--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mqwrapper.py	Sat Jul 20 05:01:05 2019 -0400
@@ -0,0 +1,148 @@
+"""
+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',
+              'exp_design', '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')
+
+# arguments for mqparam
+## global
+global_flags = ('calc_peak_properties',
+                'write_mztab',
+                'ibaq',
+                'ibaq_log_fit',
+                'separate_lfq',
+                'lfq_stabilize_large_ratios',
+                'lfq_require_msms',
+                'advanced_site_intensities',
+                'match_between_runs')
+
+global_simple_args = ('min_unique_pep',
+                      'num_threads',
+                      'min_peptide_len',
+                      'max_peptide_mass')
+
+## parameter group specific
+param_group_flags = ('lfq_skip_norm',)
+
+param_group_simple_args = ('missed_cleavages',
+                           'lfq_mode',
+                           'lfq_min_edges_per_node',
+                           'lfq_avg_edges_per_node',
+                           'lfq_min_ratio_count')
+
+param_group_silac_args = ('light_mods', 'medium_mods', 'heavy_mods')
+
+list_args = ('fixed_mods', 'var_mods', 'proteases')
+
+arguments = ['--' + el for el in (txt_output
+                                  + global_simple_args
+                                  + param_group_simple_args
+                                  + list_args
+                                  + param_group_silac_args
+                                  + other_args)]
+
+flags = ['--' + el for el in global_flags + param_group_flags]
+
+for arg in arguments:
+    parser.add_argument(arg)
+for flag in flags:
+    parser.add_argument(flag, action="store_true")
+
+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_in = os.path.join(os.getcwd(), 'mqpar.xml')
+subprocess.run(('maxquant', '-c', mqpar_in))
+mqpar_out = args['mqpar_out'] if args['mqpar_out'] != 'None' else mqpar_in
+
+
+exp_design = args['exp_design'] if args['exp_design'] != 'None' else 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], True)
+m.add_fasta_files(args['fasta_files'].split(','),
+                  identifier=args['identifier_parse_rule'],
+                  description=args['description_parse_rule'])
+
+for e in (global_simple_args
+          + param_group_simple_args
+          + global_flags
+          + param_group_flags):
+    if args[e]:
+        m.set_simple_param(e, args[e])
+
+for e in list_args:
+    if args[e]:
+        m.set_list_params(e, args[e].split(','))
+
+if args['light_mods'] or args['medium_mods'] or args['heavy_mods']:
+    m.set_silac(args['light_mods'].split(',') if args['light_mods'] else None,
+                args['medium_mods'].split(',') if args['medium_mods'] else None,
+                args['heavy_mods'].split(',') if args['heavy_mods'] else None)
+
+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'])