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comparison MUMmer/mummer_tool.sh @ 0:6753195df9e0 default tip

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Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
author abossers
date Tue, 07 Jun 2011 17:49:58 -0400
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1 #!/bin/bash
2 ## use #!/bin/bash -x for debugging
3
4 ## Galaxy wrapper for MUMmer (nucmer/promer)
5 ## Alex Bossers, CVI of Wageningen UR, NL
6 ## alex_dot_bossers_at_wur_dot_nl
7 ##
8 ## Sep 2010
9 ##
10 ## Wrapper runs MUMmer nucmer/promer and additional args
11 ## Calculates the comparison scores (delta and optional coords file)
12 ## Generates the optional STATIC comparison mummerplot to png (from delta file)
13 ##
14 ## finally the script renames (optional) output files to outfiles expected by Galaxy
15 ##
16 ##
17 ## INPUT args:
18 ## nucmer_tool.sh $input_ref $input_query $out_delta $out_coords $out_png $logfile
19 ## @0 @1 @2 @3 @4 @5
20 ## $algorithm $keep_delta $make_coords $keep_log $make_image $cmd_extra
21 ## @6 @7 @8 @9 @10 @11
22 ##
23
24 # path to where mummer suite is installed
25 # adjust this for your machine
26 # this is the only hard coded path in the scripts
27 mum_path="/opt/MUMmer/MUMmer"
28
29 # since we have more than 9 arguments we need to shift the sections or use own array
30 args=("$@")
31 # to keep things readible assign vars
32 input_ref="${args[0]}"
33 input_query="${args[1]}"
34 out_delta="${args[2]}"
35 out_coords="${args[3]}"
36 out_png="${args[4]}"
37 logfile="${args[5]}"
38 algorithm="${args[6]}"
39 keep_delta="${args[7]}"
40 make_coords="${args[8]}"
41 keep_log="${args[9]}"
42 make_image="${args[10]}"
43 cmd_extra="${args[11]}"
44
45 # enable/disable the STDOUT log file
46 if [ "$keep_log" == "yes" ]; then
47 logfile_c="2>$logfile"
48 logfile_a="2>>$logfile"
49 else
50 #dump to dev/null
51 logfile_c="2>&-"
52 logfile_a="2>&-"
53 fi
54
55 # extra mummer cmd line options
56
57 ## generate coords file on the fly?
58 if [ "$make_coords" == "yes" ]; then
59 options=" --coords"
60 fi
61 ## extra cmd line args to be concatenated in options? We need to prevent extra spaces!
62 if [ "$cmd_extra" != "" ]; then
63 if [ "$options" == "" ]; then
64 options=" $cmd_extra"
65 else
66 options="$options $cmd_extra"
67 fi
68 fi
69
70 # run nucmer/promer
71 eval "$mum_path/$algorithm$options $input_ref $input_query $logfile_c"
72
73 ## generate large png if option make_image = yes
74 ## suppress error from mummerplot since some is deprecated but not a real error
75 ## error can be easily avoided by modifying the source of mummerplot... just in case
76 ## however we need to check if a valid png was generated. This is not the case is alignment is none
77 ## 1 is stderr and 2 stdout. redirect to dev/null
78
79 if [ "${make_image}" == "yes" ]; then
80 eval "$mum_path/mummerplot --large --png out.delta 1>&- $logfile_a"
81 if [ -f "out.png" ]; then
82 mv out.png $out_png
83 #cleanup temp gnuplot file
84 rm out.gp
85 else
86 echo "not exist the req png file!"
87 fi
88
89 ## clean up remaining files
90 rm out.fplot
91 rm out.rplot
92
93 fi
94
95 # keep/rename or delete delta file
96 if [ "$keep_delta" == "yes" ]; then
97 mv out.delta "$out_delta"
98 else
99 rm out.delta
100 fi
101
102 # keep/rename coords file if it was created
103 if [ "$make_coords" == "yes" ]; then
104 mv out.coords "$out_coords"
105 fi
106
107 # end script