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comparison tools/unix_tools/cut_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 cut command.
5 ##
6
7 ##
8 ## command line arguments:
9 ## complement flag (might be empty string)
10 ## what to cut (fields or characters)
11 ## cut list (e.g. 1,2,3,4)
12 ## input_file
13 ## output_file
14
15 COMPLEMENT="$1"
16 CUTWHAT="$2"
17 CUTLIST="$3"
18 INPUT="$4"
19 OUTPUT="$5"
20
21 if [ -z "$OUTPUT" ]; then
22 echo "This script should be run from inside galaxy!" >&2
23 exit 1
24 fi
25
26 if [ ! -r "$INPUT" ]; then
27 echo "error: input file ($INPUT) not found!" >&2
28 exit 1
29 fi
30
31 # Messages printed to STDOUT will be displayed in the "INFO" field in the galaxy dataset.
32 # This way the user can tell what was the command
33 if [ -z "$COMPLEMENT" ]; then
34 echo -n "Extracting "
35 else
36 echo "Deleting "
37 fi
38
39 case $CUTWHAT in
40 -f) echo -n "field(s) "
41 ;;
42
43 -c) echo -n "character(s) "
44 ;;
45 esac
46
47 echo "$CUTLIST"
48
49
50 cut $COMPLEMENT $CUTWHAT $CUTLIST < $INPUT > $OUTPUT
51
52 exit