|
0
|
1 #!/bin/sh
|
|
|
2
|
|
|
3 ##
|
|
|
4 ## Galaxy wrapper for SED command
|
|
|
5 ##
|
|
|
6
|
|
|
7 ##
|
|
|
8 ## command line arguments:
|
|
|
9 ## input_file
|
|
|
10 ## output_file
|
|
|
11 ## sed-program
|
|
|
12 ## [other parameters passed on to sed]
|
|
|
13
|
|
|
14 INPUT="$1"
|
|
|
15 OUTPUT="$2"
|
|
|
16 PROG="$3"
|
|
|
17
|
|
|
18 shift 3
|
|
|
19
|
|
|
20 if [ -z "$PROG" ]; then
|
|
|
21 echo usage: $0 INPUTFILE OUTPUTFILE SED-PROGRAM [other sed patameters] >&2
|
|
|
22 exit 1
|
|
|
23 fi
|
|
|
24
|
|
|
25 if [ ! -r "$INPUT" ]; then
|
|
|
26 echo "error: input file ($INPUT) not found!" >&2
|
|
|
27 exit 1
|
|
|
28 fi
|
|
|
29
|
|
|
30 # Messages printed to STDOUT will be displayed in the "INFO" field in the galaxy dataset.
|
|
|
31 # This way the user can tell what was the command
|
|
|
32 echo "sed" "$@" "$PROG"
|
|
|
33
|
|
|
34 sed -r --sandbox "$@" "$PROG" "$INPUT" > "$OUTPUT"
|
|
|
35 if (( $? )); then exit; fi
|
|
|
36
|
|
|
37 exit 0
|
