Mercurial > repos > testtool > get_gr_set

changeset 27:d492a31c50f1 draft

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Uploaded
author testtool
date Mon, 10 Jul 2017 08:58:44 -0400
parents b003e02d1ea4
children ab34c2e8e533
files GRsetFromGEO/GRsetFromGEO.xml
diffstat 1 files changed, 11 insertions(+), 32 deletions(-) [+]
line wrap: on
line diff
--- a/GRsetFromGEO/GRsetFromGEO.xml	Mon Jul 10 08:58:28 2017 -0400
+++ b/GRsetFromGEO/GRsetFromGEO.xml	Mon Jul 10 08:58:44 2017 -0400
@@ -1,39 +1,18 @@
-<?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" </command>
+<tool id="getGRset" name="GRsetFromGEO">
+  <description>downloads data from GEO</description>
+  <command>Rscript $__tool_directory__/GRsetFromGEO.R $input output.RData</command>
   <inputs>
-     <param name="input" type="text" value="" label="Enter GSE ID." help="e.g. 'GSE51547'"/>
+    <param format="text" name="input" type="text" value="" label="Enter GSE ID." help="e.g. 'GSE51547'"/>
   </inputs>
   <outputs>
-    <data format="RDdata" name="output" label="GRsetFromGEO.RData"/>
+    <data format="RDdata" name="output" label="output.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>