view GRsetFromGEO/GRsetFromGEO.xml @ 32:be1ca0e7829b draft

author testtool
date Thu, 13 Apr 2017 12:50:58 -0400
parents cc4b808cb2ea
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<tool id="GRset" name="GRsetFromGEO" version="1.16.2">
         <requirement type="package" version="3.2.1">R</requirement>
   <exit_code range="1:" />
  <command> Rscript $__tool_directory__/GRsetFromGEO.R "$GSE" "$output" </command>
    <param name="GSE" type="text" value="" label="Enter GSE ID." help="e.g. 'GSE51547'"/>
     <data format="txt" name="output" label="GSMTable.txt"/>
      <param name="test">
      <element name="test-data">
           <collection type="data">
                <element name="GSE" value="GSE51547"/>
        <output format="txt"  name="output" label="test-data/GSMTable.txt"/>
Reading Illumina methylation array data from GEO.
Aryee, Martin J., et al. "Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays." Bioinformatics 30.10 (2014): 1363-1369.