annotate phastCons.xml @ 20:16ba480adf96

Uploaded
author xuebing
date Sat, 31 Mar 2012 08:31:22 -0400
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
20
16ba480adf96 Uploaded
xuebing
parents:
diff changeset
1 <tool id="getScore" name="conservation">
16ba480adf96 Uploaded
xuebing
parents:
diff changeset
2 <description>phastCons or phyloP,vertebrate30way</description>
16ba480adf96 Uploaded
xuebing
parents:
diff changeset
3 <command interpreter="python">getGenomicScore.py $input $output $score_type $score_path $nbin $strand $outplot $span</command>
16ba480adf96 Uploaded
xuebing
parents:
diff changeset
4 <inputs>
16ba480adf96 Uploaded
xuebing
parents:
diff changeset
5 <param name="input" format="interval" type="data" label="Interval file"/>
16ba480adf96 Uploaded
xuebing
parents:
diff changeset
6 <param name="score_path" type="select" label="Select score" >
16ba480adf96 Uploaded
xuebing
parents:
diff changeset
7 <option value="/Users/xuebing/galaxy-dist/tool-data/genome/mm8/phastcons" >mm8-phastCons17way</option>
16ba480adf96 Uploaded
xuebing
parents:
diff changeset
8 <option value="/Users/xuebing/galaxy-dist/tool-data/genome/mm9/phastcon" selected="true">mm9-phastCons30way-vertebrate</option>
16ba480adf96 Uploaded
xuebing
parents:
diff changeset
9 <option value="/Users/xuebing/galaxy-dist/tool-data/genome/mm9/phyloP30way">mm9-phyloP30way-vertebrate</option>
16ba480adf96 Uploaded
xuebing
parents:
diff changeset
10 <option value="/Users/xuebing/galaxy-dist/tool-data/genome/hg18/phastCons28wayPlacMam">hg18-phastCons28wayPlacMam</option> </param>
16ba480adf96 Uploaded
xuebing
parents:
diff changeset
11 <param name="score_type" type="select" label="Select score summary type" >
16ba480adf96 Uploaded
xuebing
parents:
diff changeset
12 <option value="mean" selected="true">mean</option>
16ba480adf96 Uploaded
xuebing
parents:
diff changeset
13 <option value="max">maximum</option>
16ba480adf96 Uploaded
xuebing
parents:
diff changeset
14 <option value="min">minimum</option>
16ba480adf96 Uploaded
xuebing
parents:
diff changeset
15 <option value="std">standard deviation</option>
16ba480adf96 Uploaded
xuebing
parents:
diff changeset
16 <option value="coverage">coverage:fraction covered</option>
16ba480adf96 Uploaded
xuebing
parents:
diff changeset
17 </param>
16ba480adf96 Uploaded
xuebing
parents:
diff changeset
18 <param name="nbin" type="integer" value="1" label="number of bins"/>
16ba480adf96 Uploaded
xuebing
parents:
diff changeset
19 <param name="span" size="10" type="float" value="0.1" label="loess span: smoothing parameter" help="value less then 0.1 disables smoothing"/>
16ba480adf96 Uploaded
xuebing
parents:
diff changeset
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"/>
16ba480adf96 Uploaded
xuebing
parents:
diff changeset
21 </inputs>
16ba480adf96 Uploaded
xuebing
parents:
diff changeset
22 <outputs>
16ba480adf96 Uploaded
xuebing
parents:
diff changeset
23 <data format="pdf" name="outplot" label="${tool.name} on ${on_string}[plot]"/>
16ba480adf96 Uploaded
xuebing
parents:
diff changeset
24 <data format="interval" name="output" label="${tool.name} on ${on_string}[data]"/>
16ba480adf96 Uploaded
xuebing
parents:
diff changeset
25 </outputs>
16ba480adf96 Uploaded
xuebing
parents:
diff changeset
26 <help>
16ba480adf96 Uploaded
xuebing
parents:
diff changeset
27
16ba480adf96 Uploaded
xuebing
parents:
diff changeset
28 .. class:: infomark
16ba480adf96 Uploaded
xuebing
parents:
diff changeset
29
16ba480adf96 Uploaded
xuebing
parents:
diff changeset
30 The score for each interval is added as a new column appended at the end of the original file .
16ba480adf96 Uploaded
xuebing
parents:
diff changeset
31
16ba480adf96 Uploaded
xuebing
parents:
diff changeset
32 **Example**
16ba480adf96 Uploaded
xuebing
parents:
diff changeset
33
16ba480adf96 Uploaded
xuebing
parents:
diff changeset
34 If your original data has the following format:
16ba480adf96 Uploaded
xuebing
parents:
diff changeset
35
16ba480adf96 Uploaded
xuebing
parents:
diff changeset
36 +-----+-----+---+------+
16ba480adf96 Uploaded
xuebing
parents:
diff changeset
37 |chrom|start|end|other2|
16ba480adf96 Uploaded
xuebing
parents:
diff changeset
38 +-----+-----+---+------+
16ba480adf96 Uploaded
xuebing
parents:
diff changeset
39
16ba480adf96 Uploaded
xuebing
parents:
diff changeset
40 and you choose to return the mean of phastCons scores, your output will look like this:
16ba480adf96 Uploaded
xuebing
parents:
diff changeset
41
16ba480adf96 Uploaded
xuebing
parents:
diff changeset
42 +-----+-----+---+------+----+
16ba480adf96 Uploaded
xuebing
parents:
diff changeset
43 |chrom|start|end|other2|mean|
16ba480adf96 Uploaded
xuebing
parents:
diff changeset
44 +-----+-----+---+------+----+
16ba480adf96 Uploaded
xuebing
parents:
diff changeset
45
16ba480adf96 Uploaded
xuebing
parents:
diff changeset
46
16ba480adf96 Uploaded
xuebing
parents:
diff changeset
47 </help>
16ba480adf96 Uploaded
xuebing
parents:
diff changeset
48 </tool>