Mercurial > repos > xuebing > sharplabtool

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

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author xuebing
date Fri, 09 Mar 2012 19:37:19 -0500
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:9071e359b9a3
1 #!/bin/sh
2
3 #
4 # NOTE:
5 # This is a wrapper for GNU's join under galaxy
6 # not ment to be used from command line (if you're using the command line, simply run 'join' directly...)
7 #
8 # All parameters must be supplied.
9 # the join_tool.xml file takes care of that.
10
11 JOINTYPE="$1"
12 OUTPUT_FORMAT="$2"
13 EMPTY_STRING="$3"
14 DELIMITER="$4"
15 IGNORE_CASE="$5"
16
17 INPUT1="$6"
18 COLUMN1="$7"
19 INPUT2="$8"
20 COLUMN2="$9"
21 OUTPUT="${10}"
22
23 if [ "$OUTPUT" == "" ]; then
24 echo "This script is part of galaxy. Don't run it manually.\n" >&2
25 exit 1;
26 fi
27
28 #This a TAB hack for galaxy (which can't transfer a "\t" as a parameter)
29 [ "$DELIMITER" == "tab" ] && DELIMITER=" "
30
31 #Remove spaces from the output format (if the user entered any)
32 OUTPUT_FORMAT=${OUTPUT_FORMAT// /}
33 [ "$OUTPUT_FORMAT" != "" ] && OUTPUT_FORMAT="-o $OUTPUT_FORMAT"
34
35 echo join $OUTPUT_FORMAT -t "$DELIMITER" -e "$EMPTY_STRING" $IGNORE_CASE $JOINTYPE -1 "$COLUMN1" -2 "$COLUMN2"
36 #echo join $OUTPUT_FORMAT -t "$DELIMITER" -e "$EMPTY_STRING" $IGNORE_CASE $JOINTYPE -1 "$COLUMN1" -2 "$COLUMN2" "$INPUT1" "$INPUT2" \> "$OUTPUT"
37 join $OUTPUT_FORMAT -t "$DELIMITER" -e "$EMPTY_STRING" $JOINTYPE -1 "$COLUMN1" -2 "$COLUMN2" "$INPUT1" "$INPUT2" > "$OUTPUT" || exit 1