view prediction.xml @ 103:e7115e44d8d8 draft default tip

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author nicolas
date Mon, 31 Oct 2016 07:20:49 -0400
parents 6a75b93ba5f2
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<tool id="prediction" name="prediction" version="1.0.0">
  <description>use machine learning model to predict phenotype from genotype</description>
  <command interpreter="Rscript">
	  prediction.R $config &gt; ${output1}
  </command>
  
  <inputs>
	<param name="genotype" type="data"
		  label="genotype data" help="genotype must be a .rda file 
		  containing a R dataframe/matrix called /encoded/ " 
	/>
	
	<param name="model" type="data"
		label="classifier model" help="model created by one of the classifier tool of the OGHMA suite. Represented as a .rda file, containing a dataframe called /model/" 
	/>
		  
	<!-- deprecated
	<param name="name" type="text"
			label="names" help=" prefixe given to all results of the evaluation in the output folder (see -o option) to distinguish them" 
	/>

	
	<param name="outputPath" type="data"
			label="path to the output folds" help= " a path to a FOLDER where the results will be writen" 
	/> -->
  </inputs>
  
   <configfiles>
    <configfile name="config">
## Desc: this file is sourced in encode wrapper script
##  as means to pass all galaxy params to R
"${genotype}" -> genotype
"${model}" -> model
"${output1}" -> out

    </configfile>
</configfiles>
  
<outputs>
	<data format="tabular" name = "output1" label="classifier prediction" />
</outputs>
  
  <help>
	  Use model designed by any clasifier tool from the OGHMA suite to predict the phenotype of a dataset provided as input. results are stored in a folder under a .rda file
  </help>
</tool>