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comparison README @ 0:51916b7025ba draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
author iuc
date Thu, 14 Nov 2019 06:00:39 -0500
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1 Galaxy wrapper for gprofiler2
2 =========================
3
4 g:Profiler is a widely used toolset for finding biological categories enriched in gene lists, conversions between gene identifiers and mappings to their orthologs. Mission of g:Profiler is to provide a reliable service based on up to date high quality data in a convenient manner across many evidence types, identifier spaces and organisms. g:Profiler relies on Ensembl as a primary data source and follows their quarterly release cycle while updating the other data sources simultaneously. g:Profiler provides modern responsive interactive web interface, standardised API, an R package gprofiler2 and libraries. The results are delivered through interactive and configurable interface. Results can be downloaded as publication ready visualisations or delimited text files. g:Profiler supports close to 500 species and strains, including vertebrates, plants, fungi, insects and parasites. By supporting user uploaded custom GMT files, g:Profiler is capable of analysing data from any organism. All past releases are maintained for reproducibility and transparency. g:Profiler is freely available for all users at https://biit.cs.ut.ee/gprofiler.
5
6 Installation
7 ============
8
9 The recommended installation is by means of the toolshed_.
10
11 .. _toolshed: http://toolshed.g2.bx.psu.edu/
12
13 As HTML content is blocked from display, to render optional Plotly output gProfiler GOSt (gprofiler_gost) should be allowed
14 at Admin > Tool Management > Manage whitelist.
15
16
17 History
18 =======
19
20 * v0.1.6+galaxy10 - add custom background support, fix dependencies, add messages to stdout
21 * v0.1.6+galaxy9 - add notification, fix tests
22 * v0.1.6+galaxy8 - improve formatting
23 * v0.1.6+galaxy7 - add random tool, update gprofiler2 version, major refactoring, add tests
24 * v0.1.6+galaxy6 - fix tools' names
25 * v0.1.6+galaxy5 - remove random tool
26 * v0.1.6+galaxy4 - modify commands and names to lowercase
27 * v0.1.6+galaxy3 - add r-base to requirements, fixes for suite
28 * v0.1.6+galaxy2 - remove r-base from requirements, fixes for Linux
29 * v0.1.6+galaxy1 - add r-base to requirements
30 * v0.1.6+galaxy0 - initial release
31
32
33 Licence (MIT)
34 =============
35
36 Permission is hereby granted, free of charge, to any person obtaining a copy
37 of this software and associated documentation files (the "Software"), to deal
38 in the Software without restriction, including without limitation the rights
39 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
40 copies of the Software, and to permit persons to whom the Software is
41 furnished to do so, subject to the following conditions:
42
43 The above copyright notice and this permission notice shall be included in
44 all copies or substantial portions of the Software.
45
46 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
47 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
48 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
49 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
50 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
51 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
52 THE SOFTWARE.