| Previous changeset 44:221ea7307999 (2018-07-12) Next changeset 46:20547000266a (2018-09-06) |
|
Commit message:
Uploaded |
|
modified:
bin/html.pm bin/js/filter.js sRNAPipe.xml tool_dependencies.xml |
| b |
| diff -r 221ea7307999 -r 263819fdda14 bin/html.pm --- a/bin/html.pm Thu Jul 12 08:56:18 2018 -0400 +++ b/bin/html.pm Thu Sep 06 10:21:30 2018 -0400 |
| [ |
| b'@@ -1,911 +1,911 @@\n-package html;\n-\n-use strict;\n-use warnings;\n-use File::Basename;\n-\n-use Exporter;\n-our @ISA = qw( Exporter );\n-our @EXPORT_OK = qw( &main_page &details_pages &menu_page &ppp_page );\n-\n-sub main_page\n-{\n-\tmy ( $dir, $file, $list_mainTabP, $current, $ma, $ma_uni, $dir_root ) = @_;\n-\tmy ( $futHashP, $uniqueTabP, $randTabP, $pngTabP ) = get_genome ( $dir, $dir_root );\n-\n-\topen my $h, \'>\', $file || die "cannot create $file $!\\n";\n-\theader ( $h );\n-\tnavbar ( $h, $list_mainTabP, $current );\n-\tprint $h "<div class=\\"container\\"><p><a class=\\"btn\\" href=\\"$current-sub.html\\">View details »</a></p></div>\\n";\n-\tfuturette( $h, $current, $pngTabP, $futHashP );\n-\tprint $h "<div class=\\"container\\"><h2>mappers #: $ma</h2><h2>unique mappers #: $ma_uni</h2> </div>\\n";\n-\tcarousel2( $h, $uniqueTabP, $randTabP, $dir_root );\n-\tfooter($h);\n-\tclose $h;\n-}\n-\n-sub menu_page\n-{\n-\tmy ( $dir, $file, $list_mainTabP, $current, $min, $max, $simin, $simax, $pimin, $pimax, $dir_root ) = @_;\n- my $html_ref = $1 if $dir =~ /$dir_root(.*)/;\n-\topen my $h, \'>\', $file || die "cannot create $file $!\\n";\n- header($h);\n- navbar ( $h, $list_mainTabP, $current );\n- span( $h, $current, $min, $max, $simin, $simax, $pimin, $pimax );\n- print $h " <div class=\\"container\\"> <div class=\\"row text-center\\"> <img src=\\"$html_ref/pie_chart.png\\"/><br />\\n";\n- print $h " <A HREF=\\"$html_ref/repartition.txt\\">text file</A><br/>\\n </div></div>";\n- footer($h);\n- close $h;\n-}\n-\n-sub details_pages\n-{\n-\tmy ( $dir_details, $prefix, $list_mainTabP, $current, $misTE, $dir_root, $ppp ) = @_;\n- my ($Hex, $HTE, $HG, $NonUniTE, $NonUniG, $UniG ) = get_subgroups( $dir_details, $current, $misTE, $dir_root );\n-\n- my $html_ref = $1.\'-PPP.html\' if $prefix =~ /$dir_root(.*)/;\n- open my $h, \'>\', $prefix.\'-TEs.html\' || die "cannot create $prefix-TEs.html $!\\n";\n- header($h);\n- navbar ( $h, $list_mainTabP, $current );\n- if ( $prefix =~ /piRNAs$/ && $ppp eq \'true\' )\n- {\n- \tprint $h " <div class=\\"container\\">";\n- \tprint $h " <p><a class=\\"btn\\" href=\\"$html_ref\\">Ping Pong Partners</a></p>\\n";\n- \tprint $h "</div>";\n- }\n- fut($h,\'Transposable elements\',$HTE);\n- carousel($h,$NonUniTE,$dir_root);\n- footer($h);\n- close $h;\n-\n- open $h, \'>\', $prefix.\'-genome.html\' || die "cannot create $prefix-genome.html $!\\n";\n- header($h);\n- navbar ( $h, $list_mainTabP, $current );\n- fut($h,\'Genome\',$HG);\n- carousel2($h,$UniG, $NonUniG,$dir_root);\n- footer($h);\n- close $h;\n-\n- open $h, \'>\', $prefix.\'-transcripts.html\' || die "cannot create $prefix-transcripts.html $!\\n";\n- header($h);\n- navbar ( $h, $list_mainTabP, $current );\n- fut($h,\'transcripts\',$Hex);\n- footer($h);\n- close $h;\n-}\n-\n-sub ppp_page\n-{\n-\tmy ( $dir, $file, $list_mainTabP, $current, $ppp, $dir_root ) = @_;\n-\n-\tmy $ppp_file = $ppp.\'ppp.txt\';\n-\topen my $h, \'>\', $file || die "cannot create $file $!\\n";\n-\theader($h);\n- \tnavbar ( $h, $list_mainTabP, $current );\n- \tprint $h \'<div class="container"> <table class="wb-tables table table-striped table-hover">\'."\\n";\n- \tprint $h \'<thead>\n- <tr>\n- <th data-sortable="true">ID</th>\n- <th data-sortable="true">overlap sum</th>\n- <th data-sortable="true">ten overlap sum</th>\n- <th data-sortable="true">mean</th>\n- <th data-sortable="true">standard deviation</th>\n- \t<th data-sortable="true">z-score</th>\n- \t<th data-sortable="true">p-value</th>\n-\t</tr>\n- </thead>\n- <tbody>\';\n-\n- \topen my $f, \'<\', $ppp_file || die "cannot open $ppp_file $!\\n";\n- \twhile ( <$f> )\n- \t{\n- \t\tchomp;\n- \t\tprint $h \'<tr>\';\n- \t\tmy ( $id, $sum, $ten, $mean, $sd, $zscore, $prob) = split /\\t/, $_;\n- \t\tif( -d "$ppp/$id" ) \n- \t\t{\n- \t\t\tmy $sub_html = $ppp.$id.\'.html\';\n- my $sub_html_ref = $1.$id if $ppp =~ /$dir_root(.*)/;\n- \t\t\tprint $h "<td> <a href=\\"$sub_html_ref.html\\">$id</a> </td>";\n-\n- \t\t\topen my $sub, \'>\', $sub_html || die "cannot create $sub_html\\n";\n- \t\t\t{\n- \t\t\t\theader($sub);\n- \t\t\t\tprint $sub "\n-\t\t\t\t\t<div align=\\"center\\">\n-\t\t\t\t\t<h2>$id</h2>\n-\t\t\t\t\t<'..b'@group = glob $group;\r\n+ foreach (my $g =0; $g <= $#group; $g++)\r\n+ {\r\n+ if ($group[$g] =~ /.*($name-subgroups-bonafide_reads-TE-.*distribution-.*\\.png)/ )\r\n+ {\r\n+ my $tmp = $1;\r\n+ push @out, $1;\r\n+ }\r\n+ }\r\n+ return (\\@out);\r\n+}\r\n+\r\n+sub get_PPP\r\n+{\r\n+ my ($dir,$name) = @_;\r\n+ my (%distri,@group);\r\n+ my $group = $dir.\'/\'.$name.\'-subgroups-bonafide_reads-TE-PPPartners-*\';\r\n+ @group = glob $group;\r\n+ \r\n+ foreach (my $g =0; $g <= $#group; $g++)\r\n+ {\r\n+ if ($group[$g] =~ /.*($name-subgroups-bonafide_reads-TE-PPPartners-.*)/ )\r\n+ {\r\n+ my $tmp = $1;\r\n+ if ($tmp =~ /PPPartners-(.*?)-sens\\.txt$/)\r\n+ {\r\n+ $distri{$1} = [\'\',\'\',\'\',\'\',\'\',\'\'] unless exists $distri{$1};\r\n+ $distri{$1}->[0] = $tmp;\r\n+ }\r\n+ elsif ($tmp =~ /PPPartners-(.*?)-antisens\\.txt$/)\r\n+ {\r\n+ $distri{$1} = [\'\',\'\',\'\',\'\',\'\',\'\'] unless exists $distri{$1};\r\n+ $distri{$1}->[1] = $tmp;\r\n+ }\r\n+ elsif ($tmp =~ /PPPartners-(.*?)-sensPPP\\.txt$/)\r\n+ {\r\n+ $distri{$1} = [\'\',\'\',\'\',\'\',\'\',\'\'] unless exists $distri{$1};\r\n+ $distri{$1}->[2] = $tmp;\r\n+ }\r\n+ elsif ($tmp =~ /PPPartners-(.*?)-antisensPPP\\.txt$/)\r\n+ {\r\n+ $distri{$1} = [\'\',\'\',\'\',\'\',\'\',\'\'] unless exists $distri{$1};\r\n+ $distri{$1}->[3] = $tmp;\r\n+ }\r\n+ elsif ($tmp =~ /PPPartners-(.*?)-overlap_size\\.txt$/)\r\n+ {\r\n+ $distri{$1} = [\'\',\'\',\'\',\'\',\'\',\'\'] unless exists $distri{$1};\r\n+ $distri{$1}->[4] = $tmp;\r\n+ }\r\n+ elsif ($tmp =~ /PPPartners-(.*?)-histogram\\.png$/)\r\n+ {\r\n+ $distri{$1} = [\'\',\'\',\'\',\'\',\'\',\'\'] unless exists $distri{$1};\r\n+ $distri{$1}->[5] = $tmp;\r\n+ }\r\n+ }\r\n+ }\r\n+ return \\%distri;\r\n+}\r\n+\r\n+sub PPPrint\r\n+{\r\n+ my ($h, $hash) = @_;\r\n+ my $cmp = 0;\r\n+ \r\n+ print $h "<div class=\\"container\\">\\n";\r\n+ print $h "<div class=\\"row text-center\\">";\r\n+ while ( my ($k,$v) = each %{$hash} )\r\n+ {\r\n+ print $h "</div><div class=\\"row text-center\\">" if $cmp != 0 && $cmp % 2 == 0;\r\n+ print $h "\r\n+ \r\n+ <div class=\\"span6\\">\r\n+ <h2>$k</h2>\r\n+ <p class=\\"featurette-p\\"> <img src=\\"$v->[5]\\"/></p>\r\n+ <p class=\\"featurette-p\\"><a href=\\"$v->[4]\\">ping pong signature</a></p>\r\n+ <p class=\\"featurette-p\\"><a href=\\"$v->[2]\\">sense reads with PPP</a></p>\r\n+ <p class=\\"featurette-p\\"><a href=\\"$v->[3]\\">reverse reads with PPP</a></p>\r\n+ <p class=\\"featurette-p\\"><a href=\\"$v->[0]\\">sense reads without PPP</a></p>\r\n+ <p class=\\"featurette-p\\"><a href=\\"$v->[1]\\">reverse reads without PPP</a></p>\r\n+ </div>\r\n+ ";\r\n+ $cmp++;\r\n+ }\r\n+ \r\n+ print $h "</div></div>";\r\n+}\r\n+\r\n+sub printDistri\r\n+{\r\n+ my ($h, $tab) = @_;\r\n+ my ($txt, $name);\r\n+ my $cmp = 0;\r\n+ print $h "<div class=\\"container\\">\\n";\r\n+ print $h "<div class=\\"row text-center\\">";\r\n+ foreach my $k (@{$tab})\r\n+ {\r\n+ if ($k =~ /(.*)-(.*)\\.png$/)\r\n+ {\r\n+ $txt = $1.\'-\'.$2.\'.txt\';\r\n+ $name = $2;\r\n+ }\r\n+ print $h "</div><div class=\\"row text-center\\">" if $cmp != 0 && $cmp % 2 == 0;\r\n+ print $h "\r\n+ \r\n+ <div class=\\"span6\\">\r\n+ <h2>$name</h2>\r\n+ <p> <img src=\\"$k\\"/></p>\r\n+ <p class=\\"featurette-p\\"><a href=\\"$txt\\">text file</a></p>\r\n+ </div>\r\n+ ";\r\n+ $cmp++;\r\n+ }\r\n+ \r\n+ print $h "</div></div>";\r\n+}\r\n+\r\n+sub mapnum\r\n+{\r\n+ my $dupmapnum = shift;\r\n+ my $dupnum_genome = shift;\r\n+ open (my $dupTE, $dupmapnum) || die "cannot open ".$dupmapnum."\\n";\r\n+ my %dupnum_TE = ();\r\n+ my $header = <$dupTE>;\r\n+ while (<$dupTE>)\r\n+ {\r\n+ chomp $_;\r\n+ my @dupline = split /\\t/, $_;\r\n+ $dupnum_TE{$dupline[0]} = $dupline[2];\r\n+ }\r\n+ close $dupTE;\r\n+ open (my $du_TE, \'>\'.$dupmapnum) || die "cannot open to write ".$dupmapnum."\\n";\r\n+ print $du_TE "sequence\\tduplicate\\tgenome map num\\tmap num\\n";\r\n+ while (my ($k, $v) = each %dupnum_TE )\r\n+ {\r\n+ my $hashRef = ${$dupnum_genome}{$k};\r\n+ print $du_TE "$k\\t$hashRef->[0]\\t$hashRef->[1]\\t$v\\n";\r\n+ }\r\n+ close $du_TE;\r\n+}\r\n+\r\n+1;\r\n' |
| b |
| diff -r 221ea7307999 -r 263819fdda14 bin/js/filter.js --- a/bin/js/filter.js Thu Jul 12 08:56:18 2018 -0400 +++ b/bin/js/filter.js Thu Sep 06 10:21:30 2018 -0400 |
| [ |
| @@ -1,20 +1,20 @@ -function search(input) { - // Declare variables - var elt, filter, uls, li, a, i; - elt = input.parentElement; - filter = input.value.toUpperCase(); - uls = elt.getElementsByClassName('thumbs'); - - // Loop through all list items, and hide those who don't match the search query - for (j = 0; j < uls.length; j++) { - li = uls[j].getElementsByTagName('li'); - for (i = 0; i < li.length; i++) { - a = li[i].getElementsByTagName("a")[0]; - if (a.innerHTML.toUpperCase().indexOf(filter) > -1) { - li[i].style.display = ""; - } else { - li[i].style.display = "none"; - } - } - } -} +function search(input) { + // Declare variables + var elt, filter, uls, li, a, i; + elt = input.parentElement; + filter = input.value.toUpperCase(); + uls = elt.getElementsByClassName('thumbs'); + + // Loop through all list items, and hide those who don't match the search query + for (j = 0; j < uls.length; j++) { + li = uls[j].getElementsByTagName('li'); + for (i = 0; i < li.length; i++) { + a = li[i].getElementsByTagName("a")[0]; + if (a.innerHTML.toUpperCase().indexOf(filter) > -1) { + li[i].style.display = ""; + } else { + li[i].style.display = "none"; + } + } + } +} |
| b |
| diff -r 221ea7307999 -r 263819fdda14 sRNAPipe.xml --- a/sRNAPipe.xml Thu Jul 12 08:56:18 2018 -0400 +++ b/sRNAPipe.xml Thu Sep 06 10:21:30 2018 -0400 |
| b |
| @@ -86,6 +86,14 @@ <requirement type="package" version="1.2">samtools</requirement> <requirement type="package" version="3.2.1">R</requirement> <requirement type="package" version="5.18.1">perl</requirement> + <requirement type="package" version="2.50">perl-getopt-long</requirement> + <requirement type="package" version="1.19">perl-parallel-forkmanager</requirement> + <requirement type="package" version="0.34" >perl-statistics-r</requirement> + <requirement type="package" version="0.29">perl-string-random</requirement> + <requirement type="package" version="3.6">r-plotrix</requirement> + <requirement type="package" version="1.14.0">bioconductor-sushi</requirement> + <requirement type="package" version="1.1_2">r-colorbrewer</requirement> + <requirement type="package" version="1.0.1">r-ggplot2</requirement> </requirements> <inputs> |
| b |
| diff -r 221ea7307999 -r 263819fdda14 tool_dependencies.xml --- a/tool_dependencies.xml Thu Jul 12 08:56:18 2018 -0400 +++ b/tool_dependencies.xml Thu Sep 06 10:21:30 2018 -0400 |
| b |
| @@ -1,27 +1,43 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="bwa" version="0.7.12"> - <repository changeset_revision="dcae4134cd62" name="package_bwa_0_7_12" owner="avowinkel" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="bedtools" version="2.24"> - <repository changeset_revision="3416a1d4a582" name="package_bedtools_2_24" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="samtools" version="1.2"> - <repository changeset_revision="f6ae3ba3f3c1" name="package_samtools_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="R" version="3.2.1"> - <repository changeset_revision="d9f7d84125b7" name="package_r_3_2_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="perl" version="5.18.1"> - <repository changeset_revision="35f117d7396b" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package>https://depot.galaxyproject.org/software/plotrix/plotrix_3.6_src_all.tar.gz</package> - <package>https://depot.galaxyproject.org/software/bioconductor-sushi/bioconductor-sushi_1.14.0_src_all.tar.gz</package> - <package>https://depot.galaxyproject.org/software/RColorBrewer/RColorBrewer_1.1-2_src_all.tar.gz</package> - <package>https://depot.galaxyproject.org/software/ggplot2/ggplot2_1.0.1_src_all.tar.gz</package> - <package>https://depot.galaxyproject.org/software/perl-statistics-r/perl-statistics-r_0.34_src_all.tar.gz</package> - <package>https://cpan.metacpan.org/authors/id/Y/YA/YANICK/Parallel-ForkManager-1.19.tar.gz</package> - <package>https://cpan.metacpan.org/authors/id/F/FA/FANGLY/Statistics-R-0.34.tar.gz</package> - <package>https://cpan.metacpan.org/authors/id/J/JV/JV/Getopt-Long-2.50.tar.gz</package> - <package>https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF/String-Random-0.29.tar.gz</package> -</tool_dependency> +<?xml version="1.0"?> +<tool_dependency> + <package name="bwa" version="0.7.12"> + <repository changeset_revision="dcae4134cd62" name="package_bwa_0_7_12" owner="avowinkel" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="bedtools" version="2.24"> + <repository changeset_revision="3416a1d4a582" name="package_bedtools_2_24" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="samtools" version="1.2"> + <repository changeset_revision="f6ae3ba3f3c1" name="package_samtools_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="R" version="3.2.1"> + <repository changeset_revision="d9f7d84125b7" name="package_r_3_2_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="perl" version="5.18.1"> + <repository changeset_revision="35f117d7396b" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="srnapipe" version="1.0"> + <install version="1.0"> + <actions> + <action type="setup_perl_environment"> + <repository changeset_revision="35f117d7396b" name="package_perl_5_18" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> + <package name="perl" version="5.18.1" /> + </repository> + <package>https://cpan.metacpan.org/authors/id/Y/YA/YANICK/Parallel-ForkManager-1.19.tar.gz</package> + <package>https://cpan.metacpan.org/authors/id/F/FA/FANGLY/Statistics-R-0.34.tar.gz</package> + <package>https://cpan.metacpan.org/authors/id/J/JV/JV/Getopt-Long-2.50.tar.gz</package> + <package>https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF/String-Random-0.29.tar.gz</package> + </action> + <action type="setup_r_environment"> + <repository changeset_revision="d9f7d84125b7" name="package_r_3_2_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> + <package name="R" version="3.2.1" /> + </repository> + <package>https://depot.galaxyproject.org/software/plotrix/plotrix_3.6_src_all.tar.gz</package> + <package>https://depot.galaxyproject.org/software/bioconductor-sushi/bioconductor-sushi_1.14.0_src_all.tar.gz</package> + <package>https://depot.galaxyproject.org/software/RColorBrewer/RColorBrewer_1.1-2_src_all.tar.gz</package> + <package>https://depot.galaxyproject.org/software/ggplot2/ggplot2_1.0.1_src_all.tar.gz</package> + <package>https://depot.galaxyproject.org/software/perl-statistics-r/perl-statistics-r_0.34_src_all.tar.gz</package> + </action> + </actions> + </install> + </package> +</tool_dependency> |