Mercurial > repos > testtool > get_gr_set

changeset 20:40d7bdac6322 draft

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Uploaded
author testtool
date Mon, 03 Jul 2017 07:13:53 -0400
parents 0a619d0e45fd
children 07f0fc6e4d1d
files GRsetFromGEO/GRsetFromGEO.xml
diffstat 1 files changed, 36 insertions(+), 29 deletions(-) [+]
line wrap: on
line diff
--- a/GRsetFromGEO/GRsetFromGEO.xml	Mon Jul 03 07:13:43 2017 -0400
+++ b/GRsetFromGEO/GRsetFromGEO.xml	Mon Jul 03 07:13:53 2017 -0400
@@ -1,32 +1,39 @@
-<tool id="GetGEO" name="GRsetFromGEO" version="0.1.0">
-    <requirements>
-        <requirement type="package" version="1.20.0">bioconductor-minfi</requirement>
-    </requirements>
-    <stdio>
-        <exit_code range="1:" />
-    </stdio>
-    <command><![CDATA[
-      Rscript $__tool_directory__/GRsetFromGEO.R -a "$input" > "$output"
-    ]]></command>
-    <inputs>
-        <param type="text" name="input" value="" label="Enter GSE ID." help="e.g. 'GSE51547'"/>
-    </inputs>
-    <outputs>
-        <data name="output" format="RDdata" label="GRsetFromGEO.RData"/>
-    </outputs>
-    <tests>
-        <test>
-            <param name="input" value="GSE51547"/>
-            <output name="output" file="test-data/out.RData"/>
+<?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>
+  <inputs>
+     <param name="input" type="text" value="" label="Enter GSE ID." help="e.g. 'GSE51547'"/>
+  </inputs>
+  <outputs>
+    <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</help>
-    <citations>
-        <citation type="doi">10.1093/bioinformatics/btu049</citation>
-    </citations>
+  <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
+  </help>
+  <citations>
+<citation type="doi">10.1093/bioinformatics/btu049</citation>
+  </citations>
 </tool>