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

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author xuebing
date Fri, 09 Mar 2012 19:37:19 -0500
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-1:000000000000 0:9071e359b9a3
1 #!/bin/sh
2
3 ##
4 ## Galaxy wrapper for AWK command
5 ##
6
7 ##
8 ## command line arguments:
9 ## input_file
10 ## output_file
11 ## awk-program
12 ## input-field-separator
13 ## output-field-separator
14
15 INPUT="$1"
16 OUTPUT="$2"
17 PROG="$3"
18 FS="$4"
19 OFS="$5"
20
21 shift 5
22
23 if [ -z "$OFS" ]; then
24 echo usage: $0 INPUTFILE OUTPUTFILE AWK-PROGRAM FS OFS>&2
25 exit 1
26 fi
27
28 if [ ! -r "$INPUT" ]; then
29 echo "error: input file ($INPUT) not found!" >&2
30 exit 1
31 fi
32
33 if [ "$FS" == "tab" ]; then
34 FS="\t"
35 fi
36 if [ "$OFS" == "tab" ]; then
37 OFS="\t"
38 fi
39
40 # Messages printed to STDOUT will be displayed in the "INFO" field in the galaxy dataset.
41 # This way the user can tell what was the command
42 echo "awk" "$PROG"
43
44 awk --sandbox -v OFS="$OFS" -v FS="$FS" --re-interval "$PROG" "$INPUT" > "$OUTPUT"
45 if (( $? )); then exit; fi
46
47 exit 0