view GRsetFromGEO/GRsetFromGEO.xml @ 13:6f7428f907da draft

Uploaded

<?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 $__tool_directory__/GRsetFromGEO.R "$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>