Mercurial > repos > bgruening > deeptools_bam_compare

annotate readme.rst @ 21:e4287c038599 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 3024062b63fdc502b46e4f328083493c2274182a
author bgruening
date Wed, 22 Aug 2018 17:14:20 -0400
parents 2a1b4e95bdf7
children e821645ef8fc
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
105b9da2445c planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
1 ========================
105b9da2445c planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
2 Galaxy deeptools wrapper
105b9da2445c planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
3 ========================
105b9da2445c planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
4
105b9da2445c planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
5 deepTools are user-friendly tools for the normalization and visualization of
105b9da2445c planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
6 deep-sequencing data.
105b9da2445c planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
7 They address the challenge of visualizing the large amounts of data that are now
105b9da2445c planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
8 routinely generated from sequencing centers in a meaningful way.
105b9da2445c planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
9 To do so, deepTools contain useful routines to process the mapped reads data
105b9da2445c planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
10 through removal of duplicates and different filtering options to create coverage
105b9da2445c planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
11 files in standard bedGraph and bigWig file formats. deepTools allow the creation
105b9da2445c planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
12 of normalized coverage files or the comparison between two files
105b9da2445c planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
13 (for example, treatment and control). Finally, using such normalized and
105b9da2445c planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
14 standardized files, multiple visualizations can be created to identify
105b9da2445c planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
15 enrichments with functional annotations of the genome.
105b9da2445c planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
16 For a gallery of images that can be produced and a description
105b9da2445c planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
17 of the tools see our poster_.
105b9da2445c planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
18
105b9da2445c planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
19 .. _poster: http://f1000.com/posters/browse/summary/1094053
105b9da2445c planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
20
105b9da2445c planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
21 deeptools is developed under here:
105b9da2445c planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
22
17
2a1b4e95bdf7 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents: 0
diff changeset
23 https://github.com/deeptools/deepTools
0
105b9da2445c planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
24
105b9da2445c planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
25 For support, questions, or feature requests contact: deeptools@googlegroups.com
105b9da2445c planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
26
105b9da2445c planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
27
105b9da2445c planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
28 ============
105b9da2445c planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
29 Installation
105b9da2445c planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
30 ============
105b9da2445c planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
31
105b9da2445c planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
32 Requirements: python-2.7
105b9da2445c planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
33
105b9da2445c planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
34 Galaxy should be able to automatically install all other dependencies, such as numpy or scipy.
105b9da2445c planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
35
105b9da2445c planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
36 For the best performance we recommend to install blas/lapack/atlas in your environment before
105b9da2445c planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
37 installing deepTools from the Tool Shed.
105b9da2445c planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
38
105b9da2445c planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
39
105b9da2445c planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
40 ========
105b9da2445c planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
41 Citation
105b9da2445c planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
42 ========
105b9da2445c planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
43
17
2a1b4e95bdf7 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents: 0
diff changeset
44 deeptools are currently under review. In the meantime please refere to https://github.com/deeptools/deepTools.
0
105b9da2445c planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
45
105b9da2445c planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
46
105b9da2445c planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
47 =======
105b9da2445c planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
48 History
105b9da2445c planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
49 =======
105b9da2445c planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
50
105b9da2445c planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
51 * v1.0: Initial public release
105b9da2445c planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
52 * v1.5.8.2: Include new citation tag, update version to 1.5.8.2 and change wrapper version
105b9da2445c planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
53
105b9da2445c planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
54
105b9da2445c planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
55 Licence (MIT)
105b9da2445c planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
56 =============
105b9da2445c planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
57
105b9da2445c planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
58 Permission is hereby granted, free of charge, to any person obtaining a copy
105b9da2445c planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
59 of this software and associated documentation files (the "Software"), to deal
105b9da2445c planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
60 in the Software without restriction, including without limitation the rights
105b9da2445c planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
61 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
105b9da2445c planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
62 copies of the Software, and to permit persons to whom the Software is
105b9da2445c planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
63 furnished to do so, subject to the following conditions:
105b9da2445c planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
64
105b9da2445c planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
65 The above copyright notice and this permission notice shall be included in
105b9da2445c planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
66 all copies or substantial portions of the Software.
105b9da2445c planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
67
105b9da2445c planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
68 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
105b9da2445c planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
69 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
105b9da2445c planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
70 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
105b9da2445c planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
71 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
105b9da2445c planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
72 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
105b9da2445c planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
73 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
105b9da2445c planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff changeset
74 THE SOFTWARE.