Mercurial > repos > fubar > mashmap
comparison mashmap.bash.txt @ 9:dc53eb4354a6 draft
planemo upload
| author | fubar |
|---|---|
| date | Sat, 24 Feb 2024 08:20:07 +0000 |
| parents | |
| children |
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| 8:9ba0184870ef | 9:dc53eb4354a6 |
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| 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' |