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