Mercurial > repos > galaxyp > msconvert
diff msconvert_wrapper.py @ 5:637e309295cf draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit d70aeb6f0e03a354fb8732f04dce8453b03477ea
author | galaxyp |
---|---|
date | Mon, 12 Dec 2016 17:07:11 -0500 |
parents | 158a71ee5733 |
children | 6b6bba73eadb |
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--- a/msconvert_wrapper.py Wed Dec 07 17:43:19 2016 -0500 +++ b/msconvert_wrapper.py Mon Dec 12 17:07:11 2016 -0500 @@ -88,7 +88,7 @@ #ENDTEMPLATE -to_extensions = ['mzML', 'mzXML', 'unindexed_mzML', 'unindexed_mzXML', 'mgf', 'mz5', 'txt', 'ms2', 'cms2'] +to_extensions = ['mzML', 'mzXML', 'unindexed_mzML', 'unindexed_mzXML', 'mgf', 'txt', 'ms2', 'cms2'] def str_to_bool(v): @@ -171,7 +171,7 @@ return filters_file_path -def _build_base_cmd(options,args=None): +def _build_base_cmd(options): to_extension = options.toextension if to_extension.startswith("unindexed_"): to_extension = to_extension[len("unindexed_"):] @@ -179,8 +179,6 @@ else: to_params = "" cmd = "msconvert --%s %s" % (to_extension, to_params) - if args: - cmd = "%s %s" % (cmd, ' '.join(args)) if str_to_bool(options.zlib): cmd = "%s %s" % (cmd, "--zlib") if options.binaryencoding: @@ -210,10 +208,7 @@ parser.add_option('--input', dest='inputs', action='append', default=[]) parser.add_option('--input_name', dest='input_names', action='append', default=[]) parser.add_option('--implicit', dest='implicits', action='append', default=[], help='input files that should NOT be on the msconvert command line.') - parser.add_option('--ident', dest='idents', action='append', default=[]) - parser.add_option('--ident_name', dest='ident_names', action='append', default=[]) parser.add_option('--output', dest='output') - parser.add_option('--refinement', dest='refinement') parser.add_option('--fromextension', dest='fromextension') parser.add_option('--toextension', dest='toextension', default='mzML', choices=to_extensions) parser.add_option('--binaryencoding', dest='binaryencoding', choices=['32', '64']) @@ -258,11 +253,8 @@ if input in options.implicits: continue input_files.append(input_file) - for i, ident in enumerate(options.idents): - ident_file = options.ident_names[i] - copy_to_working_directory(ident, ident_file) - cmd = _build_base_cmd(options,args=args) + cmd = _build_base_cmd(options) file_column = options.filter_table_file_column if not file_column: # Apply same filters to all files, just create a unviersal filter files @@ -283,16 +275,7 @@ cmd = "%s --merge" % cmd output_file = _run(cmd, output_dir='output', inputs=input_files, debug=options.debug) shutil.copy(output_file, options.output) - if options.refinement: - # .mzRefinement.tsv - files = os.listdir(os.getcwd()) - for fname in files: - if fname.endswith('.mzRefinement.tsv'): - shutil.copy(fname, options.refinement) - break -def __main__(): - run_script() if __name__ == '__main__': __main__()