Galaxy |

Changeset 66:d19a280323b3 (2016-10-26)

Previous changeset 65:9a6bade6e77a (2016-10-26) Next changeset 67:99e8e055ddd6 (2016-10-26)

Commit message:
Uploaded

added:
aggregation.xml

diff -r 9a6bade6e77a -r d19a280323b3 aggregation.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/aggregation.xml Wed Oct 26 18:42:20 2016 -0400

@@ -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 > ${output1}
+  </command>
+
+  <inputs>
+ <param name="lassoPred" type="data" optional="true"
+ label="lasso prediction" help="path to rds containing LASSO prediction"
+ />
+
+ <param name="rfPred" type="data" optional="true"
+ label="rf prediction" help="path to rds containing Random Forest prediction"
+ />
+
+ <param name="rrBLUPPred" type="data" optional="true"
+ label="rrBLUP prediction" help="path to rds containing rrBLUP prediction"
+ />
+
+ <param name="svmPred" type="data" optional="true"
+ label="SVM prediction" help="path to rds containing SVM prediction"
+ />
+
+ <param name="phenotype" type="data"
+ label="phenotype data" help=" a tabular datatype containing the phenotypes "
+ />
+
+ <param name="eval" type="integer" value="0"
+ label="do evaluation" help=" whether to produce a model or to use folds to evaluate the tool. 1 means the tool will be evaluate (and a folds argument is required) any other value produces a model "
+ />
+
+ <param name="folds" type="data" optional="true"
+ label="folds" help=" OPTIONAL ARGUMENT path to a folds file containing folds indexes in a R list called /folds/ such as produced by the folds tools in OGHMA suite. "
+ />
+
+ <param name="model" type="data" optional="true"
+ label="model" help= " a path to a file where the results (depending on the chosen mode) will be writen"
+ />
+ 
+ />
+ <param name="method" type="text" value="svm"
+ label="aggregation method" help= "choose among geneticMean, rrBLUP, lasso, rf or svm"
+ />
+ <param name="kernel" type="text" value="linear"
+ label="kernel for SVM" help= "choose among linear, polynomial, radial, sigmoid"
+ />
+
+  </inputs>
+
+  <configfiles>
+    <configfile name="config">
+## Desc: this file is sourced in encode wrapper script
+##  as means to pass all galaxy params to R
+"${lassoPred}" -> lassoPred
+"${rfPred}" -> rfPred
+"${rrBLUPPred}" -> rrBLUPPred
+"${svmPred}" -> svmPred
+"${phenotype}" -> phenotype
+"${model}" -> model
+"${output1}" -> 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