|
9
|
1 ln -s '$query' 'query' &&
|
|
|
2 #if len($reflist) > 1:
|
|
|
3 #for i, mash in enumerate($reflist):
|
|
|
4 #if i == 0:
|
|
|
5 echo '$mash' > 'reflist' &&
|
|
|
6 #else:
|
|
|
7 echo '$mash' >> 'reflist' &&
|
|
|
8 #end if
|
|
|
9 #end for
|
|
|
10 #end if
|
|
|
11 samtools faidx 'query' &&
|
|
|
12 mashmap --pi '$perc_identity' -s '$seqLength' -f '$filtermode' $dense \
|
|
|
13 #if int($sketchSize) > 0:
|
|
|
14 -J '$sketchSize' \
|
|
|
15 #end if
|
|
|
16 #if len($reflist) == 1:
|
|
|
17 -r '$reflist' -q 'query' &&
|
|
|
18 #else
|
|
|
19 --rl 'reflist' -q 'query' &&
|
|
|
20 #end if
|
|
|
21 cp 'mashmap.out' '$mashout'
|
