Mercurial > repos > nicolas > oghma
changeset 3:0f87be78e151 draft
Uploaded
| author | nicolas |
|---|---|
| date | Fri, 21 Oct 2016 06:25:11 -0400 |
| parents | f3f230290ffe |
| children | 62e7a8d66b1f |
| files | encode.xml |
| diffstat | 1 files changed, 45 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/encode.xml Fri Oct 21 06:25:11 2016 -0400 @@ -0,0 +1,45 @@ +<tool id="encode" name="encode" version="1.0.0"> + <description>encode genotypes for further machine learning analysis</description> + <command interpreter="Rscript"> + encode.R $config > ${output1} + </command> + + <inputs> + <param name="genotype" type="data" + label="genotype data" help="genotype must be a .csv" + /> + + <param name="separator" type="text" value="/" + label="separator of the heterozygous" help=" caracter used to separate heterozygous in the genotype" + /> + + <param name="code" type="text" value="0,1,2" + label="coding schem" help=" method to encode the genotype as minor homozygous/heterozygous/major homozygous. Three numbers separated by comma are expected " + /> + + <param name="encodedPath" type="text" + label="path to the output file" help= " a .csv extension is automatically added by OGHMA" + /> + </inputs> + + + <configfiles> + <configfile name="config"> +## Desc: this file is sourced in encode wrapper script +## as means to pass all galaxy params to R +"${genotype}" -> genotype +"${separator}" -> sep +"${code}" -> code +"${encodedPath}" -> out + + </configfile> +</configfiles> + +<outputs> + <data format="tabular" name="output1" label="encoded data" /> +</outputs> + + <help> + 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. + </help> + </tool> \ No newline at end of file