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comparison aggregation.xml @ 103:e7115e44d8d8 draft default tip

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author nicolas
date Mon, 31 Oct 2016 07:20:49 -0400
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102:7482def43360 103:e7115e44d8d8
1 <tool id="aggreg" name="aggregation" version="1.0.0">
2 <description>predict phenotype by combining multiple classifiers</description>
3 <command interpreter="Rscript">
4 aggregation.R $config &gt; ${output1}
5 </command>
6
7 <inputs>
8 <param name="lassoPred" type="data" optional="true"
9 label="lasso prediction" help="path to rds containing LASSO prediction"
10 />
11
12 <param name="rfPred" type="data" optional="true"
13 label="rf prediction" help="path to rds containing Random Forest prediction"
14 />
15
16 <param name="rrBLUPPred" type="data" optional="true"
17 label="rrBLUP prediction" help="path to rds containing rrBLUP prediction"
18 />
19
20 <param name="svmPred" type="data" optional="true"
21 label="SVM prediction" help="path to rds containing SVM prediction"
22 />
23
24 <param name="phenotype" type="data" optional="true"
25 label="phenotype data" help=" a tabular datatype containing the phenotypes "
26 />
27
28 <param name="model" type="data" optional="true"
29 label="model" help= " a path to a file where the results (depending on the chosen mode) will be writen"
30 />
31 <param name="method" type="text" value="svm"
32 label="aggregation method" help= "choose among geneticMean, dt, lasso, rf or svm"
33 />
34 <param name="kernel" type="text" value="linear"
35 label="kernel for SVM" help= "choose among linear, polynomial, radial, sigmoid"
36 />
37
38 </inputs>
39
40 <configfiles>
41 <configfile name="config">
42 ## Desc: this file is sourced in encode wrapper script
43 ## as means to pass all galaxy params to R
44 "${lassoPred}" -> lassoPred
45 "${rfPred}" -> rfPred
46 "${rrBLUPPred}" -> rrBLUPPred
47 "${svmPred}" -> svmPred
48 "${phenotype}" -> phenotype
49 "${model}" -> model
50 "${output1}" -> out
51 "${method}" -> method
52 "${kernel}" -> kernel
53
54 </configfile>
55 </configfiles>
56
57 <outputs>
58 <data format="tabular" name = "output1" label="aggregation output" />
59 </outputs>
60
61 <help>
62
63 </help>
64 </tool>