annotate bsmap_meth_caller.sh @ 27:549ff234f35e draft

Uploaded
author eiriche
date Mon, 03 Dec 2012 02:52:27 -0500
parents 98a0a60e934c
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
5
98a0a60e934c Uploaded
eiriche
parents:
diff changeset
1 #!/bin/bash
98a0a60e934c Uploaded
eiriche
parents:
diff changeset
2 #
98a0a60e934c Uploaded
eiriche
parents:
diff changeset
3 # Galaxy wrapper for BSMAP Methylation Caller
98a0a60e934c Uploaded
eiriche
parents:
diff changeset
4 #
98a0a60e934c Uploaded
eiriche
parents:
diff changeset
5
98a0a60e934c Uploaded
eiriche
parents:
diff changeset
6 set -e
98a0a60e934c Uploaded
eiriche
parents:
diff changeset
7
98a0a60e934c Uploaded
eiriche
parents:
diff changeset
8 #get parameters
98a0a60e934c Uploaded
eiriche
parents:
diff changeset
9
98a0a60e934c Uploaded
eiriche
parents:
diff changeset
10 until [ $# -eq 0 ]
98a0a60e934c Uploaded
eiriche
parents:
diff changeset
11 do
98a0a60e934c Uploaded
eiriche
parents:
diff changeset
12 case $1 in
98a0a60e934c Uploaded
eiriche
parents:
diff changeset
13 input=*)
98a0a60e934c Uploaded
eiriche
parents:
diff changeset
14 input=${1#input=}
98a0a60e934c Uploaded
eiriche
parents:
diff changeset
15 ;;
98a0a60e934c Uploaded
eiriche
parents:
diff changeset
16 method=*)
98a0a60e934c Uploaded
eiriche
parents:
diff changeset
17 method=${1#method=}
98a0a60e934c Uploaded
eiriche
parents:
diff changeset
18 ;;
98a0a60e934c Uploaded
eiriche
parents:
diff changeset
19 output=*)
98a0a60e934c Uploaded
eiriche
parents:
diff changeset
20 output=${1#output=}
98a0a60e934c Uploaded
eiriche
parents:
diff changeset
21 ;;
98a0a60e934c Uploaded
eiriche
parents:
diff changeset
22 tempdir=*)
98a0a60e934c Uploaded
eiriche
parents:
diff changeset
23 tempdir=${1#tempdir=}
98a0a60e934c Uploaded
eiriche
parents:
diff changeset
24 ;;
98a0a60e934c Uploaded
eiriche
parents:
diff changeset
25 ref=*)
98a0a60e934c Uploaded
eiriche
parents:
diff changeset
26 ref=${1#ref=}
98a0a60e934c Uploaded
eiriche
parents:
diff changeset
27 ;;
98a0a60e934c Uploaded
eiriche
parents:
diff changeset
28 esac
98a0a60e934c Uploaded
eiriche
parents:
diff changeset
29 shift
98a0a60e934c Uploaded
eiriche
parents:
diff changeset
30 done
98a0a60e934c Uploaded
eiriche
parents:
diff changeset
31
98a0a60e934c Uploaded
eiriche
parents:
diff changeset
32 methratio.py -o $output -d $ref -q $input