Mercurial > repos > nml > bundle_collections

annotate bundle_collection.pl @ 2:705ebd286b57 draft default tip

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"planemo upload commit 7761f1e59039279728185e751f1a51b56fe14cb0"
author nml
date Mon, 24 Aug 2020 12:14:15 -0400
parents bae199dc511f
children
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1 #!/usr/bin/env 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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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 <head>
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56 <style type=\"text/css\">
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57
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58 body {
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59 font-family: sans-serif;
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60 color: #000;
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61 }
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62
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63 table {
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64 margin-left: 3em;
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65 text-align: center;
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66 }
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67 th {
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68 text-align:center;
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69 background-color: #000080;
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70 color: #FFF;
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71 padding: 0.4em;
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72 }
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73 td {
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74 font-family: monospace;
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75 text-align: left;
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76 background-color: #EEE;
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77 color: #000;
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78 padding: 0.4em;
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79 }
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80 h2 {
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81 color: #800000;
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82 padding-bottom: 0;
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83 margin-bottom: 0;
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84 clear: left;
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85 }
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86 </style>
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87 </head>
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88
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89 <body>
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90
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91 <h2 id=\"M0\">Bundle Collection Summary</h2><br><br>
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92
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93 Number of keys: $num_keys<br>
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94 Number of values: $num_vals<br><br>
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95
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96 <table border=\"1\">
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97 <tr><th>File name</th><th>File type</th></tr>\n";
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98
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99 foreach my $key (sort(keys %information))
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100 {
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101
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102 foreach my $val (keys %{$information{$key}} )
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103 {
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104 printf $out " <tr><td>$key</td><td>$val</td></tr>\n";
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105 }
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106 }
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107
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108 printf $out " </table>\n</body>\n</html>";
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109
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110 close $out;
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111
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112 __END__
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113
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114 =head1 name
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115
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116 bundle_collection.pl - Downloads a collection from Galaxy
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117
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118 =head1 SYNOPSIS
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119
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120 bundle_collection.pl -h html_file -p output_path -i "key=value"
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121
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122 =back
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123 =cut