diff getGEO/getGEO.xml @ 25:e44ea6de2d4f draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/getGEO/getGEO.xml	Mon Feb 06 09:39:52 2017 -0500
@@ -0,0 +1,44 @@
+<tool id="GEO" name="getGEO" version="1.16.2">
+  <?xml version='1.0' encoding='utf-8'?>
+  <requirements>
+    <tool_dependency>
+          <package name="R" version="3.2.1">
+              <repository changeset_revision="d0bf97420fb5" name="package_r_3_2_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+          </package>
+        </tool_dependency>
+</requirements>
+<stdio>
+   <exit_code range="1:" />
+</stdio>
+  <command> Rscript $__tool_directory__/getGEO.R "$GSMTable" "$MetaTable" "$IlmnTable" "$gmTable"</command>
+  <inputs>
+    <param optional="false" format="csv" name="GSMTable" type="data" value="" help="GEO table of data." label="[required] GSMTable">
+      <validator type="empty_field" message="This field is required."/>
+    </param>
+  </inputs>
+  <outputs>
+    <data format="csv" name="MetaTable" label="MetaData.csv"/>
+    <data format="csv" name="IlmnTable" label="IlmnData.csv"/>
+    <data format="csv" name="gmTable" label="gmSet.csv"/>
+  </outputs>
+  <tests>
+    <test>
+      <param name="test">
+      <element name="test-data">
+          <collection type="data">
+              <element name="GSMTable" value="test-data/input.csv" />
+          </collection>
+        </element>
+        </param>
+        <output format="csv" name="MetaTable" label="test-data/MetaTable.csv"/>
+        <output format="csv" name="IlmnTable" label="test-data/IlmnTable.csv"/>
+        <output format="csv" name="gmTable" label="test-data/gmTable.csv"/>
+        </test>
+    </tests>
+  <help>
+**Description**
+</help>
+<citations>
+GEO
+</citations>
+</tool>