# HG changeset patch
# User jackcurragh
# Date 1653654581 0
# Node ID 1ee2d07cfb7271d828e4866208d665262e529744
# Parent  5b0c7db214140f4ff086a38b008c256ff9f19246
Uploaded

diff -r 5b0c7db21414 -r 1ee2d07cfb72 bowtie_genome_wrapper/bowtie_genomic_wrapper.py
--- 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: