Mercurial > repos > abossers > mummer_toolsuite

annotate MUMmer/mummerplot_tool.sh @ 0:59f302448cf6

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
author abossers
date Tue, 07 Jun 2011 17:22:27 -0400
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
1 #!/bin/bash
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
2
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
3 ## simple bash to generate mummerplot of MATCH file
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
4 ##
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
5 ## Galaxy wrapper by Alex Bossers, CVI of Wageningen UR, Lelystad, NL
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
6 ## alex_dot_bossers_at_wur_dot_nl
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
7 ##
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
8 ##
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
9 ## needs a rename of the fixed name to something recognised by galaxy
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
10 ## needs cleanout of temp files
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
11 ##
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
12 ## call is mummerplot $format $in_match $out_file $cmd_extra
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
13 ## $0 $1 $2 $3 $4
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
14 ##
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
15 ## since mummerplot uses some deprecated syntax which can be fixed in the source
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
16 ## we redirect STDERR to dev/null to circumvent errorstatus in galaxy
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
17 ## io redirects 0=stdin 1=stdout 2=stderr to dev/null (or &-)
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
18
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
19 # path to where mummer suite is installed
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
20 # adjust this for your machine
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
21 # this is the only hard coded path in the scripts
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
22 mum_path="/opt/MUMmer/MUMmer"
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
23
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
24 # some default options to generate a LARGE fixed PNG/POSTSCRIPT image and not an interactive one.
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
25
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
26 if [ "$1" = "png" ]; then
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
27 extension="png"
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
28 else
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
29 extension="ps"
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
30 fi
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
31
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
32 eval "$mum_path/mummerplot --large --$1 $2 1>&- 2>&-"
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
33
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
34 if [ -f "out.$extension" ]; then
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
35 #conditional move to something known by galaxy
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
36 mv out.$extension $3
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
37 #remove gnuplot file
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
38 rm out.gp
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
39 fi
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
40
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
41 ## clean up
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
42 rm out.fplot
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
43 rm out.rplot
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
44
59f302448cf6 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
abossers
parents:
diff changeset
45 #end script