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1 <tool id="evaluation" name="evaluation" version="1.0.0">
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2 <description>evaluate results of classifiers prediction</description>
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3 <command interpreter="Rscript">
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4 evaluation.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"
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10 />
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11
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12 <param name="prediction" type="data"
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13 label="results of prediction"
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14 />
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15
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16 <param name="phenotype" type="data"
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17 label="phenotype file"
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18 />
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19
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20 <param name="r2" type="integer" value="1"
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21 label="compute r-squared distance" help=" whether or not to compute the r-squared distance. 1 means the tool will compute it, any other argument means it will not be computed "
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22 />
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23
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24 <param name="cor" type="integer" value="1"
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25 label="compute correlation" help=" whether or not to compute the correlation between predictions and ture values. 1 means the tool will compute it, any other argument means it will not be computed "
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26 />
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27
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28 <param name="folds" type="data"
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29 label="folds" help=" path to a folds file containing folds indexes in a R list called /folds/ such as produced by the folds tools in OGHMA suite. "
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30 />
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31
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32 </inputs>
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33
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34
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35 <configfiles>
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36 <configfile name="config">
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37 ## Desc: this file is sourced in encode wrapper script
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38 ## as means to pass all galaxy params to R
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39 "${genotype}" -> genotype
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40 "${phenotype}" -> phenotype
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41 "${prediction}" -> prediction
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42 "${r2}" -> doR2
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43 "${cor}" -> doCor
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44 "${folds}" -> folds
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45 </configfile>
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46 </configfiles>
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47
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48 <outputs>
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49 <data format="tabular" name = "output1" label="classifier prediction" />
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50 </outputs>
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51
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52 <help>
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53 evaluate the predictions of classifiers. For now correlation between true valeus and predictions, and r-squared distance are implemeted
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54 </help>
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55 </tool> |
