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