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planemo upload
author fubar
date Sat, 24 Feb 2024 08:29:59 +0000
parents dc53eb4354a6
children
line wrap: on
line source

ln -s '$query' 'query' &&
#if len($reflist) > 1:
#for i, mash in enumerate($reflist):
   #if i == 0:
       echo '$mash' > 'reflist' &&
   #else:
       echo '$mash' >> 'reflist' &&
   #end if
#end for
#end if
samtools faidx 'query' &&
mashmap --pi '$perc_identity' -s '$seqLength' -f '$filtermode' $dense \
#if int($sketchSize) > 0:
-J '$sketchSize' \
#end if
#if len($reflist) == 1:
 -r '$reflist' -q 'query' && 
#else
--rl 'reflist' -q 'query' && 
#end if
cp 'mashmap.out'  '$mashout'