diff findDMR/findDMR.xml @ 0:ca66a1487d4a draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/findDMR/findDMR.xml	Mon Feb 06 06:10:47 2017 -0500
@@ -0,0 +1,55 @@
+<tool id="DMR" name="findDMR" version="1.16.2">
+  <requirements>
+    <package name="methyldata_1_16_2" version="1.16.2">
+        <repository name="methyldata_1_16_2" owner="testtool" prior_installation_required="True" />
+    </package>
+</requirements>
+<stdio>
+   <exit_code range="1:" />
+</stdio>
+  <command> Rscript $__tool_directory__/findDMR.R "$GSMTable" "$IlmnTable" "$gmTable" "$cutoff" "$clusterSize" "$DMR"</command>
+  <inputs>
+    <param optional="false" format="csv" 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="csv" name="IlmnTable" type="data" value="" help="CG, CHR, BP table." label="[required] IlmnTable">
+      <validator type="empty_field" message="This field is required."/>
+    </param>
+     <param optional="false" format="csv" name="gmTable" type="data" value="" help="gmSet of data." label="[required] gmTable">
+      <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.csv"/>
+              <element name="IlmnTable" value="test-data/IlmnTable.csv"/>
+              <element name="gmTable" value="test-data/gmTable.csv"/>
+              <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>