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comparison encode.xml @ 3:0f87be78e151 draft

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author nicolas
date Fri, 21 Oct 2016 06:25:11 -0400
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2:f3f230290ffe 3:0f87be78e151
1 <tool id="encode" name="encode" version="1.0.0">
2 <description>encode genotypes for further machine learning analysis</description>
3 <command interpreter="Rscript">
4 encode.R $config &gt; ${output1}
5 </command>
6
7 <inputs>
8 <param name="genotype" type="data"
9 label="genotype data" help="genotype must be a .csv"
10 />
11
12 <param name="separator" type="text" value="/"
13 label="separator of the heterozygous" help=" caracter used to separate heterozygous in the genotype"
14 />
15
16 <param name="code" type="text" value="0,1,2"
17 label="coding schem" help=" method to encode the genotype as minor homozygous/heterozygous/major homozygous. Three numbers separated by comma are expected "
18 />
19
20 <param name="encodedPath" type="text"
21 label="path to the output file" help= " a .csv extension is automatically added by OGHMA"
22 />
23 </inputs>
24
25
26 <configfiles>
27 <configfile name="config">
28 ## Desc: this file is sourced in encode wrapper script
29 ## as means to pass all galaxy params to R
30 "${genotype}" -> genotype
31 "${separator}" -> sep
32 "${code}" -> code
33 "${encodedPath}" -> out
34
35 </configfile>
36 </configfiles>
37
38 <outputs>
39 <data format="tabular" name="output1" label="encoded data" />
40 </outputs>
41
42 <help>
43 Takes the genotype and encode them in the desired schem (usually 3 integer like 1/2/3) for minor homozygous/heterozygous/major homozygous. The output is a .csv file that may be use by other tools in the OGHMA workflow.
44 </help>
45 </tool>