Mercurial > repos > refinery-platform > refinery_test

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planemo upload commit 4fb0a789956149e5a58f4e370d7fe14f4e8bcf79
author refinery-platform
date Thu, 22 Feb 2018 14:14:03 -0500
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1 #!/usr/bin/env python
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3 '''
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4 Test tool for splitting output files from Refinery Test Tools
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5
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6 @author: Scott Ouellette
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7
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8 Input: one text file
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9 Output: N output files based on the amount of input files that
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10 got concatenated from Refinery test tool runs
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11
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12 Requires Python v2.7
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13
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14 '''
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16 import re
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17 import argparse
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20 def main(args):
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21 create_many_files(args.input_file)
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24 def create_many_files(input_file):
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25 # Split file's content when we see data that wasn't added by test tool runs
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26 file_content = re.split("Output.*|Input.*", input_file.read())
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28 sanitized_data = [
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29 data.lstrip("\n") for data in file_content if data.rstrip("\n")]
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31 # Create N ouput files based on the number of inputs run through test tools
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32 for num, file_content in enumerate(sanitized_data):
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33 open("Output file {}.txt".format(num + 1), 'w').write(file_content)
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36 if __name__ == '__main__':
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37 version = "%(prog)s 0.1"
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38 description = "Test tool for running workflows on Galaxy platform from Refinery"
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39 parser = argparse.ArgumentParser(description=description, version=version)
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41 parser.add_argument('-i', '--in-file', dest='input_file',
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42 type=file, metavar='INPUT_FILE', required=True,
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43 help='name of the input file')
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45 # check argument values for errors
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46 try:
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47 args = parser.parse_args()
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48 except IOError as e:
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49 parser.error(e)
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51 main(args)