Mercurial > repos > jackcurragh > ribogalaxy_bowtie_genome

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

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Uploaded
author jackcurragh
date Fri, 27 May 2022 12:29:41 +0000
parents 5b1395ac1501
children
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line diff
--- a/bowtie_genome_wrapper/bowtie_genomic_wrapper.py	Fri May 27 10:11:51 2022 +0000
+++ b/bowtie_genome_wrapper/bowtie_genomic_wrapper.py	Fri May 27 12:29:41 2022 +0000
@@ -262,8 +262,8 @@
         mateOrient = ''
     quality_score_encoding = GALAXY_FORMAT_TO_QUALITY_SCORE_ENCODING_ARG.get( options.galaxy_input_format, DEFAULT_ASCII_ENCODING )
     if options.params == 'preSet':
-        aligning_cmds = '-q %s %s -p %s -S %s %s %s ' % \
-            ( maxInsert, mateOrient, options.threads, suppressHeader, colorspace, quality_score_encoding )
+        aligning_cmds = '-p %s -S -m 1 -n 2 --seedlen 25 -q -S' % \
+            ( options.threads)
     else:
         try:
             if options.skip and int( options.skip ) > 0: