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1 <?xml version="1.0" encoding="UTF-8"?>
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2 <tool id="findSNPs" name="findSNPs" version="1.20.0">
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3 <requirements>
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4 <requirement type="package" version="1.20.0">bioconductor-minfi</requirement>
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5 </requirements>
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6 <stdio>
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7 <exit_code range="1:" />
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8 </stdio>
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9 <command> Rscript $__tool_directory__/findSNPs.R "$input" "$output" </command>
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10 <inputs>
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11 <param format="RDdata" name="input" type="data" label="Genomic Ratio Set" help="e.g. 'GRsetFromGEO tool output'"/>
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12 </inputs>
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13 <outputs>
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14 <data format="text" type="data" name="output" label="findSNPs.txt"/>
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15 </outputs>
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16 <tests>
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17 <test>
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18 <param name="test">
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19 <element name="test-data">
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20 <collection type="data">
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21 <element name="input" type="data" format="RData" label="test-data/out.RData"> </element>
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22 </collection>
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23 </element>
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24 </param>
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25 <output name="output" type="data" format="text" label="test-data/findSNPs.txt"/>
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26 </test>
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27 </tests>
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28 <help>
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29 **What it does**
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30 Function To Retrieve The Chromosome And The Position Of Each SNP On A Given Affymetrix SNP Array
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31 **Input**
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32 GenomicRatioSet object
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33 **Output**
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34 Text file containing information on which probes contains SNPs
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35 </help>
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36 <citations>
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37 <citation type="doi">10.1093/bioinformatics/btu049</citation>
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38 </citations>
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39 </tool>
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