Mercurial > repos > proteore > proteore_venn_diagram

annotate README.rst @ 9:adb5522f1faa draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload commit e40c6dfef1c109aa2f059468881e76b923e47f9c-dirty"
author proteore
date Wed, 12 May 2021 16:08:55 +0000
parents 8d61f5ca50a4
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
8d61f5ca50a4 planemo upload commit 9760cde192a15cdf3d2dbec05dd867eaa0392bcd-dirty
proteore
parents:
diff changeset
1 Wrapper for JVenn Diagram Tool
8d61f5ca50a4 planemo upload commit 9760cde192a15cdf3d2dbec05dd867eaa0392bcd-dirty
proteore
parents:
diff changeset
2 ==============================
8d61f5ca50a4 planemo upload commit 9760cde192a15cdf3d2dbec05dd867eaa0392bcd-dirty
proteore
parents:
diff changeset
3
8d61f5ca50a4 planemo upload commit 9760cde192a15cdf3d2dbec05dd867eaa0392bcd-dirty
proteore
parents:
diff changeset
4 **Authors**
8d61f5ca50a4 planemo upload commit 9760cde192a15cdf3d2dbec05dd867eaa0392bcd-dirty
proteore
parents:
diff changeset
5
8d61f5ca50a4 planemo upload commit 9760cde192a15cdf3d2dbec05dd867eaa0392bcd-dirty
proteore
parents:
diff changeset
6 Philippe Bardou, Jérôme Mariette, Frédéric Escudié, Christophe Djemiel and Christophe Klopp. jvenn: an interactive Venn diagram viewer. BMC Bioinformatics 2014, 15:293 doi:10.1186/1471-2105-15-293
8d61f5ca50a4 planemo upload commit 9760cde192a15cdf3d2dbec05dd867eaa0392bcd-dirty
proteore
parents:
diff changeset
7
8d61f5ca50a4 planemo upload commit 9760cde192a15cdf3d2dbec05dd867eaa0392bcd-dirty
proteore
parents:
diff changeset
8 **Galaxy integration**
8d61f5ca50a4 planemo upload commit 9760cde192a15cdf3d2dbec05dd867eaa0392bcd-dirty
proteore
parents:
diff changeset
9
8d61f5ca50a4 planemo upload commit 9760cde192a15cdf3d2dbec05dd867eaa0392bcd-dirty
proteore
parents:
diff changeset
10 T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
8d61f5ca50a4 planemo upload commit 9760cde192a15cdf3d2dbec05dd867eaa0392bcd-dirty
proteore
parents:
diff changeset
11
8d61f5ca50a4 planemo upload commit 9760cde192a15cdf3d2dbec05dd867eaa0392bcd-dirty
proteore
parents:
diff changeset
12 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit,Migale Bioinformatics platform
8d61f5ca50a4 planemo upload commit 9760cde192a15cdf3d2dbec05dd867eaa0392bcd-dirty
proteore
parents:
diff changeset
13
8d61f5ca50a4 planemo upload commit 9760cde192a15cdf3d2dbec05dd867eaa0392bcd-dirty
proteore
parents:
diff changeset
14 Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool.
8d61f5ca50a4 planemo upload commit 9760cde192a15cdf3d2dbec05dd867eaa0392bcd-dirty
proteore
parents:
diff changeset
15
8d61f5ca50a4 planemo upload commit 9760cde192a15cdf3d2dbec05dd867eaa0392bcd-dirty
proteore
parents:
diff changeset
16 ------------------------------
8d61f5ca50a4 planemo upload commit 9760cde192a15cdf3d2dbec05dd867eaa0392bcd-dirty
proteore
parents:
diff changeset
17
8d61f5ca50a4 planemo upload commit 9760cde192a15cdf3d2dbec05dd867eaa0392bcd-dirty
proteore
parents:
diff changeset
18 This tool draw a venn diagram from lists/files using Jvenn plug-in (http://jvenn.toulouse.inra.fr/app/index.html). It also creates output files that contain common or specific elements between query and each compared lists/files.
8d61f5ca50a4 planemo upload commit 9760cde192a15cdf3d2dbec05dd867eaa0392bcd-dirty
proteore
parents:
diff changeset
19
8d61f5ca50a4 planemo upload commit 9760cde192a15cdf3d2dbec05dd867eaa0392bcd-dirty
proteore
parents:
diff changeset
20 **Inputs**
8d61f5ca50a4 planemo upload commit 9760cde192a15cdf3d2dbec05dd867eaa0392bcd-dirty
proteore
parents:
diff changeset
21
8d61f5ca50a4 planemo upload commit 9760cde192a15cdf3d2dbec05dd867eaa0392bcd-dirty
proteore
parents:
diff changeset
22 * **Query file:** A file containing different information of proteins, could be output of previous components.
8d61f5ca50a4 planemo upload commit 9760cde192a15cdf3d2dbec05dd867eaa0392bcd-dirty
proteore
parents:
diff changeset
23
8d61f5ca50a4 planemo upload commit 9760cde192a15cdf3d2dbec05dd867eaa0392bcd-dirty
proteore
parents:
diff changeset
24 * **File of a list of IDs:** .TXT format, each line contains 1 ID
8d61f5ca50a4 planemo upload commit 9760cde192a15cdf3d2dbec05dd867eaa0392bcd-dirty
proteore
parents:
diff changeset
25
8d61f5ca50a4 planemo upload commit 9760cde192a15cdf3d2dbec05dd867eaa0392bcd-dirty
proteore
parents:
diff changeset
26 AMY1A
8d61f5ca50a4 planemo upload commit 9760cde192a15cdf3d2dbec05dd867eaa0392bcd-dirty
proteore
parents:
diff changeset
27
8d61f5ca50a4 planemo upload commit 9760cde192a15cdf3d2dbec05dd867eaa0392bcd-dirty
proteore
parents:
diff changeset
28 ALB
8d61f5ca50a4 planemo upload commit 9760cde192a15cdf3d2dbec05dd867eaa0392bcd-dirty
proteore
parents:
diff changeset
29
8d61f5ca50a4 planemo upload commit 9760cde192a15cdf3d2dbec05dd867eaa0392bcd-dirty
proteore
parents:
diff changeset
30 IGKC
8d61f5ca50a4 planemo upload commit 9760cde192a15cdf3d2dbec05dd867eaa0392bcd-dirty
proteore
parents:
diff changeset
31
8d61f5ca50a4 planemo upload commit 9760cde192a15cdf3d2dbec05dd867eaa0392bcd-dirty
proteore
parents:
diff changeset
32 CSTA
8d61f5ca50a4 planemo upload commit 9760cde192a15cdf3d2dbec05dd867eaa0392bcd-dirty
proteore
parents:
diff changeset
33
8d61f5ca50a4 planemo upload commit 9760cde192a15cdf3d2dbec05dd867eaa0392bcd-dirty
proteore
parents:
diff changeset
34 IGHA1
8d61f5ca50a4 planemo upload commit 9760cde192a15cdf3d2dbec05dd867eaa0392bcd-dirty
proteore
parents:
diff changeset
35
8d61f5ca50a4 planemo upload commit 9760cde192a15cdf3d2dbec05dd867eaa0392bcd-dirty
proteore
parents:
diff changeset
36 ACTG1
8d61f5ca50a4 planemo upload commit 9760cde192a15cdf3d2dbec05dd867eaa0392bcd-dirty
proteore
parents:
diff changeset
37
8d61f5ca50a4 planemo upload commit 9760cde192a15cdf3d2dbec05dd867eaa0392bcd-dirty
proteore
parents:
diff changeset
38 * **List of IDs:** IDs separated by a space
8d61f5ca50a4 planemo upload commit 9760cde192a15cdf3d2dbec05dd867eaa0392bcd-dirty
proteore
parents:
diff changeset
39 AMY1A ALB IGKC CSTA IGHA1 ACTG1
8d61f5ca50a4 planemo upload commit 9760cde192a15cdf3d2dbec05dd867eaa0392bcd-dirty
proteore
parents:
diff changeset
40
8d61f5ca50a4 planemo upload commit 9760cde192a15cdf3d2dbec05dd867eaa0392bcd-dirty
proteore
parents:
diff changeset
41 If you choose a file, it is necessary to specify the column where you would like to perform the comparison.
8d61f5ca50a4 planemo upload commit 9760cde192a15cdf3d2dbec05dd867eaa0392bcd-dirty
proteore
parents:
diff changeset
42
8d61f5ca50a4 planemo upload commit 9760cde192a15cdf3d2dbec05dd867eaa0392bcd-dirty
proteore
parents:
diff changeset
43 **Outputs**
8d61f5ca50a4 planemo upload commit 9760cde192a15cdf3d2dbec05dd867eaa0392bcd-dirty
proteore
parents:
diff changeset
44
8d61f5ca50a4 planemo upload commit 9760cde192a15cdf3d2dbec05dd867eaa0392bcd-dirty
proteore
parents:
diff changeset
45 * **Summary file** (venn_diagram_summary.html):
8d61f5ca50a4 planemo upload commit 9760cde192a15cdf3d2dbec05dd867eaa0392bcd-dirty
proteore
parents:
diff changeset
46 Venn diagram: Could be downloaded as image (PNG, SVG)
8d61f5ca50a4 planemo upload commit 9760cde192a15cdf3d2dbec05dd867eaa0392bcd-dirty
proteore
parents:
diff changeset
47
8d61f5ca50a4 planemo upload commit 9760cde192a15cdf3d2dbec05dd867eaa0392bcd-dirty
proteore
parents:
diff changeset
48 * **Venn text output file**
8d61f5ca50a4 planemo upload commit 9760cde192a15cdf3d2dbec05dd867eaa0392bcd-dirty
proteore
parents:
diff changeset
49 A text file containing common/specific elements among compared lists/files.