|
0
|
1 Galaxy wrapper for sed
|
|
|
2 ======================
|
|
|
3
|
|
|
4 This wrapper is copyright 2012 by Björn Grüning.
|
|
|
5
|
|
|
6 This is a wrapper for the sed command line tool.
|
|
|
7
|
|
|
8 sed is a stream editor included in every unix-derived operating system.
|
|
|
9 That wrapper only uses a small subset of the sed functionality. Its only a wrapper for:
|
|
|
10
|
|
|
11 sed -r '$pattern' $input
|
|
|
12
|
|
|
13
|
|
|
14 WARNING:
|
|
|
15 ========
|
|
|
16
|
|
|
17 No syntax check and sanitising will happen in that wrapper. This wrapper may harm your computer ;)
|
|
|
18 Nevertheless, i think it can be useable for some installations.
|
|
|
19
|
|
|
20
|
|
|
21 Installation
|
|
|
22 ============
|
|
|
23
|
|
|
24 sed should be available on every unix derived operating system and belongs to the classical unix programms.
|
|
|
25 No further installation is requiered.
|
|
|
26
|
|
|
27 For more information have a look at the following pages:
|
|
|
28
|
|
|
29 http://en.wikipedia.org/wiki/Sed
|
|
|
30 http://www.gnu.org/software/sed/manual/sed.html
|
|
|
31
|
|
|
32 To install the wrapper copy the sed folder in the galaxy tools
|
|
|
33 folder and modify the tools_conf.xml file to make the tool available to Galaxy.
|
|
|
34 For example:
|
|
|
35
|
|
|
36 <toolbox>
|
|
|
37 <tool file="text_manipulation/sed.xml" />
|
|
|
38 </toolbox>
|
|
|
39
|
|
|
40
|
|
|
41 History
|
|
|
42 =======
|
|
|
43
|
|
|
44 v0.1 - Initial public release
|
|
|
45
|
|
|
46
|
|
|
47 Wrapper Licence (MIT/BSD style)
|
|
|
48 ===============================
|
|
|
49
|
|
|
50 Permission to use, copy, modify, and distribute this software and its
|
|
|
51 documentation with or without modifications and for any purpose and
|
|
|
52 without fee is hereby granted, provided that any copyright notices
|
|
|
53 appear in all copies and that both those copyright notices and this
|
|
|
54 permission notice appear in supporting documentation, and that the
|
|
|
55 names of the contributors or copyright holders not be used in
|
|
|
56 advertising or publicity pertaining to distribution of the software
|
|
|
57 without specific prior permission.
|
|
|
58
|
|
|
59 THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL
|
|
|
60 WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED
|
|
|
61 WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE
|
|
|
62 CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT
|
|
|
63 OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
|
|
|
64 OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE
|
|
|
65 OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE
|
|
|
66 OR PERFORMANCE OF THIS SOFTWARE.
|
|
|
67
|
