-
-
-
-
-
Uniquely mapped reads
-
-
-
-
- ";
-
- foreach my $u (@{$unique})
- {
- my $name = basename($u,'.png');
- $u = $1 if $u =~ /$dir_root(.*)/;
- print $file "
- -
- $name
-
- ";
- }
- print $file "
-
-
-
-
-
-
-
-
-
-
Reads randomly assigned
-
-
-
-
- ";
-
- foreach my $nu (@{$non_unique})
- {
- my $name = basename($nu,'.png');
- $nu = $1 if $nu =~ /$dir_root(.*)/;
- print $file "
- -
- $name
-
- ";
- }
- print $file "
-
-
-
-
-
- ";
-}
-
-sub futurette
-{
- my ($file, $name, $png, $hash) = @_;
- print $file "
-
-
-
$name
-
- ";
- foreach my $k (sort keys %{$hash})
- {
- print $file "$k
\n" ;
- }
-
- print $file "
-
";
-
- foreach my $pn (@{$png}){print $file "
![](\"$pn\"/)
";}
-
- print $file "
-
-
- ";
-}
-
-sub fut
-{
- my ($file, $name, $hash) = @_;
- print $file "
-
-
-
$name
-
- ";
-
- foreach my $k (sort { ${$hash}{$a} cmp ${$hash}{$b} } keys %{$hash})
- {
- print $file "$k
\n" ;
- }
-
- print $file "
-
-
-
- ";
-}
-
-sub get_distri_exon
-{
- my ($dir, $name) = @_;
- my (@out,@group);
- my $group = $dir.'/'.$name.'-subgroups-bonafide_reads-transcripts-*distribution-*.png';
- @group = glob $group;
- foreach (my $g =0; $g <= $#group; $g++)
- {
- if ($group[$g] =~ /.*($name-subgroups-bonafide_reads-transcripts-.*distribution-.*\.png)/ )
- {
- my $tmp = $1;
- push @out, $1;
- }
- }
- return (\@out);
-}
-
-sub get_distri_TE
-{
- my ($dir, $name) = @_;
- my (@out,@group);
- my $group = $dir.'/'.$name.'-subgroups-bonafide_reads-TE-*distribution-*.png';
- @group = glob $group;
- foreach (my $g =0; $g <= $#group; $g++)
- {
- if ($group[$g] =~ /.*($name-subgroups-bonafide_reads-TE-.*distribution-.*\.png)/ )
- {
- my $tmp = $1;
- push @out, $1;
- }
- }
- return (\@out);
-}
-
-sub get_PPP
-{
- my ($dir,$name) = @_;
- my (%distri,@group);
- my $group = $dir.'/'.$name.'-subgroups-bonafide_reads-TE-PPPartners-*';
- @group = glob $group;
-
- foreach (my $g =0; $g <= $#group; $g++)
- {
- if ($group[$g] =~ /.*($name-subgroups-bonafide_reads-TE-PPPartners-.*)/ )
- {
- my $tmp = $1;
- if ($tmp =~ /PPPartners-(.*?)-sens\.txt$/)
- {
- $distri{$1} = ['','','','','',''] unless exists $distri{$1};
- $distri{$1}->[0] = $tmp;
- }
- elsif ($tmp =~ /PPPartners-(.*?)-antisens\.txt$/)
- {
- $distri{$1} = ['','','','','',''] unless exists $distri{$1};
- $distri{$1}->[1] = $tmp;
- }
- elsif ($tmp =~ /PPPartners-(.*?)-sensPPP\.txt$/)
- {
- $distri{$1} = ['','','','','',''] unless exists $distri{$1};
- $distri{$1}->[2] = $tmp;
- }
- elsif ($tmp =~ /PPPartners-(.*?)-antisensPPP\.txt$/)
- {
- $distri{$1} = ['','','','','',''] unless exists $distri{$1};
- $distri{$1}->[3] = $tmp;
- }
- elsif ($tmp =~ /PPPartners-(.*?)-overlap_size\.txt$/)
- {
- $distri{$1} = ['','','','','',''] unless exists $distri{$1};
- $distri{$1}->[4] = $tmp;
- }
- elsif ($tmp =~ /PPPartners-(.*?)-histogram\.png$/)
- {
- $distri{$1} = ['','','','','',''] unless exists $distri{$1};
- $distri{$1}->[5] = $tmp;
- }
- }
- }
- return \%distri;
-}
-
-sub PPPrint
-{
- my ($h, $hash) = @_;
- my $cmp = 0;
-
- print $h "
\n";
- print $h "
";
- while ( my ($k,$v) = each %{$hash} )
- {
- print $h "
" if $cmp != 0 && $cmp % 2 == 0;
- print $h "
-
-
- ";
- $cmp++;
- }
-
- print $h "
";
-}
-
-sub printDistri
-{
- my ($h, $tab) = @_;
- my ($txt, $name);
- my $cmp = 0;
- print $h "
\n";
- print $h "
";
- foreach my $k (@{$tab})
- {
- if ($k =~ /(.*)-(.*)\.png$/)
- {
- $txt = $1.'-'.$2.'.txt';
- $name = $2;
- }
- print $h "
" if $cmp != 0 && $cmp % 2 == 0;
- print $h "
-
-
- ";
- $cmp++;
- }
-
- print $h "
";
-}
-
-sub mapnum
-{
- my $dupmapnum = shift;
- my $dupnum_genome = shift;
- open (my $dupTE, $dupmapnum) || die "cannot open ".$dupmapnum."\n";
- my %dupnum_TE = ();
- my $header = <$dupTE>;
- while (<$dupTE>)
- {
- chomp $_;
- my @dupline = split /\t/, $_;
- $dupnum_TE{$dupline[0]} = $dupline[2];
- }
- close $dupTE;
- open (my $du_TE, '>'.$dupmapnum) || die "cannot open to write ".$dupmapnum."\n";
- print $du_TE "sequence\tduplicate\tgenome map num\tmap num\n";
- while (my ($k, $v) = each %dupnum_TE )
- {
- my $hashRef = ${$dupnum_genome}{$k};
- print $du_TE "$k\t$hashRef->[0]\t$hashRef->[1]\t$v\n";
- }
- close $du_TE;
-}
-
-1;
+package html;
+
+use strict;
+use warnings;
+use File::Basename;
+
+use Exporter;
+our @ISA = qw( Exporter );
+our @EXPORT_OK = qw( &main_page &details_pages &menu_page &ppp_page );
+
+sub main_page
+{
+ my ( $dir, $file, $list_mainTabP, $current, $ma, $ma_uni, $dir_root ) = @_;
+ my ( $futHashP, $uniqueTabP, $randTabP, $pngTabP ) = get_genome ( $dir, $dir_root );
+
+ open my $h, '>', $file || die "cannot create $file $!\n";
+ header ( $h );
+ navbar ( $h, $list_mainTabP, $current );
+ print $h "
\n";
+ futurette( $h, $current, $pngTabP, $futHashP );
+ print $h "
mappers #: $ma
unique mappers #: $ma_uni
\n";
+ carousel2( $h, $uniqueTabP, $randTabP, $dir_root );
+ footer($h);
+ close $h;
+}
+
+sub menu_page
+{
+ my ( $dir, $file, $list_mainTabP, $current, $min, $max, $simin, $simax, $pimin, $pimax, $dir_root ) = @_;
+ my $html_ref = $1 if $dir =~ /$dir_root(.*)/;
+ open my $h, '>', $file || die "cannot create $file $!\n";
+ header($h);
+ navbar ( $h, $list_mainTabP, $current );
+ span( $h, $current, $min, $max, $simin, $simax, $pimin, $pimax );
+ print $h "
";
+ footer($h);
+ close $h;
+}
+
+sub details_pages
+{
+ my ( $dir_details, $prefix, $list_mainTabP, $current, $misTE, $dir_root, $ppp ) = @_;
+ my ($Hex, $HTE, $HG, $NonUniTE, $NonUniG, $UniG ) = get_subgroups( $dir_details, $current, $misTE, $dir_root );
+
+ my $html_ref = $1.'-PPP.html' if $prefix =~ /$dir_root(.*)/;
+ open my $h, '>', $prefix.'-TEs.html' || die "cannot create $prefix-TEs.html $!\n";
+ header($h);
+ navbar ( $h, $list_mainTabP, $current );
+ if ( $prefix =~ /piRNAs$/ && $ppp eq 'true' )
+ {
+ print $h "
";
+ }
+ fut($h,'Transposable elements',$HTE);
+ carousel($h,$NonUniTE,$dir_root);
+ footer($h);
+ close $h;
+
+ open $h, '>', $prefix.'-genome.html' || die "cannot create $prefix-genome.html $!\n";
+ header($h);
+ navbar ( $h, $list_mainTabP, $current );
+ fut($h,'Genome',$HG);
+ carousel2($h,$UniG, $NonUniG,$dir_root);
+ footer($h);
+ close $h;
+
+ open $h, '>', $prefix.'-transcripts.html' || die "cannot create $prefix-transcripts.html $!\n";
+ header($h);
+ navbar ( $h, $list_mainTabP, $current );
+ fut($h,'transcripts',$Hex);
+ footer($h);
+ close $h;
+}
+
+sub ppp_page
+{
+ my ( $dir, $file, $list_mainTabP, $current, $ppp, $dir_root ) = @_;
+
+ my $ppp_file = $ppp.'ppp.txt';
+ open my $h, '>', $file || die "cannot create $file $!\n";
+ header($h);
+ navbar ( $h, $list_mainTabP, $current );
+ print $h '
'."\n";
+ print $h '
+
+ | ID |
+ overlap sum |
+ ten overlap sum |
+ mean |
+ standard deviation |
+ z-score |
+ p-value |
+
+
+ ';
+
+ open my $f, '<', $ppp_file || die "cannot open $ppp_file $!\n";
+ while ( <$f> )
+ {
+ chomp;
+ print $h '';
+ my ( $id, $sum, $ten, $mean, $sd, $zscore, $prob) = split /\t/, $_;
+ if( -d "$ppp/$id" )
+ {
+ my $sub_html = $ppp.$id.'.html';
+ my $sub_html_ref = $1.$id if $ppp =~ /$dir_root(.*)/;
+ print $h "| $id | ";
+
+ open my $sub, '>', $sub_html || die "cannot create $sub_html\n";
+ {
+ header($sub);
+ print $sub "
+ ";
+ footer($sub);
+ }
+ close $sub;
+
+ }
+ else { print $h " $id | \n"; }
+ print $h " $sum | $ten | $mean | $sd | $zscore | $prob | \n";
+
+ print $h '
';
+ }
+ close $f;
+ print $h "
";
+ footer($h);
+ close $h;
+}
+
+sub get_genome
+{
+ my ( $dir, $dir_root ) = @_;
+ my ( %hash, @group, @Unique, @NonUnique, @png );
+
+ my $fut = $dir.'/*';
+ my @fut = glob $fut;
+
+
+ foreach my $fr ( @fut )
+ {
+ my $f = $1 if $fr =~ /$dir_root(.*)/;
+ if ( $fr =~ /.*Gviz/ )
+ {
+ my $nu = $fr.'/rand/*';
+ @NonUnique = glob $nu;
+ my $u = $fr.'/unique/*';
+ @Unique = glob $u;
+ }
+ elsif ( $f =~ /.*distribution\.txt$/ ) { $hash{'mappers size distribution (txt)'} = $f; }
+ elsif ( $f =~ /.*distribution\.png$/ ) { push @png, $f; }
+ elsif ( $f =~ /.*unique\.fastq$/ ) { $hash{'unique mappers (fastq.gz)'} = $f.'.gz'; `gzip $fr`; }
+ elsif ( $f =~ /.*rejected\.fastq$/ ) { $hash{'unmapped (fastq.gz)'} = $f.'.gz'; `gzip $fr`; }
+ elsif ( $f =~ /.*all\.fastq$/ ) { $hash{'mappers (fastq.gz)'} = $f.'.gz'; `gzip $fr`; }
+ elsif ( $f =~ /.*dup_unique\.txt$/ ) { $hash{'unique mappers (txt)'} = $f; }
+ elsif ( $f =~ /.*dup_mapnum\.txt$/ ) { $hash{'mappers (txt)'} = $f; }
+ elsif ( $f =~ /.*dup_nonmapp\.txt$/ ) { $hash{'unmapped (txt)'} = $f; }
+ elsif ( $f =~ /.*_unique_sorted\.bam$/ ) { $hash{'unique alignment (bam)'} = $f; }
+ elsif ( $f =~ /.*_sorted\.bam$/ ) { $hash{'alignment (bam)'} = $f; }
+ elsif ( $f =~ /.*unique_plus.bedgraph/) { $hash{'bedgraph unique plus strand'} = $f; }
+ elsif ( $f =~ /.*unique_minus.bedgraph/) { $hash{'bedgraph unique minus strand'} = $f; }
+ elsif ( $f =~ /.*plus.bedgraph/) { $hash{'bedgraph plus strand'} = $f; }
+ elsif ( $f =~ /.*minus.bedgraph/) { $hash{'bedgraph minus strand'} = $f; }
+ else { unlink $fr; }
+ }
+ return (\%hash, \@Unique, \@NonUnique, \@png);
+}
+
+sub span
+{
+ my ( $file, $name, $min, $max, $simin, $simax, $pimin, $pimax ) = @_;
+
+ print $file "
+
+
+
+
Bonafide
+ reads of size between $min and $max
with no mi, sn, t and r RNAs
+
Genome
+
TE
+
Transcripts
+
+
+
+
+
+";
+}
+
+sub get_subgroups
+{
+ my ( $dir, $name, $misTE, $dir_root ) = @_;
+ my (%Hex, %HTE, %HG, @group, @png, @pngTE, @NonUniTE, @UniG, @NonUniG );
+
+ my $fut = $dir.'/*';
+ my @fut = glob $fut;
+ my $f ='';
+ foreach my $fr ( @fut )
+ {
+ $f = $1 if $fr =~ /$dir_root(.*)/;
+
+ if ( $f =~ /genome_unique_sorted\.bam$/ ) { $HG{'genome unique mappers (sorted bam)'} = $f; }
+ elsif ( $f =~ /genome_sorted\.bam$/ ) { $HG{'genome mappers (sorted bam)'} = $f; }
+ elsif ( $f =~ /miRNAs_reads_counts\.txt$/ ) { $HG{'miRNAs per type (txt)'} = $f; }
+ elsif ( $f =~ /genome_unique_plus\.bedgraph$/) { $HG{'bedgraph unique plus strand'} = $f; }
+ elsif ( $f =~ /genome_unique_minus\.bedgraph$/) { $HG{'bedgraph unique minus strand'} = $f; }
+ elsif ( $f =~ /genome_plus\.bedgraph$/) { $HG{'bedgraph plus strand'} = $f; }
+ elsif ( $f =~ /genome_minus\.bedgraph$/) { $HG{'bedgraph minus strand'} = $f; }
+ elsif ( $f =~ /TEs_plus\.bedgraph$/) { $HTE{'bedgraph plus strand'} = $f; }
+ elsif ( $f =~ /TEs_minus\.bedgraph$/) { $HTE{'bedgraph minus strand'} = $f; }
+ elsif ( $f =~ /transcripts_sorted\.bam$/) { $Hex{'transcripts mappers (sorted bam)'} = $f;}
+ elsif ( $f =~ /transcripts_unique_sorted\.bam$/) { $Hex{'transcripts unique mappers (sorted bam)'} = $f;}
+ elsif ( $f =~ /transcripts_reads_counts\.txt$/) { $Hex{'read number per transcript (txt)'} = $f;}
+ elsif ( $f =~ /TEs_reads_counts\.txt$/) { $HTE{"read number per TE 0 to $misTE mismatches (txt)"} = $f; }
+ elsif ( $f =~ /TEs_reads_counts_mismatches\.txt$/) { $HTE{"read number per TE with 1 to $misTE mismatches (txt)"} = $f; }
+ elsif ( $f =~ /TEs_reads_counts_nomismatches\.txt$/) { $HTE{'read number per TE with no mismatch (txt)'} = $f; }
+ elsif ( $f =~ /TEs_unique_sorted\.bam$/) { $HTE{'TEs unique mappers (sorted bam)'} = $f; }
+ elsif ( $f =~ /TEs_sorted\.bam$/) { $HTE{'TEs mappers (sorted bam)'} = $f; }
+ elsif ( $fr =~ /.*Gviz_TEs/ )
+ {
+ my $nu = $fr.'/*';
+ @NonUniTE = glob $nu;
+ }
+ elsif ( $fr =~ /.*Gviz_genome/ )
+ {
+ my $nu = $fr.'/rand/*';
+ @NonUniG = glob $nu;
+ my $u = $fr.'/unique/*';
+ @UniG = glob $u;
+ }
+ else { unlink $fr; }
+ }
+ return (\%Hex, \%HTE, \%HG, \@NonUniTE, \@NonUniG, \@UniG);
+}
+
+sub header
+{
+ my $file = shift;
+ print $file "
+
+
+
+
+
pipeline
+
+
+
+
+
+
+
+
+
+
+ ";
+}
+
+sub navbar
+{
+ my ( $file, $fastq, $actif ) = @_;
+
+ print $file "
+
+
+
+
+
Report
+
+
+ ";
+ for (my $i = 0 ; $i <= $#{$fastq}; $i++)
+ {
+ # my $fa = basename($fastq->[$i],'.dat');
+ my $fa = $fastq->[$i];
+ if ($actif eq $fa){ print $file "- [$i].html\">$fa
";}
+ else {print $file "- [$i].html\">$fa
" ;}
+ }
+ print $file "
+
+
+
+
+
";
+}
+
+sub footer
+{
+ my $file = shift;
+ print $file "
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ ";
+}
+
+sub carousel
+{
+ my ($file, $non_unique, $dir_root) = @_;
+ my $ac = 0;
+ print $file "
+
+
+
+
+
+
+
Reads randomly assigned
+
+
+
+
+ ";
+ foreach my $u (@{$non_unique})
+ {
+ my $name = basename($u,'.png');
+ $u = $1 if $u =~ /$dir_root(.*)/;
+ print $file "
+ -
+ $name
+
+ ";
+ }
+ print $file "
+
+
+
+
+
+ ";
+}
+
+sub carousel2
+{
+ my ($file, $unique, $non_unique, $dir_root) = @_;
+ print $file "
+
+
+
+
+
+
+
Uniquely mapped reads
+
+
+
+
+ ";
+
+ foreach my $u (@{$unique})
+ {
+ my $name = basename($u,'.png');
+ $u = $1 if $u =~ /$dir_root(.*)/;
+ print $file "
+ -
+ $name
+
+ ";
+ }
+ print $file "
+
+
+
+
+
+
+
+
+
+
Reads randomly assigned
+
+
+
+
+ ";
+
+ foreach my $nu (@{$non_unique})
+ {
+ my $name = basename($nu,'.png');
+ $nu = $1 if $nu =~ /$dir_root(.*)/;
+ print $file "
+ -
+ $name
+
+ ";
+ }
+ print $file "
+
+
+
+
+
+ ";
+}
+
+sub futurette
+{
+ my ($file, $name, $png, $hash) = @_;
+ print $file "
+
+
+
$name
+
+ ";
+ foreach my $k (sort keys %{$hash})
+ {
+ print $file "$k
\n" ;
+ }
+
+ print $file "
+
";
+
+ foreach my $pn (@{$png}){print $file "
";}
+
+ print $file "
+
+
+ ";
+}
+
+sub fut
+{
+ my ($file, $name, $hash) = @_;
+ print $file "
+
+
+
$name
+
+ ";
+
+ foreach my $k (sort { ${$hash}{$a} cmp ${$hash}{$b} } keys %{$hash})
+ {
+ print $file "$k
\n" ;
+ }
+
+ print $file "
+
+
+
+ ";
+}
+
+sub get_distri_exon
+{
+ my ($dir, $name) = @_;
+ my (@out,@group);
+ my $group = $dir.'/'.$name.'-subgroups-bonafide_reads-transcripts-*distribution-*.png';
+ @group = glob $group;
+ foreach (my $g =0; $g <= $#group; $g++)
+ {
+ if ($group[$g] =~ /.*($name-subgroups-bonafide_reads-transcripts-.*distribution-.*\.png)/ )
+ {
+ my $tmp = $1;
+ push @out, $1;
+ }
+ }
+ return (\@out);
+}
+
+sub get_distri_TE
+{
+ my ($dir, $name) = @_;
+ my (@out,@group);
+ my $group = $dir.'/'.$name.'-subgroups-bonafide_reads-TE-*distribution-*.png';
+ @group = glob $group;
+ foreach (my $g =0; $g <= $#group; $g++)
+ {
+ if ($group[$g] =~ /.*($name-subgroups-bonafide_reads-TE-.*distribution-.*\.png)/ )
+ {
+ my $tmp = $1;
+ push @out, $1;
+ }
+ }
+ return (\@out);
+}
+
+sub get_PPP
+{
+ my ($dir,$name) = @_;
+ my (%distri,@group);
+ my $group = $dir.'/'.$name.'-subgroups-bonafide_reads-TE-PPPartners-*';
+ @group = glob $group;
+
+ foreach (my $g =0; $g <= $#group; $g++)
+ {
+ if ($group[$g] =~ /.*($name-subgroups-bonafide_reads-TE-PPPartners-.*)/ )
+ {
+ my $tmp = $1;
+ if ($tmp =~ /PPPartners-(.*?)-sens\.txt$/)
+ {
+ $distri{$1} = ['','','','','',''] unless exists $distri{$1};
+ $distri{$1}->[0] = $tmp;
+ }
+ elsif ($tmp =~ /PPPartners-(.*?)-antisens\.txt$/)
+ {
+ $distri{$1} = ['','','','','',''] unless exists $distri{$1};
+ $distri{$1}->[1] = $tmp;
+ }
+ elsif ($tmp =~ /PPPartners-(.*?)-sensPPP\.txt$/)
+ {
+ $distri{$1} = ['','','','','',''] unless exists $distri{$1};
+ $distri{$1}->[2] = $tmp;
+ }
+ elsif ($tmp =~ /PPPartners-(.*?)-antisensPPP\.txt$/)
+ {
+ $distri{$1} = ['','','','','',''] unless exists $distri{$1};
+ $distri{$1}->[3] = $tmp;
+ }
+ elsif ($tmp =~ /PPPartners-(.*?)-overlap_size\.txt$/)
+ {
+ $distri{$1} = ['','','','','',''] unless exists $distri{$1};
+ $distri{$1}->[4] = $tmp;
+ }
+ elsif ($tmp =~ /PPPartners-(.*?)-histogram\.png$/)
+ {
+ $distri{$1} = ['','','','','',''] unless exists $distri{$1};
+ $distri{$1}->[5] = $tmp;
+ }
+ }
+ }
+ return \%distri;
+}
+
+sub PPPrint
+{
+ my ($h, $hash) = @_;
+ my $cmp = 0;
+
+ print $h "
\n";
+ print $h "
";
+ while ( my ($k,$v) = each %{$hash} )
+ {
+ print $h "
" if $cmp != 0 && $cmp % 2 == 0;
+ print $h "
+
+
+ ";
+ $cmp++;
+ }
+
+ print $h "
";
+}
+
+sub printDistri
+{
+ my ($h, $tab) = @_;
+ my ($txt, $name);
+ my $cmp = 0;
+ print $h "
\n";
+ print $h "
";
+ foreach my $k (@{$tab})
+ {
+ if ($k =~ /(.*)-(.*)\.png$/)
+ {
+ $txt = $1.'-'.$2.'.txt';
+ $name = $2;
+ }
+ print $h "
" if $cmp != 0 && $cmp % 2 == 0;
+ print $h "
+
+
+ ";
+ $cmp++;
+ }
+
+ print $h "
";
+}
+
+sub mapnum
+{
+ my $dupmapnum = shift;
+ my $dupnum_genome = shift;
+ open (my $dupTE, $dupmapnum) || die "cannot open ".$dupmapnum."\n";
+ my %dupnum_TE = ();
+ my $header = <$dupTE>;
+ while (<$dupTE>)
+ {
+ chomp $_;
+ my @dupline = split /\t/, $_;
+ $dupnum_TE{$dupline[0]} = $dupline[2];
+ }
+ close $dupTE;
+ open (my $du_TE, '>'.$dupmapnum) || die "cannot open to write ".$dupmapnum."\n";
+ print $du_TE "sequence\tduplicate\tgenome map num\tmap num\n";
+ while (my ($k, $v) = each %dupnum_TE )
+ {
+ my $hashRef = ${$dupnum_genome}{$k};
+ print $du_TE "$k\t$hashRef->[0]\t$hashRef->[1]\t$v\n";
+ }
+ close $du_TE;
+}
+
+1;
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";
+ }
+ }
+ }
+}
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
@@ -86,6 +86,14 @@
samtools
R
perl
+
perl-getopt-long
+
perl-parallel-forkmanager
+
perl-statistics-r
+
perl-string-random
+
r-plotrix
+
bioconductor-sushi
+
r-colorbrewer
+
r-ggplot2
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
@@ -1,27 +1,43 @@
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- https://depot.galaxyproject.org/software/plotrix/plotrix_3.6_src_all.tar.gz
- https://depot.galaxyproject.org/software/bioconductor-sushi/bioconductor-sushi_1.14.0_src_all.tar.gz
- https://depot.galaxyproject.org/software/RColorBrewer/RColorBrewer_1.1-2_src_all.tar.gz
- https://depot.galaxyproject.org/software/ggplot2/ggplot2_1.0.1_src_all.tar.gz
- https://depot.galaxyproject.org/software/perl-statistics-r/perl-statistics-r_0.34_src_all.tar.gz
- https://cpan.metacpan.org/authors/id/Y/YA/YANICK/Parallel-ForkManager-1.19.tar.gz
- https://cpan.metacpan.org/authors/id/F/FA/FANGLY/Statistics-R-0.34.tar.gz
- https://cpan.metacpan.org/authors/id/J/JV/JV/Getopt-Long-2.50.tar.gz
- https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF/String-Random-0.29.tar.gz
-
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ https://cpan.metacpan.org/authors/id/Y/YA/YANICK/Parallel-ForkManager-1.19.tar.gz
+ https://cpan.metacpan.org/authors/id/F/FA/FANGLY/Statistics-R-0.34.tar.gz
+ https://cpan.metacpan.org/authors/id/J/JV/JV/Getopt-Long-2.50.tar.gz
+ https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF/String-Random-0.29.tar.gz
+
+
+
+
+
+ https://depot.galaxyproject.org/software/plotrix/plotrix_3.6_src_all.tar.gz
+ https://depot.galaxyproject.org/software/bioconductor-sushi/bioconductor-sushi_1.14.0_src_all.tar.gz
+ https://depot.galaxyproject.org/software/RColorBrewer/RColorBrewer_1.1-2_src_all.tar.gz
+ https://depot.galaxyproject.org/software/ggplot2/ggplot2_1.0.1_src_all.tar.gz
+ https://depot.galaxyproject.org/software/perl-statistics-r/perl-statistics-r_0.34_src_all.tar.gz
+
+
+
+
+
![](\"$html_ref/pie_chart.png\"/)
![](\"$id/histogram.png\"/)