Mercurial > repos > testtool > get_gr_set

changeset 29:5d796e9a96ae draft

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Uploaded
author testtool
date Mon, 10 Jul 2017 09:09:09 -0400
parents ab34c2e8e533
children 4f157ee63207
files GRsetFromGEO/GRsetFromGEO.xml
diffstat 1 files changed, 31 insertions(+), 13 deletions(-) [+]
line wrap: on
line diff
--- a/GRsetFromGEO/GRsetFromGEO.xml	Mon Jul 10 09:03:10 2017 -0400
+++ b/GRsetFromGEO/GRsetFromGEO.xml	Mon Jul 10 09:09:09 2017 -0400
@@ -1,21 +1,39 @@
-<tool id="getGRset" name="GRsetFromGEO">
-  <description>downloads data from GEO</description>
-  <requirements>
-  <requirement type="package" version="1.20.0">bioconductor-minfi</requirement>
-  </requirements>
+<?xml version="1.0" encoding="UTF-8"?>
+<tool id="GetGEO" name="GRsetFromGEO" version="1.16.2">
+<requirements>
+<requirement type="package" version="1.20.0">bioconductor-minfi</requirement>
+</requirements>
+<stdio>
+<exit_code range="1:" />
+</stdio>
   <command>Rscript $__tool_directory__/GRsetFromGEO.R $input output.RData</command>
   <inputs>
-    <param format="text" name="input" type="text" value="" label="Enter GSE ID." help="e.g. 'GSE51547'"/>
+     <param name="input" type="text" value="" label="Enter GSE ID." help="e.g. 'GSE51547'"/>
   </inputs>
   <outputs>
-    <data format="RDdata" name="output" label="output.RData" />
+    <data format="RDdata" name="output" label="GRsetFromGEO.RData"/>
   </outputs>
+  <tests>
+    <test>
+      <param name="test">
+      <element name="test-data">
+          <collection type="data">
+                <element name="input" value="GSE51547"/>
+          </collection>
+        </element>
+        </param>
+        <output type="data" format="RData"  name="output" label="test-data/out.RData"/>
+        </test>
+    </tests>
   <help>
-    **What it does**
-    This R-based tool downloads data from GEO using getGEO from the GEOquery package and then returns a GenomicRatioSet object
-    **Input**
-    The GSE ID of the dataset to be downloaded from GEO "e.g. 'GSE51547'"
-    **Output**
-    GenomicRatioSet object
+**What it does**
+This R-based tool downloads data from GEO using getGEO from the GEOquery package and then returns a GenomicRatioSet object
+**Input**
+The GSE ID of the dataset to be downloaded from GEO "e.g. 'GSE51547'"
+**Output**
+GenomicRatioSet object
   </help>
+  <citations>
+<citation type="doi">10.1093/bioinformatics/btu049</citation>
+  </citations>
 </tool>