diff getMETAdata/getMETAdata.xml @ 71:81b5c08c21e1 draft

Uploaded

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+++ b/getMETAdata/getMETAdata.xml	Mon Aug 14 09:44:57 2017 -0400
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+<tool id="META" name="getMETAdata" version="1.0.0">
+  <requirements>
+    <requirement type="package" version="1.10.4">r-data.table</requirement>
+    <requirement type="package" version="2.38.4">bioconductor-geoquery</requirement>
+  </requirements>
+<stdio>
+   <exit_code range="1:" />
+</stdio>
+  <command> Rscript $__tool_directory__/getMETAdata.R "$GSMTable" "$MetaTable" </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>
+  </inputs>
+  <outputs>
+    <data format="txt" name="MetaTable" label="MetaData.txt"/>
+</outputs>
+  <tests>
+    <test>
+      <param name="test">
+      <element name="test-data">
+          <collection type="data">
+              <element name="GSMTable" value="test-data/GSMTable.txt" />
+          </collection>
+        </element>
+        </param>
+        <output format="txt" name="MetaTable" label="test-data/MetaTable.txt"/>
+        </test>
+    </tests>
+  <help>
+**What it does**
+  This R-based tool downloads data from GEO using getGEO from the GEOquery package
+**Input**
+ A table representing ID of GEO objects for download and parsing
+**Output**
+ Get a metadata table from NCBI 
+</help>
+<citations>
+<citation type="doi">10.1093/bioinformatics/btm254</citation>
+</citations>
+</tool>