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1 #!/usr/bin/env python
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2
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3 """
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4 Wraps genetrack.scripts.peakpred so the tool can be executed from Galaxy.
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5
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6 usage: %prog input output level sigma mode exclusion strand
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7 """
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8
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9 import sys
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10 from galaxy import eggs
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11 import pkg_resources
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12 pkg_resources.require( "GeneTrack" )
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13
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14 from genetrack.scripts import peakpred
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15 from genetrack import logger
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16
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17 if __name__ == "__main__":
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18
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19 parser = peakpred.option_parser()
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20
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21 options, args = parser.parse_args()
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22
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23 logger.disable(options.verbosity)
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24
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25 from genetrack import conf
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26
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27 # trigger test mode
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28 if options.test:
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29 options.inpname = conf.testdata('test-hdflib-input.gtrack')
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30 options.outname = conf.testdata('predictions.bed')
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31
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32 # missing input file name
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33 if not options.inpname and not options.outname:
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34 parser.print_help()
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35 else:
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36 print 'Sigma = %s' % options.sigma
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37 print 'Minimum peak = %s' % options.level
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38 print 'Peak-to-peak = %s' % options.exclude
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39
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40 peakpred.predict(options.inpname, options.outname, options)
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