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1 <tool id="soft_threshold" name="wgcna soft threshold" version="1.0.0">
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2 <description>
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3 Calculate R power table and explore optimal beta value
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4 </description>
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5 <stdio>
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6 <regex match="Execution halted"
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7 source="both"
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8 level="fatal"
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9 description="Execution halted." />
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10 <regex match="Error in"
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11 source="both"
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12 level="fatal"
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13 description="An undefined error occured, please check your intput carefully and contact your administrator." />
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14 <regex match="Fatal error"
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15 source="both"
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16 level="fatal"
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17 description="An undefined error occured, please check your intput carefully and contact your administrator." />
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18 </stdio>
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19 <requirements>
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20 <requirement type="package" version="3.2.1">R</requirement>
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21 </requirements>
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22 <command>
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23 <![CDATA[
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24 Rscript '${__tool_directory__}/soft_threshold.R'
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25 -t $threads
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26 -f $expressionData
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27 -b $betaMaximum
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28 -r $rPowerTable
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29 -p $scaleFreeFitPlot
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30 ]]>
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31 </command>
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32 <inputs>
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33 <param name="threads" type="integer" value="1" label="number of threads for WGCNA"/>
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34 <param name="expressionData" type="data" format="csv" label="expression data in csv file format. Rows are samples and columns are genes"/>
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35 <param name="betaMaximum" type="integer" value="12" label="maximum beta values"/>
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36 </inputs>
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37 <outputs>
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38 <data format="csv" name="rPowerTable" label="R power table on ${on_string}" />
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39 <data format="pdf" name="scaleFreeFitPlot" label="scale free fit plot on ${on_string}" />
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40 </outputs>
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5
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41 </tool>
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