| Previous changeset 99:4af0489af821 (2016-10-31) Next changeset 101:edced3c17e3b (2016-10-31) |
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Commit message:
Uploaded |
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added:
aggregation.xml |
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| diff -r 4af0489af821 -r 09827a9f75a6 aggregation.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/aggregation.xml Mon Oct 31 06:44:04 2016 -0400 |
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| @@ -0,0 +1,64 @@ +<tool id="aggreg" name="aggregation" version="1.0.0"> + <description>predict phenotype by combining multiple classifiers</description> + <command interpreter="Rscript"> + aggregation.R $config > ${output1} + </command> + + <inputs> + <param name="lassoPred" type="data" optional="true" + label="lasso prediction" help="path to rds containing LASSO prediction" + /> + + <param name="rfPred" type="data" optional="true" + label="rf prediction" help="path to rds containing Random Forest prediction" + /> + + <param name="rrBLUPPred" type="data" optional="true" + label="rrBLUP prediction" help="path to rds containing rrBLUP prediction" + /> + + <param name="svmPred" type="data" optional="true" + label="SVM prediction" help="path to rds containing SVM prediction" + /> + + <param name="phenotype" type="data" + label="phenotype data" help=" a tabular datatype containing the phenotypes " + /> + + <param name="model" type="data" optional="true" + label="model" help= " a path to a file where the results (depending on the chosen mode) will be writen" + /> + <param name="method" type="text" value="svm" + label="aggregation method" help= "choose among geneticMean, dt, lasso, rf or svm" + /> + <param name="kernel" type="text" value="linear" + label="kernel for SVM" help= "choose among linear, polynomial, radial, sigmoid" + /> + + </inputs> + + <configfiles> + <configfile name="config"> +## Desc: this file is sourced in encode wrapper script +## as means to pass all galaxy params to R +"${lassoPred}" -> lassoPred +"${rfPred}" -> rfPred +"${rrBLUPPred}" -> rrBLUPPred +"${svmPred}" -> svmPred +"${phenotype}" -> phenotype +"${model}" -> model +"${output1}" -> out +"${method}" -> method +"${kernel}" -> kernel + + </configfile> +</configfiles> + +<outputs> + <data format="tabular" name = "output1" label="aggregation output" /> +</outputs> + + <help> + + </help> + </tool> \ No newline at end of file |