Mercurial > repos > r-lannes > cut_include_exclude

comparison README_cut_fr.txt @ 2:d28ee835a561 draft default tip

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author r-lannes
date Wed, 16 Dec 2015 08:46:37 -0500
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1:59bd6cbbeb92 2:d28ee835a561
1 ########################################
2
3 ##### french cut
4
5 ########################################
6 ##---------- Licence
7 #### FreeSoftware on GNU licence
8 ''' <cut_fr.py & cut_fr.xml are scripts allwing more convenient use of cut in galaxy environment>
9 Copyright (C) <2015> <Lannes Romain>
10
11 This program is free software: you can redistribute it and/or modify
12 it under the terms of the GNU General Public License as published by
13 the Free Software Foundation, either version 3 of the License, or
14 (at your option) any later version.
15
16 This program is distributed in the hope that it will be useful,
17 but WITHOUT ANY WARRANTY; without even the implied warranty of
18 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
19 GNU General Public License for more details.
20
21 You should have received a copy of the GNU General Public License
22 along with this program. If not, see <http://www.gnu.org/licenses/>.'''
23
24 ##########################################
25 #------- program needed
26
27 need python 3
28 and python 3 library:
29 import os
30 import argparse
31 import sys
32
33 ###########################################
34 ########------------ Install
35
36 copy cut_fr.xml and cut_fr.py in galaxy/tools/a_directory_of_your_choice/
37 not directly on tools
38
39 add in
40 config/tool_conf.xml
41
42 <tool file="a_directory_of_your_choice/cut_fr.xml" />
43
44 in the section of your choice
45
46 ############################################
47
48 input =
49 -tsv
50 -String ( "c1,c2,c3")
51 -type_cut default = Exclude
52 -extend_print default = False
53
54 output =
55 input.tsv less column 1,2,3
56
57
58 input =
59 -tsv
60 -String ( "c1,c2,c3")
61 -type_cut default = ExInclude
62 -extend_print default = False
63
64 output =
65 only column 1,2,3
66
67
68 -extend_print default = False an option allowing the sdtout to be more consistant.
69