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comparison bundle_collection.pl @ 0:bae199dc511f draft

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planemo upload commit 75c510cf71217015f3f83baf61a4a54a3a1f4bfd
author nml
date Fri, 20 Nov 2015 10:23:17 -0500
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children 705ebd286b57
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-1:000000000000 0:bae199dc511f
1 #!/usr/bin/perl
2
3 use strict;
4 use warnings;
5 use File::Copy;
6 use File::Basename;
7 use Getopt::Long;
8 use Pod::Usage;
9
10 my ($html_file, $html_path, @args, %information, $folder);
11
12 Getopt::Long::Configure('bundling');
13 GetOptions(
14 'i|input=s' => \@args,
15 'h|html=s' => \$html_file,
16 'p|path=s' => \$html_path
17 );
18
19 pod2usage(1) unless @args && $html_file && $html_path;
20
21 #At this point, the output directory does not exist yet. So we have to make it
22 mkdir $html_path or die "Could not make directory $!";
23
24 #Now make a folder for all our files
25 my $data_folder = $html_path."/Bundled_Collection";
26 mkdir $data_folder or die "Could not make directory $!";
27
28 #Go through each list item
29 foreach my $entry (@args)
30 {
31 #Get key and value. Remove any spaces
32 my ($info, $file) = split /=/, $entry;
33 my ($name, $ext) = split /,/, $info;
34 $name=~s/ /_/g;
35 my $full_name = $name.".".$ext;
36
37 #We store this for later to make the html file
38 $information{$name}{$ext}=1;
39
40 #copy each file to its directory
41
42 my $file_path = $data_folder."/".$full_name;
43
44 copy($file,$file_path) or die "Could not copy $file to $file_path: $!";
45 }
46
47 #Write out the html file
48 open my $out, ">", $html_file or die "Could not open html file: $!";
49
50 my $num_keys = scalar(keys %information);
51 my $num_vals = scalar(@args);
52
53 printf $out "<!DOCTYPE html>
54 <html>
55 <style type=\"text/css\">
56
57 body {
58 font-family: sans-serif;
59 color: #000;
60 }
61
62 table {
63 margin-left: 3em;
64 text-align: center;
65 }
66 th {
67 text-align:center;
68 background-color: #000080;
69 color: #FFF;
70 padding: 0.4em;
71 }
72 td {
73 font-family: monospace;
74 text-align: left;
75 background-color: #EEE;
76 color: #000;
77 padding: 0.4em;
78 }
79 h2 {
80 color: #800000;
81 padding-bottom: 0;
82 margin-bottom: 0;
83 clear: left;
84 }
85 </style></head>
86
87 <body>
88
89 <h2 id=\"M0\">Bundle Collection Summary</h2><br><br>
90
91 Number of keys: $num_keys<br>
92 Number of values: $num_vals<br><br>
93
94 <table border=\"1\"><tr><th>File name</th><th>File type</th></tr>";
95
96 foreach my $key (sort(keys %information))
97 {
98
99 foreach my $val (keys %{$information{$key}} )
100 {
101 printf $out "<tr><td>$key</td><td>$val</td></tr>";
102 }
103 }
104
105 printf $out "</table></body></html>";
106
107 close $out;
108
109 __END__
110
111 =head1 name
112
113 bundle_collection.pl - Downloads a collection from Galaxy
114
115 =head1 SYNOPSIS
116
117 bundle_collection.pl -h html_file -p output_path -o "key=value"
118
119 =back
120 =cut