maxquant: mqwrapper.py annotate

annotate mqwrapper.py @ 2:33c911e66d8e draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 74b5aa29e49deaaebe19ce2355a70d4f570f4951"

author	galaxyp
date	Thu, 15 Aug 2019 08:07:52 -0400
parents	461ba35a313f
children

rev	line source
0 4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	1 """
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	2 Run MaxQuant on a modified mqpar.xml.
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	3 Use maxquant conda package.
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	4 TODO: add support for parameter groups
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	5
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	6 Authors: Damian Glaetzer <d.glaetzer@mailbox.org>
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	7
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	8 based on the maxquant galaxy tool by John Chilton:
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	9 https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	10 """
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	11
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	12 import argparse
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	13 import os
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	14 import shutil
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	15 import subprocess
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	16
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	17 import mqparam
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	18
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	19 # build parser
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	20 parser = argparse.ArgumentParser()
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	21
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	22 # input, special outputs and others
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	23 other_args = ('raw_files', 'mzxml_files', 'fasta_files',
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	24 'description_parse_rule', 'identifier_parse_rule',
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	25 'exp_design', 'output_all',
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	26 'mqpar_out', 'infile_names', 'mzTab',
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	27 'version', 'substitution_rx')
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	28
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	29 # txt result files
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	30 txt_output = ('evidence', 'msms', 'parameters',
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	31 'peptides', 'proteinGroups', 'allPeptides',
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	32 'libraryMatch', 'matchedFeatures',
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	33 'modificationSpecificPeptides', 'ms3Scans',
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	34 'msmsScans', 'mzRange', 'peptideSection',
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	35 'summary')
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	36
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	37 # arguments for mqparam
2 33c911e66d8e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 74b5aa29e49deaaebe19ce2355a70d4f570f4951" galaxyp parents: 1 diff changeset	38 # global
0 4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	39 global_flags = ('calc_peak_properties',
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	40 'write_mztab',
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	41 'ibaq',
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	42 'ibaq_log_fit',
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	43 'separate_lfq',
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	44 'lfq_stabilize_large_ratios',
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	45 'lfq_require_msms',
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	46 'advanced_site_intensities',
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	47 'match_between_runs')
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	48
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	49 global_simple_args = ('min_unique_pep',
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	50 'num_threads',
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	51 'min_peptide_len',
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	52 'max_peptide_mass')
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	53
2 33c911e66d8e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 74b5aa29e49deaaebe19ce2355a70d4f570f4951" galaxyp parents: 1 diff changeset	54 # parameter group specific
0 4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	55 param_group_flags = ('lfq_skip_norm',)
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	56
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	57 param_group_simple_args = ('missed_cleavages',
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	58 'lfq_mode',
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	59 'lfq_min_edges_per_node',
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	60 'lfq_avg_edges_per_node',
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	61 'lfq_min_ratio_count')
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	62
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	63 param_group_silac_args = ('light_mods', 'medium_mods', 'heavy_mods')
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	64
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	65 list_args = ('fixed_mods', 'var_mods', 'proteases')
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	66
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	67 arguments = ['--' + el for el in (txt_output
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	68 + global_simple_args
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	69 + param_group_simple_args
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	70 + list_args
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	71 + param_group_silac_args
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	72 + other_args)]
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	73
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	74 flags = ['--' + el for el in global_flags + param_group_flags]
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	75
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	76 for arg in arguments:
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	77 parser.add_argument(arg)
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	78 for flag in flags:
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	79 parser.add_argument(flag, action="store_true")
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	80
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	81 args = vars(parser.parse_args())
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	82
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	83 # link infile datasets to names with correct extension
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	84 # for maxquant to accept them
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	85 files = (args['raw_files'] if args['raw_files']
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	86 else args['mzxml_files']).split(',')
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	87 ftype = ".thermo.raw" if args['raw_files'] else ".mzXML"
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	88 filenames = args['infile_names'].split(',')
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	89 fnames_with_ext = [(a if a.endswith(ftype)
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	90 else os.path.splitext(a)[0] + ftype)
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	91 for a in filenames]
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	92
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	93 for f, l in zip(files, fnames_with_ext):
1 461ba35a313f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 2131f017e9303599ed672797ffd6e9b00ab1245d galaxyp parents: 0 diff changeset	94 os.symlink(f, l)
0 4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	95
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	96 # build mqpar.xml
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	97 mqpar_in = os.path.join(os.getcwd(), 'mqpar.xml')
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	98 subprocess.run(('maxquant', '-c', mqpar_in))
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	99 mqpar_out = args['mqpar_out'] if args['mqpar_out'] != 'None' else mqpar_in
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	100
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	101
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	102 exp_design = args['exp_design'] if args['exp_design'] != 'None' else None
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	103 m = mqparam.MQParam(mqpar_out, mqpar_in, exp_design,
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	104 substitution_rx=args['substitution_rx'])
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	105 if m.version != args['version']:
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	106 raise Exception('mqpar version is ' + m.version +
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	107 '. Tool uses version {}.'.format(args['version']))
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	108
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	109 # modify parameters, interactive mode if no mqpar_in was specified
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	110 m.add_infiles([os.path.join(os.getcwd(), name) for name in fnames_with_ext], True)
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	111 m.add_fasta_files(args['fasta_files'].split(','),
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	112 identifier=args['identifier_parse_rule'],
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	113 description=args['description_parse_rule'])
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	114
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	115 for e in (global_simple_args
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	116 + param_group_simple_args
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	117 + global_flags
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	118 + param_group_flags):
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	119 if args[e]:
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	120 m.set_simple_param(e, args[e])
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	121
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	122 for e in list_args:
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	123 if args[e]:
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	124 m.set_list_params(e, args[e].split(','))
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	125
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	126 if args['light_mods'] or args['medium_mods'] or args['heavy_mods']:
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	127 m.set_silac(args['light_mods'].split(',') if args['light_mods'] else None,
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	128 args['medium_mods'].split(',') if args['medium_mods'] else None,
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	129 args['heavy_mods'].split(',') if args['heavy_mods'] else None)
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	130
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	131 m.write()
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	132
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	133 # build and run MaxQuant command
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	134 cmd = ['maxquant', mqpar_out]
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	135
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	136 subprocess.run(cmd, check=True, cwd='./')
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	137
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	138 # copy results to galaxy database
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	139 for el in txt_output:
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	140 destination = args[el]
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	141 source = os.path.join(os.getcwd(), "combined", "txt", "{}.txt".format(el))
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	142 if destination != 'None' and os.path.isfile(source):
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	143 shutil.copy(source, destination)
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	144
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	145 if args['mzTab'] != 'None':
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	146 source = os.path.join(os.getcwd(), "combined", "txt", "mzTab.mzTab")
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	147 if os.path.isfile(source):
4ce8694766e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: diff changeset	148 shutil.copy(source, args['mzTab'])

Mercurial > repos > galaxyp > maxquant

annotate mqwrapper.py @ 2:33c911e66d8e draft