view findSNPs/findSNPs.xml @ 3:3e5470e49ba5 draft

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<?xml version="1.0" encoding="UTF-8"?>
<tool id="findSNPs" name="findSNPs" version="1.20.0">
<requirements>
<requirement type="package" version="1.20.0">bioconductor-minfi</requirement>
</requirements>
<stdio>
<exit_code range="1:" />
</stdio>
  <command> Rscript $__tool_directory__/findSNPs.R "$input" "$output" </command>
  <inputs>
     <param format="RDdata" name="input" label="Genomic Ratio Set" help="e.g. 'GRsetFromGEO tool output'"/>
  </inputs>
  <outputs>
    <data format="text" name="output" label="findSNPs.txt"/>
  </outputs>
  <tests>
    <test>
      <param name="test">
      <element name="test-data">
          <collection type="data">
                <element name="input" format="RData" label="test-data/out.RData"> </element>
          </collection>
        </element>
        </param>
        <output name="output" type="data" format="text" label="test-data/findSNPs.txt"/>
        </test>
    </tests>
  <help>
**What it does**
Function To Retrieve The Chromosome And The Position Of Each SNP On A Given Affymetrix SNP Array
**Input**
GenomicRatioSet object
**Output**
Text file containing information on which probes contains SNPs
  </help>
  <citations>
<citation type="doi">10.1093/bioinformatics/btu049</citation>
  </citations>
</tool>