| Previous changeset 56:374c9a2bc1c2 (2016-10-26) Next changeset 58:8d8326d74f04 (2016-10-26) |
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aggregation.xml |
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| diff -r 374c9a2bc1c2 -r a7869aa2c572 aggregation.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/aggregation.xml Wed Oct 26 18:08:57 2016 -0400 |
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| @@ -0,0 +1,78 @@ +<tool id="aggreg" name="aggregation" version="1.0.0"> + <description>predict phenotype by combining multiple classifiers</description> + <command interpreter="Rscript"> + aggregation.R $config > ${output1} + </command> + + <inputs> + <param name="lassoPred" type="data" optional="true" + label="lasso prediction" help="path to rds containing LASSO prediction" + /> + + <param name="rfPred" type="data" optional="true" + label="rf prediction" help="path to rds containing Random Forest prediction" + /> + + <param name="rrBLUPPred" type="data" optional="true" + label="rrBLUP prediction" help="path to rds containing rrBLUP prediction" + /> + + <param name="svmPred" type="data" optional="true" + label="SVM prediction" help="path to rds containing SVM prediction" + /> + + <param name="phenotype" type="data" + label="phenotype data" help=" a tabular datatype containing the phenotypes " + /> + + <param name="eval" type="integer" value="0" + label="do evaluation" help=" whether to produce a model or to use folds to evaluate the tool. 1 means the tool will be evaluate (and a folds argument is required) any other value produces a model " + /> + + <param name="folds" type="data" optional="true" + label="folds" help=" OPTIONAL ARGUMENT path to a folds file containing folds indexes in a R list called /folds/ such as produced by the folds tools in OGHMA suite. " + /> + + <param name="model" type="data" optional="true" + label="model" help= " a path to a file where the results (depending on the chosen mode) will be writen" + /> + <param name="out" type="text" + label="output path" help= " a path to a rds file" + /> + <param name="method" type="text" value="svm" + label="aggregation method" help= "choose among geneticMean, rrBLUP, lasso, rf or svm" + /> + <param name="kernel" type="text" value="linear" + label="kernel for SVM" help= "choose among linear, polynomial, radial, sigmoid" + /> + + </inputs> + + <configfiles> + <configfile name="config"> +## Desc: this file is sourced in encode wrapper script +## as means to pass all galaxy params to R +"${lassoPred}" -> lassoPred +"${rfPred}" -> rfPred +"${rrBLUPPred}" -> rrBLUPPred +"${svmPred}" -> svmPred +"${phenotype}" -> phenotype +"${model}" -> model +"${out}" -> out +"${eval}" -> evaluation +"${folds}" -> folds +"${method}" -> method +"${kernel}" -> kernel +"${eval}" -> doEvaluation + + </configfile> +</configfiles> + +<outputs> + <data format="tabular" name = "output1" label="aggregation output" /> +</outputs> + + <help> + + </help> + </tool> \ No newline at end of file |