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1 <tool id="qualityControl" name="qualityControl" version="1.0.0">
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2 <description>perform QC on a dataset</description>
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3 <command interpreter="Rscript">
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4 qualityControl.R $config > ${reportPath}
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5 </command>
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6
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7 <inputs>
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8 <param name="genotype" type="data"
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9 label="genotype data" help="genotype must be a .csv"
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10 />
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11
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12 <param name="plinkFreq" type="data"
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13 label="plink files with frequencies" help=""
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14 />
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15
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16 <param name="plinkHWE" type="data"
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17 label="plink files with HardyWeinberg statistics" help=""
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18 />
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19 </inputs>
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20
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21
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22 <configfiles>
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23 <configfile name="config">
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24 ## Desc: this file is sourced in encode wrapper script
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25 ## as means to pass all galaxy params to R
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26 "${genotype}" -> genotype
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27 "${plinkFreq}" -> plinkFreq
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28 "${plinkHWE}" -> plinkHWE
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29 "${reportPath}" -> out
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30
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31 </configfile>
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32 </configfiles>
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33
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34 <outputs>
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35 <data format="plain text" name="reportPath" label="QC report" />
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36 </outputs>
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37
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38 <help>
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39 make a report with dimension of the dataset, MAF, Hardy-Weinberg test
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40 </help>
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41 </tool> |
