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author xuebing
date Tue, 13 Mar 2012 19:05:10 -0400
parents 292186c14b08
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13:292186c14b08 14:76e1b1b21cce
1 <tool id="getScore" name="conservation">
2 <description>phastCons or phyloP,vertebrate30way</description>
3 <command interpreter="python">getGenomicScore.py $input $output $score_type $score_path $nbin $strand $outplot $span</command>
4 <inputs>
5 <param name="input" format="interval" type="data" label="Interval file"/>
6 <param name="score_path" type="select" label="Select score" >
7 <option value="/Users/xuebing/galaxy-dist/tool-data/genome/mm8/phastcons" >mm8-phastCons17way</option>
8 <option value="/Users/xuebing/galaxy-dist/tool-data/genome/mm9/phastcon" selected="true">mm9-phastCons30way-vertebrate</option>
9 <option value="/Users/xuebing/galaxy-dist/tool-data/genome/mm9/phyloP30way">mm9-phyloP30way-vertebrate</option>
10 <option value="/Users/xuebing/galaxy-dist/tool-data/genome/hg18/phastCons28wayPlacMam">hg18-phastCons28wayPlacMam</option> </param>
11 <param name="score_type" type="select" label="Select score summary type" >
12 <option value="mean" selected="true">mean</option>
13 <option value="max">maximum</option>
14 <option value="min">minimum</option>
15 <option value="std">standard deviation</option>
16 <option value="coverage">coverage:fraction covered</option>
17 </param>
18 <param name="nbin" type="integer" value="1" label="number of bins"/>
19 <param name="span" size="10" type="float" value="0.1" label="loess span: smoothing parameter" help="value less then 0.1 disables smoothing"/>
20 <param name="strand" type="integer" value="0" label="Specify the strand column" help="leave 0 to ignore strand information. Only matters if using more than 1 bin"/>
21 </inputs>
22 <outputs>
23 <data format="pdf" name="outplot" label="${tool.name} on ${on_string}[plot]"/>
24 <data format="interval" name="output" label="${tool.name} on ${on_string}[data]"/>
25 </outputs>
26 <help>
27
28 .. class:: infomark
29
30 The score for each interval is added as a new column appended at the end of the original file .
31
32 **Example**
33
34 If your original data has the following format:
35
36 +-----+-----+---+------+
37 |chrom|start|end|other2|
38 +-----+-----+---+------+
39
40 and you choose to return the mean of phastCons scores, your output will look like this:
41
42 +-----+-----+---+------+----+
43 |chrom|start|end|other2|mean|
44 +-----+-----+---+------+----+
45
46
47 </help>
48 </tool>