| Previous changeset 59:eeb89c3331ad (2018-10-23) Next changeset 61:9185ca0a7b43 (2019-01-16) |
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Commit message:
Fix for spaces in datasets names. |
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modified:
bin/align.pm bin/html.pm bin/ppp.pm bin/sRNAPipe.pl sRNAPipe.xml |
| b |
| diff -r eeb89c3331ad -r 9645d995fb3c bin/align.pm --- a/bin/align.pm Tue Oct 23 11:02:17 2018 -0400 +++ b/bin/align.pm Wed Oct 24 07:40:20 2018 -0400 |
| b |
| @@ -34,7 +34,7 @@ my $to_index = shift; my $log = shift; my $index_log = $to_index.'_index.err'; - `bwa index $to_index 2> $index_log`; + `bwa index '$to_index' 2> '$index_log'`; print $log "Creating index for $to_index\n"; } @@ -412,9 +412,9 @@ $view_err = $1.'_view.err'; $sort_err = $1.'_sort.err'; } - `samtools view -Shb --threads $number_of_cpus $sam 2> $view_err | samtools sort -O BAM --threads $number_of_cpus /dev/stdin 2> $sort_err > $bam_sorted`; - `bedtools genomecov -scale $scale -strand + -bga -ibam $bam_sorted > $bedgraphP`; - `bedtools genomecov -scale $scale -strand - -bga -ibam $bam_sorted > $bedgraphM`; + `samtools view -Shb --threads $number_of_cpus '$sam' 2> '$view_err' | samtools sort -O BAM --threads $number_of_cpus /dev/stdin 2> '$sort_err' > '$bam_sorted'`; + `bedtools genomecov -scale $scale -strand + -bga -ibam '$bam_sorted' > '$bedgraphP'`; + `bedtools genomecov -scale $scale -strand - -bga -ibam '$bam_sorted' > '$bedgraphM'`; } sub sam_sorted_bam @@ -428,7 +428,7 @@ $sort_err = $1.'_sort.err'; } - `samtools view -Shb --threads $number_of_cpus $sam 2> $view_err | samtools sort -O BAM --threads $number_of_cpus /dev/stdin 2> $sort_err > $bam_sorted`; + `samtools view -Shb --threads $number_of_cpus '$sam' 2> '$view_err' | samtools sort -O BAM --threads $number_of_cpus /dev/stdin 2> '$sort_err' > '$bam_sorted'`; } sub BWA_call @@ -436,8 +436,8 @@ my ( $index, $fastq, $sam, $mismatches, $number_of_cpus, $report ) = @_; my ( $aln_err, $samse_err, $seq_num ) = ( $sam.'_aln.err', $sam.'_samse.err', 0 ); print $report "-----------------------------\n"; - print $report "bwa aln -t $number_of_cpus -n $mismatches $index $fastq 2> $aln_err | bwa samse $index /dev/stdin $fastq 2> $samse_err > $sam\n"; - `bwa aln -t $number_of_cpus -n $mismatches $index $fastq 2> $aln_err | bwa samse $index /dev/stdin $fastq 2> $samse_err > $sam `; + print $report "bwa aln -t $number_of_cpus -n $mismatches '$index' '$fastq' 2> '$aln_err' | bwa samse $index /dev/stdin '$fastq' 2> '$samse_err' > '$sam'\n"; + `bwa aln -t $number_of_cpus -n $mismatches '$index' '$fastq' 2> '$aln_err' | bwa samse $index /dev/stdin '$fastq' 2> '$samse_err' > '$sam' `; } sub rpms_rpkm |
| b |
| diff -r eeb89c3331ad -r 9645d995fb3c bin/html.pm --- a/bin/html.pm Tue Oct 23 11:02:17 2018 -0400 +++ b/bin/html.pm Wed Oct 24 07:40:20 2018 -0400 |
| [ |
| b'@@ -10,25 +10,25 @@\n \r\n sub main_page\r\n {\r\n-\tmy ( $dir, $file, $list_mainTabP, $current, $ma, $ma_uni, $dir_root ) = @_;\r\n-\tmy ( $futHashP, $uniqueTabP, $randTabP, $pngTabP ) = get_genome ( $dir, $dir_root );\r\n+ my ( $dir, $file, $list_mainTabP, $current, $ma, $ma_uni, $dir_root ) = @_;\r\n+ my ( $futHashP, $uniqueTabP, $randTabP, $pngTabP ) = get_genome ( $dir, $dir_root );\r\n \r\n-\topen my $h, \'>\', $file || die "cannot create $file $!\\n";\r\n-\theader ( $h );\r\n-\tnavbar ( $h, $list_mainTabP, $current );\r\n-\tprint $h "<div class=\\"container\\"><p><a class=\\"btn\\" href=\\"$current-sub.html\\">View details »</a></p></div>\\n";\r\n-\tfuturette( $h, $current, $pngTabP, $futHashP );\r\n-\tprint $h "<div class=\\"container\\"><h2>mappers #: $ma</h2><h2>unique mappers #: $ma_uni</h2> </div>\\n";\r\n-\tcarousel2( $h, $uniqueTabP, $randTabP, $dir_root );\r\n-\tfooter($h);\r\n-\tclose $h;\r\n+ open my $h, \'>\', $file || die "cannot create $file $!\\n";\r\n+ header ( $h );\r\n+ navbar ( $h, $list_mainTabP, $current );\r\n+ print $h "<div class=\\"container\\"><p><a class=\\"btn\\" href=\\"$current-sub.html\\">View details »</a></p></div>\\n";\r\n+ futurette( $h, $current, $pngTabP, $futHashP );\r\n+ print $h "<div class=\\"container\\"><h2>mappers #: $ma</h2><h2>unique mappers #: $ma_uni</h2> </div>\\n";\r\n+ carousel2( $h, $uniqueTabP, $randTabP, $dir_root );\r\n+ footer($h);\r\n+ close $h;\r\n }\r\n \r\n sub menu_page\r\n {\r\n-\tmy ( $dir, $file, $list_mainTabP, $current, $min, $max, $simin, $simax, $pimin, $pimax, $dir_root ) = @_;\r\n+ my ( $dir, $file, $list_mainTabP, $current, $min, $max, $simin, $simax, $pimin, $pimax, $dir_root ) = @_;\r\n my $html_ref = $1 if $dir =~ /$dir_root(.*)/;\r\n-\topen my $h, \'>\', $file || die "cannot create $file $!\\n";\r\n+ open my $h, \'>\', $file || die "cannot create $file $!\\n";\r\n header($h);\r\n navbar ( $h, $list_mainTabP, $current );\r\n span( $h, $current, $min, $max, $simin, $simax, $pimin, $pimax );\r\n@@ -40,7 +40,7 @@\n \r\n sub details_pages\r\n {\r\n-\tmy ( $dir_details, $prefix, $list_mainTabP, $current, $misTE, $dir_root, $ppp ) = @_;\r\n+ my ( $dir_details, $prefix, $list_mainTabP, $current, $misTE, $dir_root, $ppp ) = @_;\r\n my ($Hex, $HTE, $HG, $NonUniTE, $NonUniG, $UniG ) = get_subgroups( $dir_details, $current, $misTE, $dir_root );\r\n \r\n my $html_ref = $1.\'-PPP.html\' if $prefix =~ /$dir_root(.*)/;\r\n@@ -49,9 +49,9 @@\n navbar ( $h, $list_mainTabP, $current );\r\n if ( $prefix =~ /piRNAs$/ && $ppp eq \'true\' )\r\n {\r\n- \tprint $h " <div class=\\"container\\">";\r\n- \tprint $h " <p><a class=\\"btn\\" href=\\"$html_ref\\">Ping Pong Partners</a></p>\\n";\r\n- \tprint $h "</div>";\r\n+ print $h " <div class=\\"container\\">";\r\n+ print $h " <p><a class=\\"btn\\" href=\\"$html_ref\\">Ping Pong Partners</a></p>\\n";\r\n+ print $h "</div>";\r\n }\r\n fut($h,\'Transposable elements\',$HTE);\r\n carousel($h,$NonUniTE,$dir_root);\r\n@@ -76,14 +76,14 @@\n \r\n sub ppp_page\r\n {\r\n-\tmy ( $dir, $file, $list_mainTabP, $current, $ppp, $dir_root ) = @_;\r\n+ my ( $dir, $file, $list_mainTabP, $current, $ppp, $dir_root ) = @_;\r\n \r\n-\tmy $ppp_file = $ppp.\'ppp.txt\';\r\n-\topen my $h, \'>\', $file || die "cannot create $file $!\\n";\r\n-\theader($h);\r\n- \tnavbar ( $h, $list_mainTabP, $current );\r\n- \tprint $h \'<div class="container"> <table class="wb-tables table table-striped table-hover">\'."\\n";\r\n- \tprint $h \'<thead>\r\n+ my $ppp_file = $ppp.\'ppp.txt\';\r\n+ open my $h, \'>\', $file || die "cannot create $file $!\\n";\r\n+ header($h);\r\n+ navbar ( $h, $list_mainTabP, $current );\r\n+ print $h \'<div class="container"> <table class="wb-tables table table-striped table-hover">\'."\\n";\r\n+ print $h \'<thead>\r\n <tr>\r\n <th data-sortable="true">ID</th>\r\n <th data-sortable="true">overlap sum</th>\r\n@@ -96,22 +96,22 @@\n </thead>\r\n <tbody>\';\r\n \r\n- \topen my $f, \'<\', $ppp_file || die "cannot open $ppp_file $!\\n";\r\n- \twhile ( <$f> )\r\n- \t{\r\n- \t\tchomp;\r\n- \t\tprint $h \'<tr>\';\r\n- \t\tmy ( $id, $sum, $ten, $mean, $sd, $zscore, $prob) = split /\\t/, $_;\r\n- \t\tif( -d "$ppp/$id" ) \r\n- \t\t{\r\n- \t\t\tmy $sub_html = $ppp.'..b' mismatches (txt)"} = $f; }\r\n elsif ( $f =~ /TEs_reads_counts_mismatches\\.txt$/) { $HTE{"read number per TE with 1 to $misTE mismatches (txt)"} = $f; }\r\n elsif ( $f =~ /TEs_reads_counts_nomismatches\\.txt$/) { $HTE{\'read number per TE with no mismatch (txt)\'} = $f; }\r\n elsif ( $f =~ /TEs_unique_sorted\\.bam$/) { $HTE{\'TEs unique mappers (sorted bam)\'} = $f; }\r\n elsif ( $f =~ /TEs_sorted\\.bam$/) { $HTE{\'TEs mappers (sorted bam)\'} = $f; }\r\n-\t\telsif ( $fr =~ /.*Gviz_TEs/ )\r\n-\t\t{\r\n-\t\t\tmy $nu = $fr.\'/*\';\r\n-\t\t\t@NonUniTE = glob $nu;\r\n-\t\t}\r\n-\t\telsif ( $fr =~ /.*Gviz_genome/ )\r\n-\t\t{\r\n-\t\t\tmy $nu = $fr.\'/rand/*\';\r\n-\t\t\t@NonUniG = glob $nu;\r\n-\t\t\tmy $u = $fr.\'/unique/*\';\r\n-\t\t\t@UniG = glob $u;\r\n-\t\t}\r\n+ elsif ( $fr =~ /.*Gviz_TEs/ )\r\n+ {\r\n+ my $nu = "\'$fr\'".\'/*\';\r\n+ @NonUniTE = glob $nu;\r\n+ }\r\n+ elsif ( $fr =~ /.*Gviz_genome/ )\r\n+ {\r\n+ my $nu = "\'$fr\'".\'/rand/*\';\r\n+ @NonUniG = glob $nu;\r\n+ my $u = "\'$fr\'".\'/unique/*\';\r\n+ @UniG = glob $u;\r\n+ }\r\n else { unlink $fr; }\r\n }\r\n return (\\%Hex, \\%HTE, \\%HG, \\@NonUniTE, \\@NonUniG, \\@UniG);\r\n@@ -480,7 +479,7 @@\n sub navbar\r\n {\r\n my ( $file, $fastq, $actif ) = @_;\r\n- \r\n+\r\n print $file "\r\n <div class=\\"navbar navbar-inverse navbar-fixed-top\\">\r\n <div class=\\"navbar-inner\\">\r\n@@ -526,7 +525,7 @@\n <script type=\\"text/javascript\\" src=\\"js/jquery.js\\"></script>\r\n <script type=\\"text/javascript\\" src=\\"js/jquery-1.3.2.js\\"></script>\r\n <script type=\\"text/javascript\\" src=\\"js/jquery.galleriffic.js\\"></script>\r\n- <script type=\\"text/javascript\\" src=\\"js/jquery.opacityrollover.js\\"></script> \r\n+ <script type=\\"text/javascript\\" src=\\"js/jquery.opacityrollover.js\\"></script>\r\n <script type=\\"text/javascript\\" src=\\"js/bootstrap-table.js\\"></script>\r\n <script type=\\"text/javascript\\" src=\\"js/bootstrap.min.js\\"></script>\r\n <script type=\\"text/javascript\\">\r\n@@ -613,7 +612,7 @@\n ";\r\n foreach my $u (@{$non_unique})\r\n {\r\n- \tmy $name = basename($u,\'.png\');\r\n+ my $name = basename($u,\'.png\');\r\n $u = $1 if $u =~ /$dir_root(.*)/;\r\n print $file "\r\n <li>\r\n@@ -652,7 +651,7 @@\n \r\n foreach my $u (@{$unique})\r\n {\r\n- \tmy $name = basename($u,\'.png\');\r\n+ my $name = basename($u,\'.png\');\r\n $u = $1 if $u =~ /$dir_root(.*)/;\r\n print $file "\r\n <li>\r\n@@ -682,7 +681,7 @@\n \r\n foreach my $nu (@{$non_unique})\r\n {\r\n- \tmy $name = basename($nu,\'.png\');\r\n+ my $name = basename($nu,\'.png\');\r\n $nu = $1 if $nu =~ /$dir_root(.*)/;\r\n print $file "\r\n <li>\r\n@@ -750,7 +749,7 @@\n {\r\n my ($dir, $name) = @_;\r\n my (@out,@group);\r\n- my $group = $dir.\'/\'.$name.\'-subgroups-bonafide_reads-transcripts-*distribution-*.png\';\r\n+ my $group = "\'$dir\'".\'/\'."\'$name\'".\'-subgroups-bonafide_reads-transcripts-*distribution-*.png\';\r\n @group = glob $group;\r\n foreach (my $g =0; $g <= $#group; $g++)\r\n {\r\n@@ -767,7 +766,7 @@\n {\r\n my ($dir, $name) = @_;\r\n my (@out,@group);\r\n- my $group = $dir.\'/\'.$name.\'-subgroups-bonafide_reads-TE-*distribution-*.png\';\r\n+ my $group = "\'$dir\'".\'/\'."\'$name\'".\'-subgroups-bonafide_reads-TE-*distribution-*.png\';\r\n @group = glob $group;\r\n foreach (my $g =0; $g <= $#group; $g++)\r\n {\r\n@@ -784,9 +783,9 @@\n {\r\n my ($dir,$name) = @_;\r\n my (%distri,@group);\r\n- my $group = $dir.\'/\'.$name.\'-subgroups-bonafide_reads-TE-PPPartners-*\';\r\n+ my $group = "\'$dir\'".\'/\'."\'$name\'".\'-subgroups-bonafide_reads-TE-PPPartners-*\';\r\n @group = glob $group;\r\n- \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@@ -831,7 +830,7 @@\n {\r\n my ($h, $hash) = @_;\r\n my $cmp = 0;\r\n- \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@@ -851,7 +850,7 @@\n ";\r\n $cmp++;\r\n }\r\n- \r\n+\r\n print $h "</div></div>";\r\n }\r\n \r\n@@ -880,7 +879,7 @@\n ";\r\n $cmp++;\r\n }\r\n- \r\n+\r\n print $h "</div></div>";\r\n }\r\n \r\n' |
| b |
| diff -r eeb89c3331ad -r 9645d995fb3c bin/ppp.pm --- a/bin/ppp.pm Tue Oct 23 11:02:17 2018 -0400 +++ b/bin/ppp.pm Wed Oct 24 07:40:20 2018 -0400 |
| [ |
| @@ -166,7 +166,7 @@ } close $f; - open my $infile, "samtools view $in_file |"|| die "cannot open input file $! \n"; + open my $infile, "samtools view '$in_file' |"|| die "cannot open input file $! \n"; while(<$infile>) { unless ($_ =~ /^\@[A-Za-z][A-Za-z](\t[A-Za-z][A-Za-z0-9]:[ -~]+)+$/ || $_ =~ /^\@CO\t.*/ ) |
| b |
| diff -r eeb89c3331ad -r 9645d995fb3c bin/sRNAPipe.pl --- a/bin/sRNAPipe.pl Tue Oct 23 11:02:17 2018 -0400 +++ b/bin/sRNAPipe.pl Wed Oct 24 07:40:20 2018 -0400 |
| [ |
| @@ -255,14 +255,14 @@ #HTML Main Webpage my $index_page = $dir.$fastq_n[$child].'.html'; main_page ( $gen_dir, $index_page, \@fastq_n, $fastq_n[$child], $ma, $ma_uni, $dir ); - copy ($index_page, $html_out) if $child == 0; + copy ($index_page, $html_out) if $child == 0; #HTML Menu my $menu_page = $dir.$fastq_n[$child].'-sub.html'; menu_page ( $group_dir, $menu_page, \@fastq_n, $fastq_n[$child], $min, $max, $si_min, $si_max, $pi_min, $pi_max, $dir ); - unlink glob "$group_dir*.sam"; unlink glob "$group_dir*.fastq"; + unlink glob "'$group_dir'*.sam"; unlink glob "'$group_dir'*.fastq"; $pm->finish(); # pass an exit code to finish } $pm->wait_all_children; -unlink glob $dir."dataset_*symlink.fa*"; +unlink glob "'$dir'"."dataset_*symlink.fa*"; print $report "Job done!\n"; close $report; |
| b |
| diff -r eeb89c3331ad -r 9645d995fb3c sRNAPipe.xml --- a/sRNAPipe.xml Tue Oct 23 11:02:17 2018 -0400 +++ b/sRNAPipe.xml Wed Oct 24 07:40:20 2018 -0400 |
| [ |
| @@ -1,39 +1,38 @@ <tool id="sRNAPipe" name="sRNAPipe" version="1.0"> <description>In-depth study of small RNA</description> - <command interpreter="perl"> - - ./bin/sRNAPipe.pl + <command><![CDATA[ + perl '$__tool_directory__/bin/sRNAPipe.pl' - --fastq ${first_input} - --fastq_n ${first_input.name} + --fastq '${first_input}' + --fastq_n '${first_input.name}' #for $input_file in $input_files: - --fastq ${input_file.additional_input} - --fastq_n ${input_file.additional_input.name} + --fastq '${input_file.additional_input}' + --fastq_n '${input_file.additional_input.name}' #end for #if $Genome.refGenomeSource == "history": - --ref "${Genome.ownFile}" + --ref '${Genome.ownFile}' --build_index #else: - --ref "${Genome.indices.fields.path}" + --ref '${Genome.indices.fields.path}' #end if #if $tRNAs.refGenomeSource == "history": - --tRNAs "${tRNAs.ownFile}" + --tRNAs '${tRNAs.ownFile}' --build_tRNAs #elif $tRNAs.refGenomeSource == "none": --tRNAs "None" #else: - --tRNAs "${tRNAs.indices.fields.path}" + --tRNAs '${tRNAs.indices.fields.path}' #end if #if $snRNAs.refGenomeSource == "history": - --snRNAs "${snRNAs.ownFile}" + --snRNAs '${snRNAs.ownFile}' --build_snRNAs #elif $snRNAs.refGenomeSource == "none": --snRNAs "None" #else: - --snRNAs "${snRNAs.indices.fields.path}" + --snRNAs '${snRNAs.indices.fields.path}' #end if #if $rRNAs.refGenomeSource == "history": @@ -42,28 +41,28 @@ #elif $rRNAs.refGenomeSource == "none": --rRNAs "None" #else: - --rRNAs "${rRNAs.indices.fields.path}" + --rRNAs '${rRNAs.indices.fields.path}' #end if #if $miRNAs.refGenomeSource == "history": - --miRNAs "${miRNAs.ownFile}" + --miRNAs '${miRNAs.ownFile}' --build_miRNAs #else: - --miRNAs "${miRNAs.indices.fields.path}" + --miRNAs '${miRNAs.indices.fields.path}' #end if #if $transcripts.refGenomeSource == "history": - --transcripts "${transcripts.ownFile}" + --transcripts '${transcripts.ownFile}' --build_transcripts #else: - --transcripts "${transcripts.indices.fields.path}" + --transcripts '${transcripts.indices.fields.path}' #end if #if $TE.refGenomeSource == "history": - --TE "${TE.ownFile}" + --TE '${TE.ownFile}' --build_TE #else: - --TE "${TE.indices.fields.path}" + --TE '${TE.indices.fields.path}' #end if --si_min $si_min @@ -78,6 +77,7 @@ --dir $html_out.files_path --html $html_out --PPPon $PPPon + ]]> </command> <requirements> |