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randomForest.xml |
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| diff -r f311dc86809f -r 502fbb316d2d randomForest.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/randomForest.xml Fri Oct 21 06:28:31 2016 -0400 |
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| @@ -0,0 +1,59 @@ +<tool id="randomForest" name="randomForest" version="1.0.1"> + <description>predict phenotype using a random forest approach</description> + <command interpreter="Rscript"> + randomForest.R $config > ${output1} + </command> + + <inputs> + <param name="genotype" type="data" + label="genotype data" help="a tabular datatype containing the encoded genotypes" + /> + + <param name="phenotype" type="data" + label="phenotype data" help=" a tabular datatype containing the phenotypes " + /> + + <param name="eval" type="integer" value="1" + label="do evaluation" help=" whether to produce a model or to use folds to evaluate the tool. 1 means the tool will be evaluate (and a folds argument is required) any other value produces a model " + /> + + <param name="ntree" type="float" value="1000" + label="ntree" help="the ntree parameter of Random Forest. Suitable value could be around 1000. " + /> + + <param name="mtry" type="float" value="-1" + label="mtry" help="the mtry parameter of Random Forest (number of node per tree). default value are around nuber_of_variable/3 through optimization is highly desirable. -1 means the parameter must be optimized by the tool" + /> + + <param name="folds" type="data" optional="true" + label="folds" help=" OPTIONAL ARGUMENT path to a folds file containing folds indexes in a R list called /folds/ such as produced by the folds tools in OGHMA suite. " + /> + + <param name="model" type="text" + label="path to the output folds" help= " a path to a file where the results (depending on the chosen mode) will be writen" + /> + </inputs> + + <configfiles> + <configfile name="config"> +## Desc: this file is sourced in encode wrapper script +## as means to pass all galaxy params to R +"${genotype}" -> genotype +"${phenotype}" -> phenotype +"${eval}" -> doEvaluation +"${folds}" -> folds +"${model}" -> out +"${mtry}" -> mtry +"${ntree}" -> ntree + + </configfile> +</configfiles> + +<outputs> + <data format="tabular" name = "output1" label="random forest output" /> +</outputs> + + <help> + make the classification using the random forest method + </help> +</tool> \ No newline at end of file |