Mercurial > repos > testtool > get_gr_set

changeset 1:af176b97c4ac draft

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Deleted selected files
author testtool
date Sun, 11 Jun 2017 06:37:18 -0400
parents 457c1fc71f64
children 39f1afe94ef4
files getGRsetFromGEO/getGRsetFromGEO.xml
diffstat 1 files changed, 0 insertions(+), 39 deletions(-) [+]
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--- a/getGRsetFromGEO/getGRsetFromGEO.xml	Sun Jun 11 06:21:37 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,39 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<tool id="getGRsetFromGEO" name="getGRsetFromGEO" version="1.18.4">
-  <requirements>
-          <requirement type="package" version="1.20.0">bioconductor-minfi</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="RDdata" name="output" label="GRsetFromGEO.RData"/>
-  </outputs>
-  <tests>
-    <test>
-      <param name="test">
-      <element name="test-data">
-          <collection type="data">
-                <element name="GSE" 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>
-</tool>