|
88
|
1 <tool id="rrBLUP" name="rrBLUP" version="1.0.0">
|
|
|
2 <description>predict phenotype using a rrBLUP approach</description>
|
|
|
3 <command interpreter="Rscript">
|
|
|
4 rrBLUP.R $config > ${output1}
|
|
|
5 </command>
|
|
|
6
|
|
|
7 <inputs>
|
|
|
8 <param name="genotype" type="data"
|
|
|
9 label="genotype data" help="a tabular datatype containing the encoded genotypes"
|
|
|
10 />
|
|
|
11
|
|
|
12 <param name="phenotype" type="data"
|
|
|
13 label="phenotype data" help=" a tabular datatype containing the phenotypes "
|
|
|
14 />
|
|
|
15
|
|
|
16 <param name="eval" type="integer" value="0"
|
|
|
17 label="do evaluation" help=" whether to produce a model or to use folds to evaluate the tool. 1 means the tool will be evaluate (and a folds argument is required) any other value produces a model "
|
|
|
18 />
|
|
|
19
|
|
|
20 <param name="folds" type="data" optional="true"
|
|
|
21 label="folds" help=" OPTIONAL ARGUMENT path to a folds file containing folds indexes in a R list called /folds/ such as produced by the folds tools in OGHMA suite. "
|
|
|
22 />
|
|
|
23
|
|
|
24 <!-- <param name="model" type="text"
|
|
|
25 label="path to the output folds" help= " a path to a file where the results (depending on the chosen mode) will be writen"
|
|
|
26 /> -->
|
|
|
27 </inputs>
|
|
|
28
|
|
|
29 <configfiles>
|
|
|
30 <configfile name="config">
|
|
|
31 ## Desc: this file is sourced in encode wrapper script
|
|
|
32 ## as means to pass all galaxy params to R
|
|
|
33 "${genotype}" -> genotype
|
|
|
34 "${phenotype}" -> phenotype
|
|
|
35 "${output1}" -> out
|
|
|
36 "${eval}" -> evaluation
|
|
|
37 "${folds}" -> folds
|
|
|
38
|
|
|
39
|
|
|
40 </configfile>
|
|
|
41 </configfiles>
|
|
|
42
|
|
|
43 <outputs>
|
|
|
44 <data format="tabular" name = "output1" label="rrBLUP output" />
|
|
|
45 </outputs>
|
|
|
46
|
|
|
47 <help>
|
|
|
48 make the classification using the rrBLUP method
|
|
|
49 </help>
|
|
|
50 </tool> |
