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comparison evaluate_aggregation.xml @ 97:642ffa1b1467 draft

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author nicolas
date Mon, 31 Oct 2016 05:55:59 -0400
parents d1e92ce799c1
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96:5c895aa6d820 97:642ffa1b1467
1 <tool id="aggregEval" name="aggregation_evaluation" version="1.0.0">
2 <description>tool to evaluate aggregation accuracy</description>
3 <command interpreter="Rscript">
4 evaluate_aggregation.R $config &gt; ${output1}
5 </command>
6
7 <inputs>
8
9 <param name="genotype" type="data"
10 label="genotype data" help="path to a file containing the encoded genotypes"
11 />
12
13 <param name="lasso" type="data" optional="true"
14 label="lasso model" help="path to rds containing LASSO model"
15 />
16
17 <param name="rf" type="data" optional="true"
18 label="rf model" help="path to rds containing Random Forest model"
19 />
20
21 <param name="rrBLUP" type="data" optional="true"
22 label="rrBLUP model" help="path to rds containing rrBLUP model"
23 />
24
25 <param name="svm" type="data" optional="true"
26 label="SVM model" help="path to rds containing SVM model"
27 />
28
29 <param name="phenotype" type="data"
30 label="phenotype data" help=" a tabular datatype containing the phenotypes "
31 />
32
33 <param name="folds" type="data"
34 label="folds" help=" OPTIONAL ARGUMENT path to a folds file containing folds indexes in a R list called /folds/ such as produced by the folds tools in OGHMA suite. "
35 />
36 <param name="method" type="text" value="svm"
37 label="aggregation method" help= "choose among geneticMean, dt, lasso, rf or svm"
38 />
39 <param name="kernel" type="text" value="linear"
40 label="kernel for SVM" help= "choose among linear, polynomial, radial, sigmoid"
41 />
42
43 </inputs>
44
45 <configfiles>
46 <configfile name="config">
47 ## Desc: this file is sourced in encode wrapper script
48 ## as means to pass all galaxy params to R
49 "${genotype}" -> genotype
50 "${lasso}" -> lassoModel
51 "${rf}" -> rfModel
52 "${rrBLUP}" -> rrBLUPModel
53 "${svm}" -> svmModel
54 "${phenotype}" -> phenotype
55 "${output1}" -> out
56 "${folds}" -> folds
57 "${method}" -> method
58 "${kernel}" -> kernel
59
60 </configfile>
61 </configfiles>
62
63 <outputs>
64 <data format="tabular" name = "output1" label="aggregation evaluation" />
65 </outputs>
66
67 <help>
68
69 </help>
70 </tool>