view findBlocks/findBlocks.xml @ 0:fea57210de6c draft

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<tool id="findBlocks" name="findBlocks" version="1.18.4">
  <requirements>
        <requirement type="package" version="1.20.0">bioconductor-minfi</requirement>
    </requirements>
<stdio>
   <exit_code range="1:" />
</stdio>
  <command> Rscript $__tool_directory__/findBlocks.R "$input" "$output" </command>
  <inputs>
    <param name="input" format="RData"label="getGenomicRatioSet.RData" help="e.g. 'GSE51547'"/>
  </inputs>
  <outputs>
    <data format="txt" name="output" label="findBlocks.txt"/>
  </outputs>
  <tests>
    <test>
      <param name="test">
      <element name="test-data">
           <collection type="data">
                <element format="RData" name="input" label="test-data/GenomicRatioSet.Rdata"/>
          </collection>
        </element>
        </param>
        <output format="txt" name="output" label="test-data/findBlocks.txt"/>
        </test>
    </tests>
  <help>
**What it does**
Finds blocks (large scale regions) of methylation differences for Illumina methylation arrays.
**Input**
GenomicRatioSet object e.g. output from getGRsetFromGEO tool
**Output**
Text file
</help>
<citations>
<citation type="doi">10.1093/bioinformatics/btu049</citation>
</citations>
</tool>