view GRsetFromGEO/GRsetFromGEO.xml @ 27:2d4a97506931 draft

author testtool
date Thu, 13 Apr 2017 11:01:46 -0400
parents c7bab1a516ce
children 3d281ad15b83
line wrap: on
line source

<tool id="GRset" name="GRsetFromGEO" version="1.16.2">
   Reading Illumina methylation array data from GEO.
         <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="RData" name="output" label="GenomicRatioSet.RData"/>
      <param name="test">
      <element name="test-data">
          <collection type="data">
                <element name="GSE" value="GSE51547"/>
        <output format="RData" name="output" label="test-data/GenomicRatioSet.RData"/>
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 3010 (2014): 1363-1369