<tool id="encode" name="encode" version="1.0.0">
  <description>encode genotypes for further machine learning analysis</description>
  <command interpreter="Rscript">
	  encode.R $config &gt; ${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>