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1 <tool id="predict2genetrack" name="Peak predictor">
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2
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3 <description>on GeneTrack index</description>
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4
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5 <command interpreter="python">
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6 genetrack_peak_prediction.py -i $input -o $output --level=$level --sigma=$sigma --mode=$mode --exclusion=$exclusion --strand=$strand -v 0 -x
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7 </command>
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8
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9 <inputs>
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10
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11 <param format="genetrack" name="input" type="data" help="Input data" label="Select input data"/>
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12
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13 <param name="method" type="select" label="Smoothing method" help="The function used to average nearby read values">
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14 <option value="gauss">Gaussian kernel</option>
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15 <!-- <option value="yes">Moving averages</option> -->
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16 </param>
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17
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18 <param name="sigma" size="4" type="integer" value="10" label="Smoothing factor" help="The interval over which each read is averaged" />
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19
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20
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21 <param name="mode" type="select" label="Peak prediction" help="Peak prediction method">
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22 <option value="nolap">Maximal non-overlapping</option>
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23 <!-- <option value="above">Above a threshold</option> -->
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24 <option value="all">All peaks</option>
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25 </param>
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26
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27 <param name="exclusion" type="integer" size="4" value="0" help="The minimal distance between peaks" label="Peak-to-peak distance">
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28 </param>
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29
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30 <param name="level" size="4" type="float" value="1" label="Threshold" help="Return only peaks above this value" />
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31
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32 <param name="strand" type="select" label="Strands" help="Combine strand data or predict on each strand separately">
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33 <option value="all">Merge strands</option>
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34 <!-- <option value="yes1">Above a threshold</option> -->
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35 <option value="two">Separate strands</option>
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36 </param>
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37
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38 </inputs>
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39
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40 <outputs>
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41 <data format="bed" name="output" />
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42 </outputs>
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43
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44 <help>
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45 **Help**
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46
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47 This tool will generate genome wide peak prediction from an index file.
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48
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49 **Parameters**
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50
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51 - **Smoothing method** the function used to average nearby values
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52
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53 - **Smoothing value** the factor used in the method
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54
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55 - **Prediction method** the function used to average nearby values
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56
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57 </help>
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58
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59 </tool>
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