|
0
|
1 motif_tools
|
|
|
2 ===========
|
|
|
3
|
|
|
4 Galaxy tools for various motif-finding utilities developed by Ian Donaldson.
|
|
|
5
|
|
|
6 There are five tools available:
|
|
|
7
|
|
|
8 * **IUPAC scan and output each match** Returns all matches to a given IUPAC in
|
|
|
9 GFF format
|
|
|
10
|
|
|
11 * **IUPAC scan and output matches per seq** Counts the matches to a given IUPAC
|
|
|
12
|
|
|
13 * **Count unique seq in GFF** Gives the non-redundant count of sequences
|
|
|
14
|
|
|
15 * **TFBScluster two TFBS** Identifies clusters of two TFBS
|
|
|
16
|
|
|
17 * **TFBScluster three TFBS** Identifies clusters of three TFBS
|
|
|
18
|
|
|
19 Automated installation
|
|
|
20 ======================
|
|
|
21
|
|
|
22 Installation via the Galaxy Tool Shed will take of installing the tools
|
|
|
23 and the underlying dependencies.
|
|
|
24
|
|
|
25 Manual Installation
|
|
|
26 ===================
|
|
|
27
|
|
|
28 To add these to Galaxy put the following lines in tool_conf.xml for each:
|
|
1
|
29 tool that you want::
|
|
0
|
30
|
|
|
31 <tool file="motif_tools/Scan_IUPAC_output_each_match.xml" />
|
|
|
32 <tool file="motif_tools/Scan_IUPAC_output_matches_per_seq.xml" />
|
|
|
33 <tool file="motif_tools/CountUniqueIDs.xml" />
|
|
|
34 <tool file="motif_tools/TFBScluster_candidates_2TFBS.xml" />
|
|
|
35 <tool file="motif_tools/TFBScluster_candidates_3TFBS.xml" />
|
|
|
36
|
|
|
37 The tools also require Perl and ``Bioperl`` to be installed.
|
|
|
38
|
|
|
39 History
|
|
|
40 =======
|
|
|
41
|
|
2
|
42 ========== ======================================================================
|
|
0
|
43 Version Changes
|
|
1
|
44 ---------- ----------------------------------------------------------------------
|
|
4
|
45 - 1.0.2 Update bioperl dependency to 1.7.2
|
|
0
|
46 - 1.0.1 Updates to use conda dependency resolution and tidy up XML
|
|
|
47 - 1.0.0 Initial version
|
|
2
|
48 ========== ======================================================================
|
|
0
|
49
|
|
|
50 Developers
|
|
|
51 ==========
|
|
|
52
|
|
|
53 This tool is developed on the following GitHub repository:
|
|
|
54 https://github.com/fls-bioinformatics-core/galaxy-tools/tree/master/tools/macs21
|
|
|
55
|
|
|
56
|
|
|
57 Licence (MIT)
|
|
|
58 =============
|
|
|
59
|
|
|
60 Permission is hereby granted, free of charge, to any person obtaining a copy
|
|
|
61 of this software and associated documentation files (the "Software"), to deal
|
|
|
62 in the Software without restriction, including without limitation the rights
|
|
|
63 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
|
|
|
64 copies of the Software, and to permit persons to whom the Software is
|
|
|
65 furnished to do so, subject to the following conditions:
|
|
|
66
|
|
|
67 The above copyright notice and this permission notice shall be included in
|
|
|
68 all copies or substantial portions of the Software.
|
|
|
69
|
|
|
70 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
|
|
|
71 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
|
|
|
72 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
|
|
|
73 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
|
|
|
74 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
|
|
|
75 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
|
|
|
76 THE SOFTWARE.
|
