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comparison glang-galaxy-conf/kbws/acdgalaxy.pl @ 2:8947fca5f715 draft default tip

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author ktnyt
date Fri, 26 Jun 2015 05:21:44 -0400
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1:84a17b3fad1f 2:8947fca5f715
1 #!/usr/bin/env perl
2 use strict;
3 use warnings;
4
5 my $progname = shift;
6 $progname =~ s/\.acd$//g;
7 my $progfile = "/usr/local/share/EMBOSS/acd/$progname.acd";
8 open my $acdfh, "<", $progfile;
9 open my $xmlfh, ">", "$progname.xml";
10
11 my $tool;
12 my $description;
13 my $command;
14 my @params;
15 my @args;
16 my $help;
17 my $plot = 0+`grep -c 'toggle: plot' $progfile`;
18 my $pngout = 0+`grep -c 'string: format' $progfile`;
19
20 while(<$acdfh>) {
21 chomp;
22 if(/\s*application\s*:\s*\w+\s*\[\s*$/../^\s*\]\s*$/) {
23 if(/\s*application\s*:\s*(\w+)\s*\[\s*$/) {
24 $tool = qq(<tool id="EMBOSS: $1" name="$1" version="1.0.2">);
25 }
26
27 if(/\s*documentation:\s*"([^"]+)"?\s*/) {
28 my $tmp = $1;
29 if(/\s*documentation:\s*".+"\s*/) {
30 $description = qq( <description>$tmp</description>);
31 } else {
32 while(<$acdfh>) {
33 if(/\s*(.*)"/) {
34 $tmp.= " $1";
35 last;
36 } elsif(/\s*(.*)\s*/) {
37 $tmp .= " $1";
38 }
39 }
40 $description = qq( <description>$tmp</description>);
41 }
42 }
43 }
44
45 if(/\s*section\s*:\s*advanced\s*\[/../\s*endsection:\s*advanced/) {
46 if(/\s*section\s*:\s*advanced\s*\[/../\]/ or /\s*endsction:\s*advanced/) {
47 next;
48 }
49
50 if(/\s*\w+\s*:\s*\w+\s*\[/../\s*\]/) {
51 if(/\s*(\w+)\s*:\s*(\w+)\s*\[/) {
52 my ($type, $name) = ($1, $2);
53 my $information;
54 my $default;
55 my @values;
56
57 next if $name eq "accid";
58 next if $name eq "plot";
59
60 push @args, $name;
61
62 while(<$acdfh>) {
63 chomp;
64 if(/\]/) {
65 last;
66 }
67 if(/\s*information:\s*"([^"]+)"?\s*/) {
68 my $tmp = $1;
69 if(/\s*information:\s*".+"\s*/) {
70 $information = $tmp;
71 } else {
72 while(<$acdfh>) {
73 if(/\s*(.*)"/) {
74 $tmp.= " $1";
75 last;
76 } elsif(/\s*(.*)\s*/) {
77 $tmp .= " $1";
78 }
79 }
80 $information = $tmp;
81 }
82 }
83
84 if(/\s*default:\s*"(.+)"\s*/) {
85 $default = $1;
86 }
87
88 if(/\s*values:\s*"(.+)"\s*/) {
89 @values = split ";", $1;
90 }
91 }
92 #print "$type\t$name\t$information";
93 #print "\t$default" if defined $default;
94 #print "\n";
95 my $param;
96
97 if($default) {
98 $default = "yes" if $default eq "Y";
99 $default = "no" if $default eq "N";
100 $default = "[^ACDEFGHIKLMNPQRSTVWYacgtU]" if $name eq "delkey";
101 } else {
102 $default = "";
103 }
104
105 if($type eq "boolean") {
106 $param = <<EOS;
107 <param name="$name" type="select" value="$default">
108 <label>$information</label>
109 <option value="no">No</option>
110 <option value="yes">Yes</option>
111 </param>
112 EOS
113 }
114
115 if($type =~ /(integer)|(float)|(string)/) {
116 $type =~ s/string/text/g;
117 $param = <<EOS;
118 <param name="$name" size="4" type="$type" value="$default">
119 <label>$information</label>
120 </param>
121 EOS
122 }
123
124 if($type =~ /selection/) {
125 my $vals = join "\n", map{
126 " <option value=\"$_\">". ucfirst($_) ."</option>"
127 }@values;
128 $param = <<EOS
129 <param name="$name" type="select" value="$default">
130 <label>$information</label>
131 $vals
132 </param>
133 EOS
134 }
135
136 print "$type: $name\n";
137 if($param && length $param) {
138 chomp($param);
139 push @params, $param;
140 }
141 }
142 }
143 }
144 }
145 close $acdfh;
146
147 my $args = join(" ", map{"-$_ \$$_"}@args);
148
149 my $paramstr = "";
150 foreach my $param (@params) {
151 $paramstr .= "$param\n";
152 }
153
154 my $outputs;
155
156 if($plot) {
157 $command = "<command interpreter=\"perl\">gembassy_calcandplot_wrapper.pl $progname -sequence \$input1 $args -auto \$out_file1 \$out_file2</command>";
158 $outputs = <<EOS;
159 <data format="csv" name="out_file1" label="\${tool.name} data for \${input1.name}" />
160 <data format="png" name="out_file2" label="\${tool.name} plot for \${input1.name}" />
161 EOS
162 } elsif($pngout) {
163 $command = "<command interpreter=\"perl\">emboss_single_outputfile_wrapper.pl $progname -sequence \$input1 -format png -goutfile \$out_file1 -auto $args</command>";
164 $outputs = <<EOS;
165 <data format="png" name="out_file1" label="\${tool.name} for \${input1.name}" />
166 EOS
167 } else {
168 $command = "<command>$progname -sequence \$input1 $args -auto -outfile \$out_file1</command>";
169 printf(STDERR "Enter output data format of $progname (1: txt 2: csv): ");
170 chomp(my $format = <>);
171 $format = $format == 1 ? "txt" : "csv";
172 $outputs = <<EOS;
173 <data format="$format" name="out_file1" label="\${tool.name} for \${input1.name}" />
174 EOS
175 }
176 chomp $outputs;
177
178 print $xmlfh <<EOS;
179 $tool
180 $description
181 $command
182 <inputs>
183 <param format="data" name="input1" type="data">
184 <label>Sequence</label>
185 </param>
186 $paramstr
187 </inputs>
188 <outputs>
189 $outputs
190 </outputs>
191 </tool>
192 EOS
193
194 close $xmlfh;