Mercurial > repos > abossers > mummer_toolsuite
comparison MUMmer/mummerplot_tool.sh @ 0:59f302448cf6
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
| author | abossers |
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| date | Tue, 07 Jun 2011 17:22:27 -0400 |
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| -1:000000000000 | 0:59f302448cf6 |
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| 1 #!/bin/bash | |
| 2 | |
| 3 ## simple bash to generate mummerplot of MATCH file | |
| 4 ## | |
| 5 ## Galaxy wrapper by Alex Bossers, CVI of Wageningen UR, Lelystad, NL | |
| 6 ## alex_dot_bossers_at_wur_dot_nl | |
| 7 ## | |
| 8 ## | |
| 9 ## needs a rename of the fixed name to something recognised by galaxy | |
| 10 ## needs cleanout of temp files | |
| 11 ## | |
| 12 ## call is mummerplot $format $in_match $out_file $cmd_extra | |
| 13 ## $0 $1 $2 $3 $4 | |
| 14 ## | |
| 15 ## since mummerplot uses some deprecated syntax which can be fixed in the source | |
| 16 ## we redirect STDERR to dev/null to circumvent errorstatus in galaxy | |
| 17 ## io redirects 0=stdin 1=stdout 2=stderr to dev/null (or &-) | |
| 18 | |
| 19 # path to where mummer suite is installed | |
| 20 # adjust this for your machine | |
| 21 # this is the only hard coded path in the scripts | |
| 22 mum_path="/opt/MUMmer/MUMmer" | |
| 23 | |
| 24 # some default options to generate a LARGE fixed PNG/POSTSCRIPT image and not an interactive one. | |
| 25 | |
| 26 if [ "$1" = "png" ]; then | |
| 27 extension="png" | |
| 28 else | |
| 29 extension="ps" | |
| 30 fi | |
| 31 | |
| 32 eval "$mum_path/mummerplot --large --$1 $2 1>&- 2>&-" | |
| 33 | |
| 34 if [ -f "out.$extension" ]; then | |
| 35 #conditional move to something known by galaxy | |
| 36 mv out.$extension $3 | |
| 37 #remove gnuplot file | |
| 38 rm out.gp | |
| 39 fi | |
| 40 | |
| 41 ## clean up | |
| 42 rm out.fplot | |
| 43 rm out.rplot | |
| 44 | |
| 45 #end script |