Mercurial > repos > bgruening > osra
view osra.py @ 3:e44dda38e6ae draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/osra commit 83e947d9a1921939ba3b2c3d7067b8a0e72e2757-dirty
author | bgruening |
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date | Tue, 01 Mar 2016 10:41:20 -0500 |
parents | 34ae5f2ae450 |
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#!usr/bin/env python import os, sys import subprocess """ OSRA_DATA_FILES is set during the toolshed Installation If it is not set, use the standard configuration of OSRA. That means we need to delete argument 4-7. That script is a hack, because we do not know the content of OSRA_DATA_FILES at xml evaluation time. osra -f $oformat $infile -l \$OSRA_DATA_FILES/spelling.txt -a \$OSRA_DATA_FILES/superatom.txt > $outfile """ if not os.path.exists(sys.argv[7]): # OSRA_DATA_FILES path is not set or the spelling file is not existent sys.argv.pop(7) # superatom.txt path sys.argv.pop(6) # -a sys.argv.pop(5) # speling.txt path sys.argv.pop(4) # -l sys.argv[0] = 'osra' subprocess.call(sys.argv, stdout=sys.stdout)