| Previous changeset 96:5c895aa6d820 (2016-10-31) Next changeset 98:b04f764a52bd (2016-10-31) |
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added:
evaluate_aggregation.xml |
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| diff -r 5c895aa6d820 -r 642ffa1b1467 evaluate_aggregation.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/evaluate_aggregation.xml Mon Oct 31 05:55:59 2016 -0400 |
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| @@ -0,0 +1,70 @@ +<tool id="aggregEval" name="aggregation_evaluation" version="1.0.0"> + <description>tool to evaluate aggregation accuracy</description> + <command interpreter="Rscript"> + evaluate_aggregation.R $config > ${output1} + </command> + + <inputs> + + <param name="genotype" type="data" + label="genotype data" help="path to a file containing the encoded genotypes" + /> + + <param name="lasso" type="data" optional="true" + label="lasso model" help="path to rds containing LASSO model" + /> + + <param name="rf" type="data" optional="true" + label="rf model" help="path to rds containing Random Forest model" + /> + + <param name="rrBLUP" type="data" optional="true" + label="rrBLUP model" help="path to rds containing rrBLUP model" + /> + + <param name="svm" type="data" optional="true" + label="SVM model" help="path to rds containing SVM model" + /> + + <param name="phenotype" type="data" + label="phenotype data" help=" a tabular datatype containing the phenotypes " + /> + + <param name="folds" type="data" + label="folds" help=" OPTIONAL ARGUMENT path to a folds file containing folds indexes in a R list called /folds/ such as produced by the folds tools in OGHMA suite. " + /> + <param name="method" type="text" value="svm" + label="aggregation method" help= "choose among geneticMean, dt, lasso, rf or svm" + /> + <param name="kernel" type="text" value="linear" + label="kernel for SVM" help= "choose among linear, polynomial, radial, sigmoid" + /> + + </inputs> + + <configfiles> + <configfile name="config"> +## Desc: this file is sourced in encode wrapper script +## as means to pass all galaxy params to R +"${genotype}" -> genotype +"${lasso}" -> lassoModel +"${rf}" -> rfModel +"${rrBLUP}" -> rrBLUPModel +"${svm}" -> svmModel +"${phenotype}" -> phenotype +"${output1}" -> out +"${folds}" -> folds +"${method}" -> method +"${kernel}" -> kernel + + </configfile> +</configfiles> + +<outputs> + <data format="tabular" name = "output1" label="aggregation evaluation" /> +</outputs> + + <help> + + </help> + </tool> \ No newline at end of file |