Mercurial > repos > matces > carpet_toolsuite

comparison carpet-src-1/tools/CARPET/genecentrico.xml @ 0:cdd489d98766

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
author matces
date Tue, 07 Jun 2011 16:50:41 -0400
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:cdd489d98766
1 <tool id="BECorrelation" name="BEC" version="1.0.0">
2 <description>Binding-Expression-Correlation</description>
3 <command interpreter="perl">genecentrico.pl $expr $chip_gff ${prom_choice.prom_start} ${prom_choice.type} $result $output ${prom_choice.prom_end}</command>
4 <inputs>
5 <param format="tabular" name="expr" type="data" label="expression file"/>
6 <param format="bed" name="chip_gff" type="data" label="ChIP on chip GFF results"/>
7 <conditional name="prom_choice">
8 <param name="type" type="select" label="Analysis type">
9 <option value="promoter">only promoter</option>
10 <option value="all">all gene</option>
11 </param>
12 <when value="promoter">
13 <param name="prom_start" type="integer" size="10" value="-2000" label="Promoter start"/>
14 <param name="prom_end" type="integer" size="10" value="1000" label="Promoter end"/>
15 </when>
16 <when value="all">
17 <param name="prom_start" type="integer" size="10" value="-2000" label="Promoter start"/>
18 <param name="prom_end" type="text" size="12" value="NOT-NEEDED" label="Promoter end"/>
19 </when>
20 </conditional>
21 <param name="result" type="select" label="result output">
22 <option value="number"># of matches</option>
23 <option value="max_value">max value</option>
24 </param>
25 </inputs>
26 <outputs>
27 <data format="tabular" name="output" />
28 </outputs>
29 <help>
30 .. class:: infomark
31
32 **What it does**
33
34 BEC integrates the results of expression analysis and ChIP-chip analysis. For each transcript the number of peaks matching in the promoter and/or within the gene body is calculated.
35
36 PLEASE, for more detailed information refer to the CARPET user Manual:
37 click to download_ it.
38
39 .. _download: /static/example_file/CARPET_userManual.zip
40
41 -----
42
43 **Parameters:**
44
45 - **Analysis type:**
46 - **promoter:** only the peaks matching in the promoter region (defined by user) are associated with the transcript
47 - **all gene:** peaks matching in the promoter and within the gene body are associated with the transcript
48 - **result output:**
49 - **# of matches:** the number of matching peaks are reported
50 - **max value:** the highest score among all matching peaks is reported
51
52 --------
53
54 .. class:: warningmark
55
56 If a peak matches with more than one transcript, it is associated with both.
57
58 -----
59
60 **INPUT FILES**
61
62 - Expression file: file created by TEA
63 - ChIP on chip GFF results: file create by PeakPicker (or any GFF file)
64
65 **OUTPUT FILES**
66
67 .. image:: static/images/CARPET/bec_output.png
68
69 .. class:: infomark
70
71 This results table can be used again as input expression file, to add another ChIP-chip experiment.
72
73 </help>
74
75 </tool>