Mercurial > repos > dereeper > sniplay

annotate SNP_density/calculateSlidingWindowsSNPdensitiesFromVCF.sh @ 11:15b23cdde685 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 305985afd3b7c3d47f531149c2f1a279af2d12aa-dirty
author dereeper
date Fri, 20 Apr 2018 09:04:25 -0400
parents ebb0ac9b6fa9
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
6
ebb0ac9b6fa9 planemo upload
gandres
parents:
diff changeset
1 #!/bin/bash
ebb0ac9b6fa9 planemo upload
gandres
parents:
diff changeset
2
ebb0ac9b6fa9 planemo upload
gandres
parents:
diff changeset
3 tool_path=$(dirname $0)
ebb0ac9b6fa9 planemo upload
gandres
parents:
diff changeset
4 input=$1
ebb0ac9b6fa9 planemo upload
gandres
parents:
diff changeset
5 fileout=$2
ebb0ac9b6fa9 planemo upload
gandres
parents:
diff changeset
6 fileout_bysample=$3
ebb0ac9b6fa9 planemo upload
gandres
parents:
diff changeset
7 step=$4
ebb0ac9b6fa9 planemo upload
gandres
parents:
diff changeset
8
ebb0ac9b6fa9 planemo upload
gandres
parents:
diff changeset
9 perl $tool_path/CalculateSlidingWindowsSNPdensitiesFromVCF.pl -i $input -o $fileout -s $step
ebb0ac9b6fa9 planemo upload
gandres
parents:
diff changeset
10
ebb0ac9b6fa9 planemo upload
gandres
parents:
diff changeset
11 cp $fileout.by_sample $fileout_bysample
ebb0ac9b6fa9 planemo upload
gandres
parents:
diff changeset
12 rm $fileout.by_sample
ebb0ac9b6fa9 planemo upload
gandres
parents:
diff changeset
13