ 33:2c799524e1d3 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/findDMR/findDMR.xml	Fri Apr 14 06:44:35 2017 -0400
@@ -0,0 +1,56 @@
+<tool id="DMR" name="findDMR" version="1.16.2">
+  <description>
+from series of samples
+  </description>
+  <requirements>
+         <requirement type="package" version="3.2.1">R</requirement>
+     </requirements>
+<stdio>
+   <exit_code range="1:" />
+</stdio>
+  <command> Rscript $__tool_directory__/findDMR.R "$GSMTable" "$platform" "$Data_Table" "$cutoff" "$clusterSize" "$DMR"</command>
+  <inputs>
+    <param optional="false" format="txt" name="GSMTable" type="data" value="" help="GSM ID and phenotype table." label="[required] GSMTable">
+      <validator type="empty_field" message="This field is required."/>
+    </param>
+     <param optional="false" format="txt" name="platform" type="data" value="" help="CG, CHR, BP table." label="[required] platform">
+      <validator type="empty_field" message="This field is required."/>
+    </param>
+     <param optional="false" format="txt" name="Data_Table" type="data" value="" help="Matrix of data." label="[required] Data_Table">
+      <validator type="empty_field" message="This field is required."/>
+    </param>
+    <param name="cutoff" type="float" value=""
+	       label="Enter cutoff size (number)"
+	       help="e.g. '0.2'" >
+      </param>
+    <param name="clusterSize" type="float" value=""
+	       label="Enter cluster size (number)"
+	       help="e.g. '2'" >
+      </param>
+  </inputs>
+  <outputs>
+    <data format="bed" name="DMR" label="DMR.bed"/>
+  </outputs>
+  <tests>
+    <test>
+      <param name="test">
+      <element name="test-data">
+          <collection type="data">
+              <element name="GSMTable" value="test-data/input.txt"/>
+              <element name="platform" value="test-data/platform.txt"/>
+              <element name="Data_Table" value="test-data/Data_Table.txt"/>
+              <element name="cutoff" value="0.2"/>
+              <element name="clusterSize" value="2"/>
+          </collection>
+        </element>
+        </param>
+        <output format="bed" name="DMR" label="test-data/DMR.bed"/>
+        </test>
+    </tests>
+  <help>
+**Description**
+</help>
+<citations>
+DMR
+</citations>
+</tool>