Mercurial > repos > nml > bundle_collections

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