annotate osra.py @ 3:e44dda38e6ae draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/osra commit 83e947d9a1921939ba3b2c3d7067b8a0e72e2757-dirty
author bgruening
date Tue, 01 Mar 2016 10:41:20 -0500
parents 34ae5f2ae450
children
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1 #!usr/bin/env python
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3 import os, sys
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4 import subprocess
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5
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6 """
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7 OSRA_DATA_FILES is set during the toolshed Installation
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8 If it is not set, use the standard configuration of OSRA.
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9 That means we need to delete argument 4-7.
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10 That script is a hack, because we do not know the content of OSRA_DATA_FILES at xml evaluation time.
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12 osra -f $oformat $infile
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13 -l \$OSRA_DATA_FILES/spelling.txt -a \$OSRA_DATA_FILES/superatom.txt
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14 > $outfile
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15 """
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16
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17 if not os.path.exists(sys.argv[7]):
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18 # OSRA_DATA_FILES path is not set or the spelling file is not existent
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19 sys.argv.pop(7) # superatom.txt path
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20 sys.argv.pop(6) # -a
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21 sys.argv.pop(5) # speling.txt path
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22 sys.argv.pop(4) # -l
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24 sys.argv[0] = 'osra'
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25 subprocess.call(sys.argv, stdout=sys.stdout)
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