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1 <tool id="SNPs" name="SNPs" version="1.16.2">
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2 <requirements>
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3 <requirement type="package" version="1.20.0">bioconductor-minfi</requirement>
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4 </requirements>
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5 <stdio>
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6 <exit_code range="1:" />
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7 </stdio>
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8 <command> Rscript $__tool_directory__/findSNPs.R "$input" "$output" </command>
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9 <inputs>
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10 <param name="input" format="Rdata"label="GenomicRatioSet.Rdata" help="e.g. 'GSE51547'"/>
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11 </inputs>
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12 <outputs>
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13 <data format="txt" name="output" label="SNPs.txt"/>
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14 </outputs>
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15 <tests>
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16 <test>
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17 <param name="test">
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18 <element name="test-data">
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19 <collection type="data">
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20 <element format="Rdata" name="input" label="test-data/GenomicRatioSet.Rdata"/>
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21 </collection>
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22 </element>
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23 </param>
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24 <output format="txt" name="output" label="test-data/findSNP.txt"/>
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25 </test>
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26 </tests>
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27 <help>
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28 **What it does**
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29 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
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30 **Input**
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31 GenomicRatioSet object e.g. output from getGRsetFromGEO tool
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32 **Output**
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33 Text file with columns containing the SNP information about the probes
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34 </help>
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35 <citations>
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36 <citation type="doi">10.1093/bioinformatics/btu049</citation>
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37 </citations>
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38 </tool>
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