Mercurial > repos > xuebing > sharplabtool
comparison tools/genetrack/genetrack_peak_prediction.xml @ 0:9071e359b9a3
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| author | xuebing |
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| date | Fri, 09 Mar 2012 19:37:19 -0500 |
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| -1:000000000000 | 0:9071e359b9a3 |
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| 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> |