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annotate create_mqpar.py @ 9:37d669de2828 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 5e4f8567c0145de8c6f9344fe4ee4c3bf2a81e59"
author galaxyp
date Fri, 19 Feb 2021 21:24:41 +0000
parents dcd39bcc7481
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dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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1 """Create paramter xml file for a specific MaxQuant version from yaml or command line input
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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2 and a template parameter file.
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3 """
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5 import argparse
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6 import os
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37d669de2828 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 5e4f8567c0145de8c6f9344fe4ee4c3bf2a81e59"
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8 import yaml
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9 from mqparam import MQParam
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11 parser = argparse.ArgumentParser()
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13 parser.add_argument('--yaml', '-y', help="""Yaml config file. Only those parameters differing
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14 from the template need to be specified.""")
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16 parser.add_argument('--exp_design', '-e', help="Experimental design template as it is created by the MaxQuant GUI.")
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18 parser.add_argument('template', help="Template Parameter File.")
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20 parser.add_argument('--mqpar_out', '-o', help="Output file, will be ./mqpar.xml if omitted.")
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22 parser.add_argument('--substitution_rx', '-s', help="""Regular expression for filename substitution.
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23 Necessary for usage in the Galaxy tool. Can usually be ignored.""")
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25 parser.add_argument('--version', '-v', help="""A version number. Raises exception if it doesn't
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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26 match the MaxQuant version of the template. For usage in the Galaxy tool.""")
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28 # in case numThreads is a environment variable, otherwise it can be specified in the yaml file as well
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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29 parser.add_argument('--num_threads', '-t', help="Number of threads to specify in mqpar.")
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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30 args = parser.parse_args()
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32 # edit file names, working dir is unknown at the time of galaxy tool configfile creation
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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33 if args.yaml:
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34 with open(args.yaml) as f:
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35 conf_dict = yaml.safe_load(f.read())
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37 for n, pg in enumerate(conf_dict['paramGroups']):
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38 for num, fl in enumerate(pg['files']):
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39 if not fl.startswith('/'):
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40 conf_dict['paramGroups'][n]['files'][num] = os.path.join(os.getcwd(), fl)
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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41 with open('yaml', 'w') as f:
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42 yaml.safe_dump(conf_dict, stream=f)
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43 args.yaml = 'yaml'
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45 kwargs = dict(yaml=args.yaml)
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46 if args.substitution_rx:
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47 kwargs['substitution_rx'] = args.substitution_rx
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48 mqparam = MQParam(args.template, args.exp_design, **kwargs)
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49 if args.version and mqparam.version != args.version:
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50 raise Exception('mqpar version is ' + mqparam.version + '. Tool uses version {}.'.format(args.version))
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51 mqparam.set_simple_param('numThreads', args.num_threads)
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53 mqparam.write(args.mqpar_out if args.mqpar_out else 'mqpar.xml')