Mercurial > repos > jackcurragh > ribogalaxy_bowtie_genome

comparison bowtie_genome_wrapper/bowtie_genomic_wrapper.py @ 11:1ee2d07cfb72 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author jackcurragh
date Fri, 27 May 2022 12:29:41 +0000
parents 5b1395ac1501
children
comparison
equal deleted inserted replaced
10:5b0c7db21414 11:1ee2d07cfb72
260 mateOrient = '--%s' % options.mateOrient 260 mateOrient = '--%s' % options.mateOrient
261 else: 261 else:
262 mateOrient = '' 262 mateOrient = ''
263 quality_score_encoding = GALAXY_FORMAT_TO_QUALITY_SCORE_ENCODING_ARG.get( options.galaxy_input_format, DEFAULT_ASCII_ENCODING ) 263 quality_score_encoding = GALAXY_FORMAT_TO_QUALITY_SCORE_ENCODING_ARG.get( options.galaxy_input_format, DEFAULT_ASCII_ENCODING )
264 if options.params == 'preSet': 264 if options.params == 'preSet':
265 aligning_cmds = '-q %s %s -p %s -S %s %s %s ' % \ 265 aligning_cmds = '-p %s -S -m 1 -n 2 --seedlen 25 -q -S' % \
266 ( maxInsert, mateOrient, options.threads, suppressHeader, colorspace, quality_score_encoding ) 266 ( options.threads)
267 else: 267 else:
268 try: 268 try:
269 if options.skip and int( options.skip ) > 0: 269 if options.skip and int( options.skip ) > 0:
270 skip = '-s %s' % options.skip 270 skip = '-s %s' % options.skip
271 else: 271 else: