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1 import sys
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2 import subprocess
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3
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4 """
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5 We only need that file because galaxy do not understand the -t $'\t' term.
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6 Otherwise that would be the right XML-only solution:
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7 sort -u
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8 $ignore_case
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9 $is_numeric
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10 -t \$'\t'
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11 #if $adv_opts.adv_opts_selector=="advanced":
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12 -k$adv_opts.column_start,$adv_opts.column_end
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13 #end if
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14 -o $outfile
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15 $input
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16 """
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17
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18 if sys.argv[1].strip() != 'false':
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19 ignore_case = sys.argv[1]
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20 else:
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21 ignore_case = ''
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22
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23 if sys.argv[2].strip() != 'false':
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24 is_numeric = sys.argv[2]
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25 else:
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26 is_numeric = ''
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27
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28 try:
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29 col_start = sys.argv[3]
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30 col_end = sys.argv[4]
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31 com = "sort -u %s %s -t ' ' -k%s,%s -o %s %s" % (is_numeric, ignore_case, col_start, col_end, sys.argv[5], sys.argv[6])
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32 except:
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33 # no advanced options selected
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34 com = "sort -u %s %s -t ' ' -o %s %s" % (is_numeric, ignore_case, sys.argv[3], sys.argv[4])
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35
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36 subprocess.call(com, shell=True)
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