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changeset 29:118e636a5f95 draft

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Uploaded
author testtool
date Thu, 13 Apr 2017 11:49:05 -0400
parents 3d281ad15b83
children ceced09589d9
files GRsetFromGEO/GRsetFromGEO.R GRsetFromGEO/GRsetFromGEO.xml
diffstat 2 files changed, 9 insertions(+), 17 deletions(-) [+]
line wrap: on
line diff
--- a/GRsetFromGEO/GRsetFromGEO.R	Thu Apr 13 11:26:43 2017 -0400
+++ b/GRsetFromGEO/GRsetFromGEO.R	Thu Apr 13 11:49:05 2017 -0400
@@ -1,14 +1,9 @@
 require("minfi", quietly = TRUE)
 
-options(warn = -1)
-options("download.file.method"="wget")
-
 args <- commandArgs(trailingOnly = TRUE)
 GSE = args[1] 
 output = args[2] 
 
 GRset <- getGenomicRatioSetFromGEO(GSE)
-a<-"stefan"
-write.table(a,output)
 
-#save(GRset,file = output)
+save(GRset,output)
--- a/GRsetFromGEO/GRsetFromGEO.xml	Thu Apr 13 11:26:43 2017 -0400
+++ b/GRsetFromGEO/GRsetFromGEO.xml	Thu Apr 13 11:49:05 2017 -0400
@@ -1,36 +1,33 @@
 <tool id="GRset" name="GRsetFromGEO" version="1.16.2">
-  <description>
-   Reading Illumina methylation array data from GEO.
-  </description>
   <requirements>
-         <requirement type="package" version="3.2.1">R</requirement>
-     </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'"/>
+    <param name="GSE" type="text" value="" label="Enter GSE ID." help="e.g. 'GSE51547'"/>
   </inputs>
   <outputs>
-   <data format="txt" name="output" label="GenomicRatioSet.txt"/>
+    <data type="galaxy.datatypes.binary:RData" name="output" label="GenomicRatioSet.RData"/>
   </outputs>
   <tests>
     <test>
       <param name="test">
       <element name="test-data">
-          <collection type="data">
+           <collection type="data">
                 <element name="GSE" value="GSE51547"/>
           </collection>
         </element>
         </param>
-        <output format="txt" name="output" label="test-data/GenomicRatioSet.txt"/>
+        <output  type="galaxy.datatypes.binary:RData" name="output" label="test-data/GenomicRatioSet.RData"/>
         </test>
     </tests>
   <help>
-Reading Illumina methylation array data from GEO.
+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 3010 (2014): 1363-1369
+xxx
 </citations>
 </tool>