Mercurial > repos > galaxyp > maxquant

comparison mqwrapper.py @ 2:666f3453a99d draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 2131f017e9303599ed672797ffd6e9b00ab1245d
author galaxyp
date Wed, 07 Aug 2019 10:50:06 -0400
parents 8bac3cc5c5de
children 175e062b6a17
comparison
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1:8bac3cc5c5de 2:666f3453a99d
89 fnames_with_ext = [(a if a.endswith(ftype) 89 fnames_with_ext = [(a if a.endswith(ftype)
90 else os.path.splitext(a)[0] + ftype) 90 else os.path.splitext(a)[0] + ftype)
91 for a in filenames] 91 for a in filenames]
92 92
93 for f, l in zip(files, fnames_with_ext): 93 for f, l in zip(files, fnames_with_ext):
94 os.link(f, l) 94 os.symlink(f, l)
95 95
96 # build mqpar.xml 96 # build mqpar.xml
97 mqpar_in = os.path.join(os.getcwd(), 'mqpar.xml') 97 mqpar_in = os.path.join(os.getcwd(), 'mqpar.xml')
98 subprocess.run(('maxquant', '-c', mqpar_in)) 98 subprocess.run(('maxquant', '-c', mqpar_in))
99 mqpar_out = args['mqpar_out'] if args['mqpar_out'] != 'None' else mqpar_in 99 mqpar_out = args['mqpar_out'] if args['mqpar_out'] != 'None' else mqpar_in