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1 <tool id="prediction" name="prediction" version="1.0.0">
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2 <description>use machine learning model to predict phenotype from genotype</description>
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3 <command interpreter="Rscript">
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4 prediction.R $config > ${output1}
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5 </command>
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6
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7 <inputs>
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8 <param name="genotype" type="data"
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9 label="genotype data" help="genotype must be a .rda file
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10 containing a R dataframe/matrix called /encoded/ "
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11 />
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12
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13 <param name="model" type="data"
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14 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/"
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15 />
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16
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17 <!-- deprecated
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18 <param name="name" type="text"
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19 label="names" help=" prefixe given to all results of the evaluation in the output folder (see -o option) to distinguish them"
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20 />
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21
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22
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23 <param name="outputPath" type="data"
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24 label="path to the output folds" help= " a path to a FOLDER where the results will be writen"
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25 /> -->
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26 </inputs>
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27
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28 <configfiles>
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29 <configfile name="config">
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30 ## Desc: this file is sourced in encode wrapper script
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31 ## as means to pass all galaxy params to R
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32 "${genotype}" -> genotype
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33 "${model}" -> model
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34 "${output1}" -> out
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35
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36 </configfile>
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37 </configfiles>
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38
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39 <outputs>
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40 <data format="tabular" name = "output1" label="classifier prediction" />
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41 </outputs>
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42
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43 <help>
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44 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
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45 </help>
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46 </tool> |
