diff create_mqpar.py @ 4:dcd39bcc7481 draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/create_mqpar.py	Sat Apr 11 11:49:19 2020 -0400
@@ -0,0 +1,53 @@
+"""Create paramter xml file for a specific MaxQuant version from yaml or command line input
+and a template parameter file.
+"""
+
+import argparse
+import os
+import yaml
+
+from mqparam import MQParam
+
+parser = argparse.ArgumentParser()
+
+parser.add_argument('--yaml', '-y', help="""Yaml config file. Only those parameters differing
+from the template need to be specified.""")
+
+parser.add_argument('--exp_design', '-e', help="Experimental design template as it is created by the MaxQuant GUI.")
+
+parser.add_argument('template', help="Template Parameter File.")
+
+parser.add_argument('--mqpar_out', '-o', help="Output file, will be ./mqpar.xml if omitted.")
+
+parser.add_argument('--substitution_rx', '-s', help="""Regular expression for filename substitution.
+Necessary for usage in the Galaxy tool. Can usually be ignored.""")
+
+parser.add_argument('--version', '-v', help="""A version number. Raises exception if it doesn't
+match the MaxQuant version of the template. For usage in the Galaxy tool.""")
+
+# in case numThreads is a environment variable, otherwise it can be specified in the yaml file as well
+parser.add_argument('--num_threads', '-t', help="Number of threads to specify in mqpar.")
+args = parser.parse_args()
+
+# edit file names, working dir is unknown at the time of galaxy tool configfile creation
+if args.yaml:
+    with open(args.yaml) as f:
+        conf_dict = yaml.safe_load(f.read())
+
+        for n, pg in enumerate(conf_dict['paramGroups']):
+            for num, fl in enumerate(pg['files']):
+                if not fl.startswith('/'):
+                    conf_dict['paramGroups'][n]['files'][num] = os.path.join(os.getcwd(), fl)
+    with open('yaml', 'w') as f:
+        yaml.safe_dump(conf_dict, stream=f)
+        args.yaml = 'yaml'
+
+kwargs = dict(yaml=args.yaml)
+if args.substitution_rx:
+    kwargs['substitution_rx'] = args.substitution_rx
+mqparam = MQParam(args.template, args.exp_design, **kwargs)
+if args.version and mqparam.version != args.version:
+    raise Exception('mqpar version is ' + mqparam.version + '. Tool uses version {}.'.format(args.version))
+mqparam.set_simple_param('numThreads', args.num_threads)
+
+mqparam.write(args.mqpar_out if args.mqpar_out else 'mqpar.xml')