| Next changeset 1:b434ba108e9b (2017-02-27) |
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Commit message:
Uploaded |
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added:
soft-threshold.xml |
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| diff -r 000000000000 -r 29be657758be soft-threshold.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/soft-threshold.xml Mon Feb 27 22:36:21 2017 -0500 |
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| @@ -0,0 +1,42 @@ +<tool id="soft_threshold" name="wgcna soft threshold" version="1.0.0"> + <description> + Calculate R power table and explore optimal beta value + </description> + <stdio> + <regex match="Execution halted" + source="both" + level="fatal" + description="Execution halted." /> + <regex match="Error in" + source="both" + level="fatal" + description="An undefined error occured, please check your intput carefully and contact your administrator." /> + <regex match="Fatal error" + source="both" + level="fatal" + description="An undefined error occured, please check your intput carefully and contact your administrator." /> + </stdio> + <requirements> + <requirement type="package" version="3.2.1">R</requirement> + <requirement type="package" version="1.0.0">wgcna</requirement> + </requirements> + <command> + <![CDATA[ + Rscript '${__tool_directory__}/soft_threshold.R' + -t $threads + -f $expressionData + -b $betaMaximum + -r $rPowerTable + -p $scaleFreeFitPlot + ]]> + </command> + <inputs> + <param name="threads" type="integer" value="1" label="number of threads for WGCNA"/> + <param name="expressionData" type="data" format="csv" label="expression data in csv file format. Rows are samples and columns are genes"/> + <param name="betaMaximum" type="integer" value="12" label="maximum beta values"/> + </inputs> + <outputs> + <data format="csv" name="rPowerTable" label="R power table on ${on_string}" /> + <data format="pdf" name="scaleFreeFitPlot" label="scale free fit plot on ${on_string}" /> + </outputs> +</tool> \ No newline at end of file |