--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mqwrapper.py	Sat Jul 20 04:53:23 2019 -0400
@@ -0,0 +1,99 @@
+"""
+Run MaxQuant on a modified mqpar.xml.
+Use maxquant conda package.
+TODO: add support for parameter groups
+
+Authors: Damian Glaetzer <d.glaetzer@mailbox.org>
+
+based on the maxquant galaxy tool by John Chilton:
+https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant
+"""
+
+import argparse
+import os
+import shutil
+import subprocess
+
+import mqparam
+
+# build parser
+parser = argparse.ArgumentParser()
+
+# input, special outputs and others
+other_args = ('raw_files', 'mzxml_files', 'fasta_files',
+              'description_parse_rule', 'identifier_parse_rule',
+              'mqpar_in', 'output_all',
+              'mqpar_out', 'infile_names', 'mzTab',
+              'version', 'substitution_rx')
+
+# txt result files
+txt_output = ('evidence', 'msms', 'parameters',
+              'peptides', 'proteinGroups', 'allPeptides',
+              'libraryMatch', 'matchedFeatures',
+              'modificationSpecificPeptides', 'ms3Scans',
+              'msmsScans', 'mzRange', 'peptideSection',
+              'summary')
+
+global_simple_args = ('num_threads',)
+
+arguments = ['--' + el for el in (txt_output
+                                  + other_args
+                                  + global_simple_args)]
+
+for arg in arguments:
+    parser.add_argument(arg)
+
+args = vars(parser.parse_args())
+
+# link infile datasets to names with correct extension
+# for maxquant to accept them
+files = (args['raw_files'] if args['raw_files']
+         else args['mzxml_files']).split(',')
+ftype = ".thermo.raw" if args['raw_files'] else ".mzXML"
+filenames = args['infile_names'].split(',')
+fnames_with_ext = [(a if a.endswith(ftype)
+                    else os.path.splitext(a)[0] + ftype)
+                   for a in filenames]
+
+for f, l in zip(files, fnames_with_ext):
+    os.link(f, l)
+
+# build mqpar.xml
+mqpar_temp = os.path.join(os.getcwd(), 'mqpar.xml')
+mqpar_out = args['mqpar_out'] if args['mqpar_out'] != 'None' else mqpar_temp
+mqpar_in = args['mqpar_in']
+
+exp_design = None
+m = mqparam.MQParam(mqpar_out, mqpar_in, exp_design,
+                    substitution_rx=args['substitution_rx'])
+if m.version != args['version']:
+    raise Exception('mqpar version is ' + m.version +
+                    '. Tool uses version {}.'.format(args['version']))
+
+# modify parameters, interactive mode if no mqpar_in was specified
+m.add_infiles([os.path.join(os.getcwd(), name) for name in fnames_with_ext], False)
+m.add_fasta_files(args['fasta_files'].split(','),
+                  identifier=args['identifier_parse_rule'],
+                  description=args['description_parse_rule'])
+
+m.write()
+
+# build and run MaxQuant command
+cmd = ['maxquant', mqpar_out]
+
+subprocess.run(cmd, check=True, cwd='./')
+
+# copy results to galaxy database
+for el in txt_output:
+    destination = args[el]
+    source = os.path.join(os.getcwd(), "combined", "txt", "{}.txt".format(el))
+    if destination != 'None' and os.path.isfile(source):
+        shutil.copy(source, destination)
+
+if args['mzTab'] != 'None':
+    source = os.path.join(os.getcwd(), "combined", "txt", "mzTab.mzTab")
+    if os.path.isfile(source):
+        shutil.copy(source, args['mzTab'])
+
+if args['output_all'] != 'None':
+    subprocess.run(('tar', '-zcf', args['output_all'], './combined/txt/'))