Mercurial > repos > dereeper > snmf
annotate snmf.sh @ 6:0ba60156e25f draft
planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
| author | dereeper |
|---|---|
| date | Mon, 16 Apr 2018 08:57:17 -0400 |
| parents | 9a1729b89405 |
| children | c94c31bde773 |
| rev | line source |
|---|---|
| 0 | 1 #!/bin/bash |
| 2 vcf=$1 | |
| 3 outputs=$2 | |
| 4 logs=$3 | |
| 5 best_k_output=$4 | |
| 6 best_k_logfile=$5 | |
| 7 kmin=$6 | |
| 8 kmax=$7 | |
| 9 groups=$8 | |
| 10 threshold_group=$9 | |
| 11 | |
| 12 directory=`dirname $0` | |
| 13 mkdir tmpdir$$ | |
| 14 | |
| 15 | |
| 16 perl $directory/Snmf.pl -i $vcf -o $outputs -k $kmin -m $kmax -d tmpdir$$ -t $threshold_group | |
| 17 | |
| 18 mv tmpdir$$/output $best_k_output | |
| 19 mv tmpdir$$/log $best_k_logfile | |
| 20 mv tmpdir$$/outputs.Q $outputs | |
| 21 mv tmpdir$$/logs $logs | |
| 22 mv tmpdir$$/groups $groups | |
| 23 | |
| 24 |