Mercurial > repos > jvolkening > nanopore_qc

annotate yaml_to_html.pl @ 2:5c7848b91964 draft default tip

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planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit efc73adf2038b9c6504c60f35202e91dbc7f4d48-dirty
author jvolkening
date Sat, 02 Mar 2024 05:33:33 +0000
parents e0006d8bf849
children
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e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
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1 #!/usr/bin/env perl
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
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3 use strict;
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
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4 use warnings;
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
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5 use 5.012;
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
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6
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
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7 use YAML::XS qw/LoadFile/;
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
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8 use MIME::Base64;
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
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9 use autodie;
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
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e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
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11 my ($fn_yaml, $dir_in, $fn_out) = @ARGV;
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
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e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
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13 die "Can't find or read input file: $!\n"
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
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14 if (! -r $fn_yaml);
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
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16 # set output filehandle based on arguments
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
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17 my $fh = \*STDOUT;
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
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18 if (defined $fn_out) {
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
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19 open $fh, '>', $fn_out;
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
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20 }
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
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22 my $yaml = LoadFile($fn_yaml);
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
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24 convert($yaml, $dir_in);
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
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26 sub convert {
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
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28 my ($yaml) = @_;
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
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30 print {$fh} header();
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
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32 say {$fh} " <h3>Summary statistics</h3>";
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
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34 for my $grp (sort keys %$yaml) {
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
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36 my $ref = $yaml->{$grp};
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
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37
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
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38 next if (! ref $ref);
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
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39 next if (! defined $ref->{'total.gigabases'});
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
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40
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41 print {$fh} <<"CONTENT"
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
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42 <table>
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43 <caption>$grp</caption>
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
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44 <tr>
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
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45 <td>Total Yield (Gb)</td>
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46 <td>$ref->{'total.gigabases'}</td>
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47 </tr>
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
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48 <tr>
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49 <td>Total Reads</td>
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50 <td>$ref->{'total.reads'}</td>
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51 </tr>
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52 <tr>
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53 <td>Mean Length</td>
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54 <td>$ref->{'mean.length'}</td>
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55 </tr>
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56 <tr>
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57 <td>Median Length</td>
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58 <td>$ref->{'median.length'}</td>
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59 </tr>
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60 <tr>
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61 <td>Max Length</td>
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62 <td>$ref->{'max.length'}</td>
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63 </tr>
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64 <tr>
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65 <td>Mean Q</td>
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66 <td>$ref->{'mean.q'}</td>
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67 </tr>
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68 <tr>
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69 <td>Median Q</td>
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70 <td>$ref->{'median.q'}</td>
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71 </tr>
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72 </table>
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73 CONTENT
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74
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75 }
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76
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77 my %figs = (
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78 'length_histogram' => "Read length distribution",
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79 'q_histogram' => "Mean quality score distribution",
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
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80 'reads_per_hour' => "Yield over time",
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
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81 'cumulative_yield' => "Cumulative yield over time",
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82 'yield_summary' => "Yield by read length cutoff",
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83 'flowcell_overview' => "Median read quality per channel",
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
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84 'length_by_hour' => "Read length over time",
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85 'q_by_hour' => "Read quality over time",
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
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parents:
diff changeset
86 'length_vs_q' => "Read length vs. quality",
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
jvolkening
parents:
diff changeset
87 );
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
jvolkening
parents:
diff changeset
88
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
jvolkening
parents:
diff changeset
89 my @order = qw/
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
jvolkening
parents:
diff changeset
90 length_histogram
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
jvolkening
parents:
diff changeset
91 q_histogram
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
jvolkening
parents:
diff changeset
92 reads_per_hour
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
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parents:
diff changeset
93 cumulative_yield
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
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parents:
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94 yield_summary
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
jvolkening
parents:
diff changeset
95 flowcell_overview
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
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diff changeset
96 length_by_hour
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
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diff changeset
97 q_by_hour
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
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diff changeset
98 length_vs_q
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
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parents:
diff changeset
99 /;
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
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parents:
diff changeset
100
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
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101
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
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102 say {$fh} " <h3>QC plots</h3>";
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
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103 say {$fh} " <p>(Click on plot for high-resolution version, or in Chrome \"Open link in new tab\")</p>";
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
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diff changeset
104
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
jvolkening
parents:
diff changeset
105 for my $base (@order) {
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
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diff changeset
106
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
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107 my $caption = $figs{$base} // die "No caption found for $base";
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
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parents:
diff changeset
108
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
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parents:
diff changeset
109 # Base64-encode images
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
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diff changeset
110 my $fn_img_full = "$dir_in/$base.png";
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
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parents:
diff changeset
111 my $fn_img_screen = "$dir_in/$base.screen.png";
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
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parents:
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112 die "Failed to find or read $fn_img_full"
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
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parents:
diff changeset
113 if (! -r $fn_img_full);
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
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parents:
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114 die "Failed to find or read $fn_img_screen"
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
jvolkening
parents:
diff changeset
115 if (! -r $fn_img_screen);
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
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parents:
diff changeset
116 my $img_full = encode($fn_img_full);
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
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parents:
diff changeset
117 my $img_screen = encode($fn_img_screen);
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
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diff changeset
118
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
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119 print {$fh} <<"CONTENT"
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
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120 <a href="data:image/png;base64,$img_full">
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
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parents:
diff changeset
121 <figure>
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
jvolkening
parents:
diff changeset
122 <img src="data:image/png;base64,$img_screen" alt="$base" />
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
jvolkening
parents:
diff changeset
123 <figcaption>$caption</figcaption>
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
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parents:
diff changeset
124 </figure>
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
jvolkening
parents:
diff changeset
125 </a>
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
jvolkening
parents:
diff changeset
126 CONTENT
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
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diff changeset
127
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
jvolkening
parents:
diff changeset
128 }
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
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diff changeset
129
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
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parents:
diff changeset
130 print {$fh} footer();
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
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diff changeset
131
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
jvolkening
parents:
diff changeset
132 }
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
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diff changeset
133
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
jvolkening
parents:
diff changeset
134 sub encode {
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
jvolkening
parents:
diff changeset
135
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
jvolkening
parents:
diff changeset
136 my ($fn) = @_;
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
jvolkening
parents:
diff changeset
137 open my $in, '<:raw', $fn;
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
jvolkening
parents:
diff changeset
138 local($/) = undef;
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
jvolkening
parents:
diff changeset
139 return encode_base64(<$in>);
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
jvolkening
parents:
diff changeset
140
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
jvolkening
parents:
diff changeset
141 }
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
jvolkening
parents:
diff changeset
142
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
jvolkening
parents:
diff changeset
143 sub header {
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
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parents:
diff changeset
144
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
jvolkening
parents:
diff changeset
145 return <<'HEADER';
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
jvolkening
parents:
diff changeset
146 <?xml version="1.0" encoding="utf-8"?>
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
jvolkening
parents:
diff changeset
147 <!DOCTYPE html>
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
jvolkening
parents:
diff changeset
148 <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
jvolkening
parents:
diff changeset
149 <head>
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
jvolkening
parents:
diff changeset
150 <title></title>
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
jvolkening
parents:
diff changeset
151 <meta http-equiv="content-type" content="application/xhtml+xml; charset=utf-8" />
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
jvolkening
parents:
diff changeset
152 <style>
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
jvolkening
parents:
diff changeset
153 h2 {
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
jvolkening
parents:
diff changeset
154 padding: 0.3em;
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
jvolkening
parents:
diff changeset
155 background-color: #000000;
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
jvolkening
parents:
diff changeset
156 color: #ffffff;
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
jvolkening
parents:
diff changeset
157 margin: 1em 0 2em 0;
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
jvolkening
parents:
diff changeset
158 }
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
jvolkening
parents:
diff changeset
159 h3 {
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
jvolkening
parents:
diff changeset
160 padding: 0em 0.2em 0em 0.2em;
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
jvolkening
parents:
diff changeset
161 color: #555555;
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
jvolkening
parents:
diff changeset
162 border: solid 1px black;
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
jvolkening
parents:
diff changeset
163 border-width: 0px 0px 1px 0px;
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
jvolkening
parents:
diff changeset
164 margin: 2em 0 0.4em 0;
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
jvolkening
parents:
diff changeset
165 }
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
jvolkening
parents:
diff changeset
166 tr {
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
jvolkening
parents:
diff changeset
167 margin: 0;
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
jvolkening
parents:
diff changeset
168 }
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
jvolkening
parents:
diff changeset
169 tr:nth-child(even) {
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
jvolkening
parents:
diff changeset
170 background-color: #bbbbbb;
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
jvolkening
parents:
diff changeset
171 }
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
jvolkening
parents:
diff changeset
172 tr:nth-child(odd) {
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173 background-color: #eeeeee;
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174 }
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175 caption {
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176 text-align: left;
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177 font-weight: bold;
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178 background-color: #550000;
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179 color: #ffffff;
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
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180 padding: 0.1em 0.2em;
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181 }
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182 table {
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
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183 margin: 1em;
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184 padding: 0.3em;
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
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185 }
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186 td {
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
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187 margin: 0;
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188 padding: 0 0.4em;
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189 }
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
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190 tr td:nth-child(1) {
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
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191 color: #550000;
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
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192 }
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
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193 figure {
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194 display: table;
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195 margin: 2em 0;
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196 }
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
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197 figcaption {
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198 display: table-caption;
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199 caption-side: top;
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200 font-size: 1.1em;
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201 text-decoration: none;
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202 text-align: center;
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203 font-weight: bold;
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204 background-color: #550000;
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205 color: #ffffff;
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
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206 padding: 0.1em 0.2em;
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207 margin: 2em 0 0.7em 0;
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208 }
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209
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
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210 </style>
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211 </head>
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212 <body>
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213
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214 <h2>NanoporeQC Report</h2>
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215 HEADER
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216
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217 }
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218
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219 sub footer {
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220
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221 return <<'FOOTER';
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222
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
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223 </body>
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224 </html>
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225 FOOTER
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226
e0006d8bf849 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit b99a7d95d62b95ececc9d808f5f183b9eb718f80-dirty
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227 }