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

リビジョン 2, 2.0 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central

行番号 
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
47This 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>
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