Mercurial > repos > matces > carpet_toolsuite

annotate carpet-src-1/tools/CARPET/genecentrico.xml @ 1:78770028dcf1 default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
author matces
date Tue, 07 Jun 2011 16:59:33 -0400
parents cdd489d98766
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
1 <tool id="BECorrelation" name="BEC" version="1.0.0">
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
2 <description>Binding-Expression-Correlation</description>
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
3 <command interpreter="perl">genecentrico.pl $expr $chip_gff ${prom_choice.prom_start} ${prom_choice.type} $result $output ${prom_choice.prom_end}</command>
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
4 <inputs>
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
5 <param format="tabular" name="expr" type="data" label="expression file"/>
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
6 <param format="bed" name="chip_gff" type="data" label="ChIP on chip GFF results"/>
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
7 <conditional name="prom_choice">
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
8 <param name="type" type="select" label="Analysis type">
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
9 <option value="promoter">only promoter</option>
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
10 <option value="all">all gene</option>
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
11 </param>
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
12 <when value="promoter">
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
13 <param name="prom_start" type="integer" size="10" value="-2000" label="Promoter start"/>
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
14 <param name="prom_end" type="integer" size="10" value="1000" label="Promoter end"/>
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
15 </when>
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
16 <when value="all">
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
17 <param name="prom_start" type="integer" size="10" value="-2000" label="Promoter start"/>
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
18 <param name="prom_end" type="text" size="12" value="NOT-NEEDED" label="Promoter end"/>
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
19 </when>
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
20 </conditional>
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
21 <param name="result" type="select" label="result output">
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
22 <option value="number"># of matches</option>
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
23 <option value="max_value">max value</option>
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
24 </param>
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
25 </inputs>
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
26 <outputs>
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
27 <data format="tabular" name="output" />
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
28 </outputs>
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
29 <help>
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
30 .. class:: infomark
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
31
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
32 **What it does**
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
33
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
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.
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
35
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
36 PLEASE, for more detailed information refer to the CARPET user Manual:
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
37 click to download_ it.
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
38
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
39 .. _download: /static/example_file/CARPET_userManual.zip
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
40
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
41 -----
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
42
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
43 **Parameters:**
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
44
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
45 - **Analysis type:**
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
46 - **promoter:** only the peaks matching in the promoter region (defined by user) are associated with the transcript
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
47 - **all gene:** peaks matching in the promoter and within the gene body are associated with the transcript
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
48 - **result output:**
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
49 - **# of matches:** the number of matching peaks are reported
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
50 - **max value:** the highest score among all matching peaks is reported
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
51
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
52 --------
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
53
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
54 .. class:: warningmark
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
55
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
56 If a peak matches with more than one transcript, it is associated with both.
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
57
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
58 -----
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
59
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
60 **INPUT FILES**
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
61
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
62 - Expression file: file created by TEA
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
63 - ChIP on chip GFF results: file create by PeakPicker (or any GFF file)
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
64
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
65 **OUTPUT FILES**
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
66
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
67 .. image:: static/images/CARPET/bec_output.png
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
68
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
69 .. class:: infomark
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
70
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
71 This results table can be used again as input expression file, to add another ChIP-chip experiment.
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
72
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
73 </help>
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
74
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
75 </tool>