<tool id="SNPs" name="SNPs" version="1.16.2">
  <requirements>
   <requirement name="package_r_3_2_1" type="package" version="3.2.1">R</requirement>
</requirements>
<stdio>
   <exit_code range="1:" />
</stdio>
  <command> Rscript $__tool_directory__/findSNPs.R "$input" "$output" </command>
  <inputs>
    <param name="input" format="Rdata"label="GenomicRatioSet.Rdata" help="e.g. 'GSE51547'"/>
  </inputs>
  <outputs>
    <data format="txt" name="output" label="SNPs.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/findSNP.txt"/>
        </test>
    </tests>
  <help>
**What it does**
SNPs inside the probe body or at the nucleotide extension can have important consequences on the downstream analysis, these tool offers the possibility to remove such probes
**Input**
GenomicRatioSet object e.g. output from getGRsetFromGEO tool
**Output**
Text file with columns containing the SNP information about the probes
</help>
<citations>
<citation type="doi">10.1093/bioinformatics/btu049</citation>
</citations>
</tool>