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diff GRsetFromGEO/GRsetFromGEO.xml @ 12:0631845b906d draft

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author testtool
date Wed, 12 Apr 2017 08:29:45 -0400
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children cf1e6aa2caea
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/GRsetFromGEO/GRsetFromGEO.xml	Wed Apr 12 08:29:45 2017 -0400
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+<tool id="GRset" name="GRsetFromGEO" version="1.16.2">
+  <requirements>
+   <requirement name="package_r_3_2_1" type="package" version="3.2.1">R</requirement>
+</requirements>
+<stdio>
+   <exit_code range="1:" />
+</stdio>
+  <command> Rscript $__tool_directory__/GRsetFromGEO.R "$GSE" "$output" </command>
+  <inputs>
+    <param name="GSE" type="text" value="" label="Enter GSE ID." help="e.g. 'GSE51547'"/>
+  </inputs>
+  <outputs>
+    <data format="Rdata" name="output" label="GenomicRatioSet.Rdata"/>
+  </outputs>
+  <tests>
+    <test>
+      <param name="test">
+      <element name="test-data">
+           <collection type="data">
+                <element name="GSE" value="GSE51547"/>
+          </collection>
+        </element>
+        </param>
+        <output format="Rdata" name="output" label="test-data/GenomicRatioSet.Rdata"/>
+        </test>
+    </tests>
+  <help>
+Reading Illumina methylation array data from GEO.
+</help>
+<citations>
+Aryee, Martin J., et al. "Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays." Bioinformatics 30.10 (2014): 1363-1369.
+</citations>
+</tool>