root/galaxy-central/tools/genetrack/genetrack_peak_prediction.xml @ 3

<tool id="predict2genetrack" name="Peak predictor">
  
  <description>on GeneTrack index</description>

  <command interpreter="python">
      genetrack_peak_prediction.py -i $input -o $output --level=$level --sigma=$sigma --mode=$mode --exclusion=$exclusion --strand=$strand -v 0 -x
  </command>
    
  <inputs>
    
    <param format="genetrack" name="input" type="data" help="Input data" label="Select input data"/>
 
    <param name="method" type="select" label="Smoothing method" help="The function used to average nearby read values">
      <option value="gauss">Gaussian kernel</option>
      <!-- <option value="yes">Moving averages</option> -->
    </param>
  
    <param name="sigma" size="4" type="integer" value="10" label="Smoothing factor" help="The interval over which each read is averaged" />
        

    <param name="mode" type="select" label="Peak prediction" help="Peak prediction method"> 
      <option value="nolap">Maximal non-overlapping</option>
      <!-- <option value="above">Above a threshold</option> -->
      <option value="all">All peaks</option>
    </param>
  
    <param name="exclusion" type="integer" size="4" value="0" help="The minimal distance between peaks"  label="Peak-to-peak distance">
    </param>

    <param name="level" size="4" type="float" value="1" label="Threshold" help="Return only peaks above this value" />
    
    <param name="strand" type="select" label="Strands" help="Combine strand data or predict on each strand separately">
      <option value="all">Merge strands</option>
      <!-- <option value="yes1">Above a threshold</option> -->
      <option value="two">Separate strands</option>
    </param>

  </inputs>

  <outputs>  
    <data format="bed" name="output" />
  </outputs>
   
<help>
**Help**

This tool will generate genome wide peak prediction from an index file.

**Parameters**

- **Smoothing method** the function used to average nearby values

- **Smoothing value** the factor used in the method

- **Prediction method** the function used to average nearby values

</help>

</tool>