Mercurial > repos > yhoogstrate > featurecounts

annotate README.rst @ 3:e04fbcc4e91a draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit 597fa3df643b54ea93a17448c722f657e3d68b60
author yhoogstrate
date Wed, 07 Oct 2015 11:38:41 -0400
parents b5c93611d2c5
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
ab0323782bb5 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/featurecounts commit cc900436bad9c6cca1f73d438c1f158d3bfc4318-dirty
yhoogstrate
parents:
diff changeset
1 FeatureCounts wrapper for Galaxy
ab0323782bb5 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/featurecounts commit cc900436bad9c6cca1f73d438c1f158d3bfc4318-dirty
yhoogstrate
parents:
diff changeset
2 ================================
ab0323782bb5 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/featurecounts commit cc900436bad9c6cca1f73d438c1f158d3bfc4318-dirty
yhoogstrate
parents:
diff changeset
3
2
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
4 * http://bioinf.wehi.edu.au/featureCounts/
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
5 * http://subread.sourceforge.net/
0
ab0323782bb5 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/featurecounts commit cc900436bad9c6cca1f73d438c1f158d3bfc4318-dirty
yhoogstrate
parents:
diff changeset
6
ab0323782bb5 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/featurecounts commit cc900436bad9c6cca1f73d438c1f158d3bfc4318-dirty
yhoogstrate
parents:
diff changeset
7 FeatureCounts as part of the SUBREAD package is "a highly efficient and
ab0323782bb5 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/featurecounts commit cc900436bad9c6cca1f73d438c1f158d3bfc4318-dirty
yhoogstrate
parents:
diff changeset
8 accurate read summarization program".
ab0323782bb5 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/featurecounts commit cc900436bad9c6cca1f73d438c1f158d3bfc4318-dirty
yhoogstrate
parents:
diff changeset
9
ab0323782bb5 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/featurecounts commit cc900436bad9c6cca1f73d438c1f158d3bfc4318-dirty
yhoogstrate
parents:
diff changeset
10 Development
ab0323782bb5 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/featurecounts commit cc900436bad9c6cca1f73d438c1f158d3bfc4318-dirty
yhoogstrate
parents:
diff changeset
11 -----------
ab0323782bb5 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/featurecounts commit cc900436bad9c6cca1f73d438c1f158d3bfc4318-dirty
yhoogstrate
parents:
diff changeset
12
ab0323782bb5 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/featurecounts commit cc900436bad9c6cca1f73d438c1f158d3bfc4318-dirty
yhoogstrate
parents:
diff changeset
13 * Repository-Maintainer: Youri Hoogstrate
ab0323782bb5 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/featurecounts commit cc900436bad9c6cca1f73d438c1f158d3bfc4318-dirty
yhoogstrate
parents:
diff changeset
14 * Repository-Developers: Youri Hoogstrate, Marius van den Beek
ab0323782bb5 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/featurecounts commit cc900436bad9c6cca1f73d438c1f158d3bfc4318-dirty
yhoogstrate
parents:
diff changeset
15
2
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
16 * Repository-Development: https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper
0
ab0323782bb5 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/featurecounts commit cc900436bad9c6cca1f73d438c1f158d3bfc4318-dirty
yhoogstrate
parents:
diff changeset
17
ab0323782bb5 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/featurecounts commit cc900436bad9c6cca1f73d438c1f158d3bfc4318-dirty
yhoogstrate
parents:
diff changeset
18 The tool wrapper has been written by Youri Hoogstrate from the Erasmus
ab0323782bb5 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/featurecounts commit cc900436bad9c6cca1f73d438c1f158d3bfc4318-dirty
yhoogstrate
parents:
diff changeset
19 Medical Center (Rotterdam, Netherlands) on behalf of the Translational
ab0323782bb5 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/featurecounts commit cc900436bad9c6cca1f73d438c1f158d3bfc4318-dirty
yhoogstrate
parents:
diff changeset
20 Research IT (TraIT) project:
ab0323782bb5 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/featurecounts commit cc900436bad9c6cca1f73d438c1f158d3bfc4318-dirty
yhoogstrate
parents:
diff changeset
21
ab0323782bb5 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/featurecounts commit cc900436bad9c6cca1f73d438c1f158d3bfc4318-dirty
yhoogstrate
parents:
diff changeset
22 http://www.ctmm.nl/en/programmas/infrastructuren/traitprojecttranslationeleresearch
ab0323782bb5 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/featurecounts commit cc900436bad9c6cca1f73d438c1f158d3bfc4318-dirty
yhoogstrate
parents:
diff changeset
23
ab0323782bb5 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/featurecounts commit cc900436bad9c6cca1f73d438c1f158d3bfc4318-dirty
yhoogstrate
parents:
diff changeset
24 License
ab0323782bb5 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/featurecounts commit cc900436bad9c6cca1f73d438c1f158d3bfc4318-dirty
yhoogstrate
parents:
diff changeset
25 -------
ab0323782bb5 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/featurecounts commit cc900436bad9c6cca1f73d438c1f158d3bfc4318-dirty
yhoogstrate
parents:
diff changeset
26
ab0323782bb5 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/featurecounts commit cc900436bad9c6cca1f73d438c1f158d3bfc4318-dirty
yhoogstrate
parents:
diff changeset
27 **featureCounts**:
ab0323782bb5 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/featurecounts commit cc900436bad9c6cca1f73d438c1f158d3bfc4318-dirty
yhoogstrate
parents:
diff changeset
28
ab0323782bb5 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/featurecounts commit cc900436bad9c6cca1f73d438c1f158d3bfc4318-dirty
yhoogstrate
parents:
diff changeset
29 GPL (>=3)
ab0323782bb5 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/featurecounts commit cc900436bad9c6cca1f73d438c1f158d3bfc4318-dirty
yhoogstrate
parents:
diff changeset
30
ab0323782bb5 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/featurecounts commit cc900436bad9c6cca1f73d438c1f158d3bfc4318-dirty
yhoogstrate
parents:
diff changeset
31 **featurecounts2bed**:
ab0323782bb5 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/featurecounts commit cc900436bad9c6cca1f73d438c1f158d3bfc4318-dirty
yhoogstrate
parents:
diff changeset
32
ab0323782bb5 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/featurecounts commit cc900436bad9c6cca1f73d438c1f158d3bfc4318-dirty
yhoogstrate
parents:
diff changeset
33 GPL (>=3)
ab0323782bb5 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/featurecounts commit cc900436bad9c6cca1f73d438c1f158d3bfc4318-dirty
yhoogstrate
parents:
diff changeset
34
ab0323782bb5 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/featurecounts commit cc900436bad9c6cca1f73d438c1f158d3bfc4318-dirty
yhoogstrate
parents:
diff changeset
35 **This wrapper**:
ab0323782bb5 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/featurecounts commit cc900436bad9c6cca1f73d438c1f158d3bfc4318-dirty
yhoogstrate
parents:
diff changeset
36
2
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
37 ``Copyright (C) 2013-2015 Youri Hoogstrate``
0
ab0323782bb5 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/featurecounts commit cc900436bad9c6cca1f73d438c1f158d3bfc4318-dirty
yhoogstrate
parents:
diff changeset
38
2
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
39 ``This program is free software: you can redistribute it and/or modify
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
40 it under the terms of the GNU General Public License as published by
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
41 the Free Software Foundation, either version 3 of the License, or
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
42 (at your option) any later version.``
0
ab0323782bb5 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/featurecounts commit cc900436bad9c6cca1f73d438c1f158d3bfc4318-dirty
yhoogstrate
parents:
diff changeset
43
2
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
44 ``This program is distributed in the hope that it will be useful,
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
45 but WITHOUT ANY WARRANTY; without even the implied warranty of
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
46 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
47 GNU General Public License for more details.``
0
ab0323782bb5 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/featurecounts commit cc900436bad9c6cca1f73d438c1f158d3bfc4318-dirty
yhoogstrate
parents:
diff changeset
48
2
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
49 ``You should have received a copy of the GNU General Public License
b5c93611d2c5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit b05640a41e2106782ac7f88f858b0a256918fa6f
yhoogstrate
parents: 1
diff changeset
50 along with this program. If not, see <http://www.gnu.org/licenses/>.``
0
ab0323782bb5 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/featurecounts commit cc900436bad9c6cca1f73d438c1f158d3bfc4318-dirty
yhoogstrate
parents:
diff changeset
51
ab0323782bb5 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/featurecounts commit cc900436bad9c6cca1f73d438c1f158d3bfc4318-dirty
yhoogstrate
parents:
diff changeset
52 Acknowledgements
ab0323782bb5 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/featurecounts commit cc900436bad9c6cca1f73d438c1f158d3bfc4318-dirty
yhoogstrate
parents:
diff changeset
53 ----------------
ab0323782bb5 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/featurecounts commit cc900436bad9c6cca1f73d438c1f158d3bfc4318-dirty
yhoogstrate
parents:
diff changeset
54
3
e04fbcc4e91a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit 597fa3df643b54ea93a17448c722f657e3d68b60
yhoogstrate
parents: 2
diff changeset
55 I would like to thank Marius van den Beek and Björn Grüning for their contributions to this project.