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comparison tools/unix_tools/sed_wrapper.sh @ 0:9071e359b9a3

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author xuebing
date Fri, 09 Mar 2012 19:37:19 -0500
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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