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svdetect/BAM_preprocessingPairs.pl svdetect/BAM_preprocessingPairs.xml svdetect/SVDetect_compare.pl svdetect/SVDetect_compare.xml svdetect/SVDetect_import.sh svdetect/SVDetect_import.xml svdetect/SVDetect_run_parallel.pl svdetect/SVDetect_run_parallel.xml svdetect/circos_graph.xml |
| b |
| diff -r 105e78d03f35 -r eb65c0fa5542 svdetect/BAM_preprocessingPairs.pl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/svdetect/BAM_preprocessingPairs.pl Thu Jul 12 12:19:40 2012 -0400 |
| [ |
| b'@@ -0,0 +1,340 @@\n+#!/usr/bin/perl -w\n+\n+use strict;\n+use warnings;\n+use Getopt::Std;\n+my $version = \'0.4b_galaxy\';\n+\n+my $SAMTOOLS_BIN_DIR="/bioinfo/local/samtools";\n+\n+my %opts = ( t=>1, p=>1, n=>1000000, f=>3, s=>0, S=>10000, o=>"." );\n+\n+getopts(\'dt:p:n:f:s:S:o:b:l:x:N:\', \\%opts); #GALAXY \n+\n+my $working_dir=($opts{o} ne ".")? $opts{o}:"working directory";\n+\n+my $pt_bad_mates_file=$opts{b}; #GALAXY \n+my $pt_log_file=$opts{l}; #GALAXY \n+my $pt_good_mates_file=$opts{x} if($opts{d}); #GALAXY \n+\n+\n+die(qq/\n+ \n+Description:\n+ \n+ Preprocessing of mates to get anomalously mapped mate-pair\\/paired-end reads as input\n+ for SVDetect.\n+\n+ From all pairs mapped onto the reference genome, this script outputs abnormal pairs:\n+ - mapped on two different chromosomes\n+ - with an incorrect strand orientation and\\/or pair order\n+ - with an insert size distance +- sigma threshold\n+ into a file <prefix.ab.bam\\/sam> sorted by read names\n+ \n+ -BAM\\/SAM File input format only.\n+\n+ Version : $version\n+ SAMtools required for BAM files\n+ \n+ \n+Usage: BAM_preprocessingPairs.pl [options] <all_mate_file.sorted.bam\\/sam>\n+\n+Options: -t BOOLEAN read type: =1 (Illumina), =0 (SOLiD) [$opts{t}]\n+ -p BOOLEAN pair type: =1 (paired-end), =0 (mate-pair) [$opts{p}]\n+ -n INTEGER number of pairs for calculating mu and sigma lengths [$opts{n}]\n+\t -s INTEGER minimum value of ISIZE for calculating mu and sigma lengths [$opts{s}]\n+\t -S INTEGER maximum value of ISIZE for calculating mu and sigma lengths [$opts{S}]\n+ -f REAL minimal number of sigma fold for filtering pairs [$opts{f}]\n+ -d dump normal pairs into a file [<prefix.norm.bam\\/sam>] (optional)\n+\t -o STRING output directory [$working_dir]\n+\n+\\n/) if (@ARGV == 0 && -t STDIN);\n+\n+unless (-d $opts{o}){\n+\tmkdir $opts{o} or die;\n+}\n+$opts{o}.="/" if($opts{o}!~/\\/$/);\n+\n+my $mates_file=shift(@ARGV);\n+\n+$mates_file=readlink($mates_file);\n+\n+my $bad_mates_file=(split(/\\//,$mates_file))[$#_];\n+\n+if($bad_mates_file=~/.(s|b)am$/){\n+ $bad_mates_file=~s/.(b|s)am$/.ab.sam/;\n+ $bad_mates_file=$opts{o}.$bad_mates_file;\n+}\n+\n+else{\n+ die "Error: mate_file with the extension <.bam> or <.sam> needed !\\n";\n+}\n+\n+my $good_mates_file;\n+if($opts{d}){\n+ $good_mates_file=(split(/\\//,$mates_file))[$#_];\n+ $good_mates_file=~s/.(b|s)am$/.norm.sam/;\n+ $good_mates_file=$opts{o}.$good_mates_file;\n+}\n+\n+my $log_file=$opts{o}.$opts{N}.".svdetect_preprocessing.log"; #GALAXY \n+\n+#------------------------------------------------------------------------------#\n+#Calculate mu and sigma\n+\n+open LOG,">$log_file" or die "$0: can\'t open ".$log_file.":$!\\n";\n+\n+print LOG "\\# Calculating mu and sigma lengths...\\n";\n+print LOG "-- file=$mates_file\\n";\n+print LOG "-- n=$opts{n}\\n";\n+print LOG "-- ISIZE min=$opts{s}, max=$opts{S}\\n";\n+\n+my ($record, $sumX,$sumX2) = (0,0,0);\n+my $warn=$opts{n}/10;\n+my $prev_pair="FIRST";\n+\n+my $bam=($mates_file =~ /.bam$/)? 1:0;\n+\n+if($bam){\n+ open(MATES, "${SAMTOOLS_BIN_DIR}/samtools view $mates_file |") or die "$0: can\'t open ".$mates_file.":$!\\n";\n+}else{\n+ open MATES, "<".$mates_file or die "$0: can\'t open ".$mates_file.":$!\\n";\n+}\n+\n+while(<MATES>){\n+ \n+ my @t=split;\n+ \n+ next if ($t[0]=~/^@/);\n+ \n+ my $current_pair=$t[0];\n+ next if($current_pair eq $prev_pair);\n+ $prev_pair=$current_pair; \n+ \n+ my ($chr1,$chr2,$length)=($t[2],$t[6],abs($t[8]));\n+ \n+ next if ($chr1 eq "*" || $chr2 eq "*");\n+ next if ($length<$opts{s} || $length>$opts{S}) ;\n+ \n+ if($chr2 eq "="){\n+\n+ $sumX += $length;\t\t\t\t\t\t\t#add to sum and sum^2 for mean and variance calculation\n+\t$sumX2 += $length*$length;\n+ $record++;\n+ }\n+\n+ if($record>$warn){\n+\tprint LOG "-- $warn pairs analysed\\n";\n+ $warn+=$warn;\n+ }\n+ \n+ last if ($record>$opts{n});\n+ \n+}\n+close (MATES);\n+\n+$record--;\n+my $m'..b'ad=-1;\n+ $count{unmap}++;\n+ $record++;\n+ next;\n+ \n+ }\n+ \n+ my $strand1 = (($t[1]&0x0010))? \'R\':\'F\';\n+ my $strand2 = (($t[1]&0x0020))? \'R\':\'F\';\n+ my $order1 = (($t[1]&0x0040))? \'1\':\'2\';\n+ my $order2 = (($t[1]&0x0080))? \'1\':\'2\';\n+ \n+ if($order1 == 2){\n+ ($strand1,$strand2)=($strand2,$strand1);\n+ ($chr1,$chr2)=($chr2,$chr1);\n+ ($pos1,$pos2)=($pos2,$pos1);\n+ ($order1,$order2)=($order2,$order1);\n+ }\n+ \n+ my $sense=$strand1.$strand2;\n+ \n+ if($chr1 ne "=" && $chr2 ne "="){\n+ $bad=1;\n+ $count{chr}++;\n+ }\n+ \n+ if($opts{p}){ #paired-end\n+ if(!(($sense eq "FR" && $pos1<$pos2) || ($sense eq "RF" && $pos2<$pos1))){\n+ $bad=1;\n+ $count{sense}++;\n+ }\n+ }else{ #mate-pair\n+ if($opts{t}){ #Illumina\n+ if(!(($sense eq "FR" && $pos2<$pos1) || ($sense eq "RF" && $pos1<$pos2))){\n+ $bad=1;\n+ $count{sense}++;\n+ }\n+ }else{ #SOLiD\n+ if(!(($sense eq "FF" && $pos2<$pos1) || ($sense eq "RR" && $pos1<$pos2))){\n+ $bad=1;\n+ $count{sense}++;\n+ }\n+ }\n+ }\n+ \n+ if(($chr1 eq "=" || $chr2 eq "=") && ($length <$mu - $opts{f}*$sigma || $length>$mu + $opts{f}*$sigma)){\n+ $bad=1;\n+ $count{dist}++;\n+ }\n+ \n+ if($bad){\n+ print AB;\n+ $count{ab}++;\n+ $prev_bad=$bad;\n+ }else{\n+ print NORM if ($opts{d});\n+ $count{norm}++;\n+ $prev_bad=$bad;\n+ }\n+ \n+ $record++;\n+ \n+ if($record>$warn){\n+ print LOG "-- $warn pairs analysed\\n";\n+ $warn+=100000;\n+ }\n+}\n+\n+close AB;\n+close NORM if($opts{d});\n+\n+print LOG "-- Total : $record pairs analysed\\n";\n+print LOG "-- $count{unmap} pairs whose one or both reads are unmapped\\n";\n+print LOG "-- ".($count{ab}+$count{norm})." mapped pairs\\n";\n+print LOG "---- $count{ab} abnormal mapped pairs\\n";\n+print LOG "------ $count{chr} pairs mapped on two different chromosomes\\n";\n+print LOG "------ $count{sense} pairs with incorrect strand orientation and\\/or pair order\\n";\n+print LOG "------ $count{dist} pairs with incorrect insert size distance\\n";\n+print LOG "--- $count{norm} correct mapped pairs\\n";\n+\n+#------------------------------------------------------------------------------#\n+#------------------------------------------------------------------------------#\n+#OUTPUT\n+\n+if($bam){\n+ \n+ my $bam_file=$bad_mates_file;\n+ $bam_file=~s/.sam$/.bam/;\n+ print LOG "\\# Converting sam to bam for abnormal mapped pairs\\n";\n+ system("${SAMTOOLS_BIN_DIR}/samtools view -bS $bad_mates_file > $bam_file 2>".$opts{o}."samtools.log");\n+ unlink($bad_mates_file);\n+ print LOG "-- output created: $bam_file\\n";\n+\n+ system "rm $pt_bad_mates_file ; ln -s $bam_file $pt_bad_mates_file"; #GALAXY\n+ \n+ if($opts{d}){\n+ $bam_file=$good_mates_file;\n+ $bam_file=~s/.sam$/.bam/;\n+ print LOG "\\# Converting sam to bam for correct mapped pairs\\n";\n+ system("${SAMTOOLS_BIN_DIR}/samtools view -bS $good_mates_file > $bam_file 2>".$opts{o}."samtools.log");\n+ unlink($good_mates_file);\n+ print LOG "-- output created: $bam_file\\n";\n+\n+\tsystem "rm $pt_good_mates_file ; ln -s $bam_file $pt_good_mates_file"; #GALAXY\n+\n+ }\n+\n+}\n+\n+else{\n+ print LOG "-- output created: $bad_mates_file\\n";\n+ print LOG "-- output created: $good_mates_file\\n" if($opts{d});\n+}\n+\n+close LOG;\n+\n+system "rm $pt_log_file ; ln -s $log_file $pt_log_file"; #GALAXY\n+\n+\n+#------------------------------------------------------------------------------#\n+#------------------------------------------------------------------------------#\n+sub decimal{\n+ \n+ my $num=shift;\n+ my $digs_to_cut=shift;\n+\n+ $num=sprintf("%.".($digs_to_cut-1)."f", $num) if ($num=~/\\d+\\.(\\d){$digs_to_cut,}/);\n+\n+ return $num;\n+}\n+#------------------------------------------------------------------------------#\n' |
| b |
| diff -r 105e78d03f35 -r eb65c0fa5542 svdetect/BAM_preprocessingPairs.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/svdetect/BAM_preprocessingPairs.xml Thu Jul 12 12:19:40 2012 -0400 |
| [ |
| @@ -0,0 +1,77 @@ +<tool id="svdetect_preprocessing" name="BAM preprocessing"> + + <description>to get abnormal pairs</description> + + <command interpreter="perl"> BAM_preprocessingPairs.pl -t '$readType' -p '$pairType' -n '$nbrePair' -s '$isizeMin' -S '$isizeMax' -f '$foldPair' -o $__new_file_path__/svdetect -b '$abBAM' -l '$log' -N $sample_name + #if $newBam.pairNormal=="yes" + -d -x '$normBAM' + #end if + '$inputBam' + </command> + + <inputs> + <param name="sample_name" type="text" value="sample" label="Sample Name"/> + <param name="inputBam" type="data" format="bam" label="BAM input file"/> + <param name="readType" type="select" label="Read type"> + <option value="1">Illumina</option> + <option value="0">SOLiD</option> + </param> + <param name="pairType" type="select" label="Library type"> + <option value="1">Paired-end</option> + <option value="0">Mate-Pair</option> + </param> + <conditional name="newBam"> + <param name="pairNormal" type="select" label="Do you want an additional bam file listing concordant mapped pairs?" help="Dump normal pairs into a file sample_name.norm.bam/sam"> + <option value="no">No</option> + <option value="yes">Yes</option> + </param> + <when value="yes"> + <!-- do nothing here --> + </when> + <when value="no"> + <!-- do nothing here --> + </when> + </conditional> + <param name="nbrePair" value="1000000" type="integer" size="30" label="Number of pairs for calculating mu (µ) and sigma (σ) lengths"/> + <param name="isizeMin" value="0" type="integer" size="30" label="Minimum value of ISIZE for calculating mu (µ) and sigma (σ) lengths"/> + <param name="isizeMax" value="10000" type="integer" size="30" label="Maximum value of ISIZE for calculating mu (µ)and sigma( σ) lengths"/> + <param name="foldPair" value="3" type="float" size="30" label="Minimal number of sigma (σ) fold for filtering pairs"/> + </inputs> + + <outputs> + <data format="bam" name="abBAM" label="${$sample_name}.ab.bam"/> + <data format="txt" name="log" label="${$sample_name}.svdetect_preprocessing.log"/> + <data format="bam" name="normBAM" label="${$sample_name}.norm.bam"> + <filter>newBam['pairNormal'] == 'yes'</filter> + </data> + </outputs> + + <help> + +**What it does** + +Bam_preprocessingPairs - Version 0.4b + +Preprocessing of mates to get anomalously mapped mate-pair/paired-end reads as input for SVDetect. + +From all pairs mapped onto the reference genome, this script outputs abnormal pairs: + + * mapped on two different chromosomes + * with an incorrect strand orientation and/or pair order + * with an insert size distance +- sigma threshold + +into a file prefix.ab.bam/sam sorted by read names + +-BAM/SAM File input format only. + +SAMtools required for BAM files + +----- + +.. class:: infomark + +Contact Bruno Zeitouni (svdetect@curie.fr) for any questions or concerns about the Galaxy implementation of SVDetect. + + </help> + +</tool> |
| b |
| diff -r 105e78d03f35 -r eb65c0fa5542 svdetect/SVDetect_compare.pl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/svdetect/SVDetect_compare.pl Thu Jul 12 12:19:40 2012 -0400 |
| [ |
| b'@@ -0,0 +1,716 @@\n+#!/usr/bin/perl -w\n+\n+=pod\n+\n+=head1 NAME\n+\n+SVDetect Compare for Galaxy\n+\n+Version: 0.8 for Galaxy\n+\n+=head1 SYNOPSIS\n+\n+SVDetect_compare.pl links2compare -conf <configuration_file> [-help] [-man]\n+\n+=cut\n+\n+# -------------------------------------------------------------------\n+\n+use strict;\n+use warnings;\n+\n+use Pod::Usage;\n+use Getopt::Long;\n+\n+use Config::General;\n+use Tie::IxHash;\n+\n+#::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::#\n+#PARSE THE COMMAND LINE\n+my %OPT;\n+GetOptions(\\%OPT,\n+\t \'conf=s\',\n+\t \'out1=s\', #GALAXY\n+\t \'out2=s\', #GALAXY\n+\t \'out3=s\', #GALAXY\n+\t \'out4=s\', #GALAXY\n+\t \'out5=s\', #GALAXY\n+\t \'out6=s\', #GALAXY\n+\t \'out7=s\', #GALAXY\n+\t \'out8=s\', #GALAXY\n+\t \'out9=s\', #GALAXY\n+\t \'l=s\', #GALAXY\n+\t \'N=s\', #GALAXY\n+\t \'help\',\n+ \'man\'\n+\t );\n+\n+pod2usage() if $OPT{help};\n+pod2usage(-verbose=>2) if $OPT{man};\n+pod2usage(-message=> "$!", -exitval => 2) if (!defined $OPT{conf});\n+\n+\n+pod2usage() if(@ARGV<1);\n+\n+tie (my %func, \'Tie::IxHash\',links2compare=>\\&links2compare);\n+\n+foreach my $command (@ARGV){\n+ pod2usage(-message=> "Unknown command \\"$command\\"", -exitval => 2) if (!defined($func{$command}));\n+}\n+#::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::#\n+\n+#::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::#\n+#READ THE CONFIGURATION FILE\n+my $conf=Config::General->new( -ConfigFile => $OPT{conf},\n+ -Tie => "Tie::IxHash",\n+ -AllowMultiOptions => 1,\n+\t\t\t\t -LowerCaseNames => 1,\n+\t\t\t\t -AutoTrue => 1);\n+my %CONF= $conf->getall;\n+validateconfiguration(\\%CONF);\t\t\t\t\t\t\t#validation of the configuration parameters\n+\n+\n+my $SAMTOOLS_BIN_DIR="/bioinfo/local/samtools"; #GALAXY\n+my $BEDTOOLS_BIN_DIR="/bioinfo/local/BEDTools/bin"; #GALAXY\n+\n+my $pt_log_file=$OPT{l}; #GALAXY\n+my $log_file=$CONF{general}{output_dir}.$OPT{N}.".svdetect_compare.log"; #GALAXY\n+open LOG,">$log_file" or die "$0: can\'t open ".$log_file.":$!\\n";#GALAXY\n+\n+my @pt_sv_file=($OPT{out1},$OPT{out2},$OPT{out3}) if($OPT{out1}); #GALAXY common,sample,reference\n+my @pt_circos_file=($OPT{out4},$OPT{out5},$OPT{out6}) if($OPT{out4}); #GALAXY common,sample,reference\n+my @pt_bed_file=($OPT{out7},$OPT{out8},$OPT{out9}) if($OPT{out7}); #GALAXY common,sample,reference\n+\n+$CONF{compare}{sample_link_file}=readlink($CONF{compare}{sample_link_file});#GALAXY\n+$CONF{compare}{sample_link_file}=~s/.sv.txt//; #GALAXY\n+\n+$CONF{compare}{reference_link_file}=readlink($CONF{compare}{reference_link_file});#GALAXY\n+$CONF{compare}{reference_link_file}=~s/.sv.txt//; #GALAXY\n+\n+#::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::#\n+\n+#::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::#\n+#COMMAND EXECUTION\n+foreach my $command (@ARGV){\n+ &{$func{$command}}();\n+}\n+print LOG "-- end\\n";\n+\n+close LOG;#GALAXY\n+system "rm $pt_log_file ; ln -s $log_file $pt_log_file"; #GALAXY\n+\n+exit(0);\n+#::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::#\n+\n+#::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::#\n+#FUNCTIONS\n+\n+# -----------------------------------------------------------------------------#\n+#MAIN FUNCTION number 5:Comparison between samples, common or specific links\n+sub links2compare{\n+ \n+ my @compare_files;\n+ \n+ compareSamples($CONF{general}{output_dir},\n+\t\t $CONF{compare}{list_samples},\n+\t\t $CONF{compare}{sample_link_file},\n+\t\t $CONF{compare}{reference_link_file},\n+\t\t $CONF{compare}{min_overlap},\n+\t\t $CONF{compare}{same_sv_type},\n+\t\t \\@compare_files);\n+\n+ my $pt_ind=0;\n+ \n+ for my $input_file (@compa'..b'->[$i] eq \'F\'){\n+\t $starts->[$i]=$positions->[$i];\n+\t $ends->[$i]=$positions->[$i]+$tag_length->{$end_order->[$i]}-1;\n+\t}else{\n+\t $starts->[$i]=$positions->[$i]-$tag_length->{$end_order->[$i]}+1;\n+\t $ends->[$i]=$positions->[$i];\n+\t}\n+ } \n+}\n+#------------------------------------------------------------------------------#\n+#------------------------------------------------------------------------------#\n+sub floor {\n+ my $nb = $_[0];\n+ $nb=~ s/\\..*//;\n+ return $nb;\n+}\n+#------------------------------------------------------------------------------#\n+#------------------------------------------------------------------------------#\n+sub decimal{\n+ \n+ my $num=shift;\n+ my $digs_to_cut=shift;\n+\n+ $num=sprintf("%.".($digs_to_cut-1)."f", $num) if ($num=~/\\d+\\.(\\d){$digs_to_cut,}/);\n+\n+ return $num;\n+}\n+\n+#------------------------------------------------------------------------------#\n+#------------------------------------------------------------------------------#\n+#Sort links according the concerned chromosomes and their coordinates\n+sub sortLinks{\n+ \n+ my ($links_file,$sortedlinks_file,$unique)=@_;\n+ \n+ print LOG "# Sorting links...\\n";\n+ \n+ my $pipe=($unique)? "| sort -u":"";\n+ system "sort -k 1,1 -k 4,4 -k 2,2n -k 5,5n -k 8,8n $links_file $pipe > $sortedlinks_file";\n+\n+}\n+#------------------------------------------------------------------------------#\n+#------------------------------------------------------------------------------#\n+sub getColor{\n+\n+ my($count,$hcolor,$format)=@_;\n+ for my $col ( keys % { $hcolor} ) {\n+ return $col if($count>=$hcolor->{$col}->[0] && $count<=$hcolor->{$col}->[1]);\n+ }\n+ return "white" if($format eq "circos");\n+ return "255,255,255" if($format eq "bed");\n+}\n+#------------------------------------------------------------------------------#\n+#------------------------------------------------------------------------------#\n+#check if the configuration file is correct\n+sub validateconfiguration{\n+ \n+ my %conf=%{$_[0]};\n+ my $list_prgs="@ARGV";\n+ \n+ my @circos_params=qw(organism_id colorcode);\n+ my @bed_params=qw(colorcode);\n+ my @compare_params=qw(list_samples list_read_lengths sample_link_file reference_link_file);\n+ \n+ unless (defined($conf{general}{output_dir})) {\n+\t$conf{general}{output_dir} = ".";\n+ }\n+ unless (-d $conf{general}{output_dir}){\n+\tmkdir $conf{general}{output_dir} or die;\n+ }\n+ $conf{general}{output_dir}.="/" if($conf{general}{output_dir}!~/\\/$/);\n+\n+ \n+ if($list_prgs=~/links2compare/){\n+\tforeach my $p (@compare_params) {\n+\t die("Error Config : The compare parameter \\"$p\\" is not defined\\n") if (!defined $conf{compare}{$p});\n+\t}\n+\t\n+\tunless (defined($conf{compare}{same_sv_type})) {\n+\t $conf{compare}{same_sv_type} = 0;\n+\t}\n+\t\n+\tunless (defined($conf{compare}{min_overlap})) {\n+\t $conf{compare}{min_overlap} = 1E-9;\n+\t}\n+\t\n+\tif($conf{compare}{circos_output}){\n+\t foreach my $p (@circos_params) {\n+\t\tnext if($list_prgs=~/^ratio/ && $p eq "colorcode");\n+\t\tdie("Error Config : The circos parameter \\"$p\\" is not defined\\n") if (!defined $conf{circos}{$p});\n+\t }\n+\t}\n+\tif($conf{compare}{bed_output}){\n+\t foreach my $p (@bed_params) {\n+\t\tdie("Error Config : The bed parameter \\"$p\\" is not defined\\n") if (!defined $conf{bed}{$p});\n+\t }\n+\t die("Error Config : The compare parameter \\"list_read_lengths\\" is not defined\\n") if (!defined $conf{compare}{list_read_lengths});\n+\n+\t my @samples=split(",",$conf{compare}{list_samples});\n+\t my @read_lengths=split(",",$conf{compare}{list_read_lengths});\n+\t for my $i (0..$#samples){\n+\t\tmy @l=split("-",$read_lengths[$i]);\n+\t\t$conf{compare}{read_lengths}{$samples[$i]}={ 1=> $l[0], 2=> $l[1]};\n+\t }\n+\t}\n+ }\n+ \n+ \n+}\n+#------------------------------------------------------------------------------#\n+#::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::#\n' |
| b |
| diff -r 105e78d03f35 -r eb65c0fa5542 svdetect/SVDetect_compare.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/svdetect/SVDetect_compare.xml Thu Jul 12 12:19:40 2012 -0400 |
| [ |
| @@ -0,0 +1,218 @@ +<tool id="svdetect_compare" name="Compare"> + +<description>structural variants between two samples</description> + +<command interpreter="perl">SVDetect_compare.pl links2compare -conf '$config_file' -l '$log_file' -N '$sample_name.$reference_name' + +#if $links2SV +-out1 '$common_sv_file' +-out2 '$sample_sv_file' +-out3 '$reference_sv_file' +#end if + +#if $file_conversion.file_conversion_select=="convert" and $file_conversion.links2circos +-out4 '$common_circos_file' +-out5 '$sample_circos_file' +-out6 '$reference_circos_file' +#end if + +#if $file_conversion.file_conversion_select=="convert" and $file_conversion.links2bed +-out7 '$common_bed_file' +-out8 '$sample_bed_file' +-out9 '$reference_bed_file' +#end if + +</command> + +<inputs> + <param name="sample_name" type="text" size="20" value="sample" label="Sample Name"/> + <param name="sample_read1_length" type="integer" size="10" value="50" label="Sample read 1 length (bp)"/> + <param name="sample_read2_length" type="integer" size="10" value="50" label="Sample read 2 length (bp)"/> + <param name="sample_mates_file" type="data" format="sv" label="Sample input file" help=".sv file"/> + + <param name="reference_name" type="text" size="20" value="reference" label="Reference Name"/> + <param name="reference_read1_length" type="integer" size="10" value="50" label="Reference read 1 length (bp)"/> + <param name="reference_read2_length" type="integer" size="10" value="50" label="Reference read 2 length (bp)"/> + <param name="reference_mates_file" type="data" format="sv" label="Reference input file" help=".sv file"/> + + <param name="min_overlap" type="float" size="10" value="0.05" label="Minimum overlap of links required as a fraction"/> + <param name="same_sv_type" label="Comparison of SVs with the same type only ?" type="boolean" truevalue="1" falsevalue="0" checked="True"/> + + <param name="links2SV" label="Do you want to have filtered links in a tabulated file format showing significant SVs?" type="boolean" truevalue="1" falsevalue="0" checked="True"/> + + <conditional name="file_conversion"> + <param name="file_conversion_select" type="select" label="Output file conversion" help="Converts filtered links to Circos/BED files format for graphical view of SVs"> + <option value="do_not_convert">No</option> + <option value="convert">Yes</option> + </param> + <when value="do_not_convert"> + <!-- do nothing here --> + </when> + <when value="convert"> + <param name="links2circos" label="Converts the link list to the Circos link format" type="boolean" truevalue="1" falsevalue="0" checked="True"/> + <param name="links2bed" label="Converts the link list to the UCSC BED format" type="boolean" truevalue="1" falsevalue="0" checked="False"/> + <param name="organism_id" type="text" size="10" value="hs" label="Organism ID"/> + <repeat name="color_code" title="Color-code" min="1" max="7"> + <param name="color" type="select" label="Color"> + <option value="grey">grey</option> + <option value="black">black</option> + <option value="blue">blue</option> + <option value="green">green</option> + <option value="purple">purple</option> + <option value="orange">orange</option> + <option value="red">red</option> + </param> + <param name="interval" type="text" value="1,3" label="Interval"/> + </repeat> + </when> + </conditional> +</inputs> + + + +<outputs> + <data format="sv" name="common_sv_file" label="common.compared.sv"> + <filter>links2SV is True</filter> + </data> + <data format="sv" name="sample_sv_file" label="${sample_name}.compared.sv"> + <filter>links2SV is True</filter> + </data> + <data format="sv" name="reference_sv_file" label="${reference_name}.compared.sv"> + <filter>links2SV is True</filter> + </data> + + <data format="segdup" name="common_circos_file" label="common.compared.segdup"> + <filter>( + file_conversion['file_conversion_select']=="convert" and + file_conversion['links2circos'] is True + ) + </filter> + </data> + <data format="segdup" name="sample_circos_file" label="${sample_name}.compared.segdup"> + <filter>( + file_conversion['file_conversion_select']=="convert" and + file_conversion['links2circos'] is True + ) + </filter> + </data> + <data format="segdup" name="reference_circos_file" label="${reference_name}.compared.segdup"> + <filter>( + file_conversion['file_conversion_select']=="convert" and + file_conversion['links2circos'] is True + ) + </filter> + </data> + + <data format="bed" name="common_bed_file" label="common.compared.bed"> + <filter>( + file_conversion['file_conversion_select']=="convert" and + file_conversion['links2bed'] is True + ) + </filter> + </data> + <data format="bed" name="sample_bed_file" label="${sample_name}.compared.bed"> + <filter>( + file_conversion['file_conversion_select']=="convert" and + file_conversion['links2bed'] is True + ) + </filter> + </data> + <data format="bed" name="reference_bed_file" label="${reference_name}.compared.bed"> + <filter>( + file_conversion['file_conversion_select']=="convert" and + file_conversion['links2bed'] is True + ) + </filter> + </data> + + <data format="txt" name="log_file" label="${sample_name}.${reference_name}.svdetect_compare.log"/> +</outputs> + + + +<configfiles> + <configfile name="config_file"> +<general> +output_dir=$__new_file_path__/svdetect +</general> + +#if $file_conversion.file_conversion_select == "convert" +#if $file_conversion.links2circos +<circos> +organism_id=${file_conversion.organism_id} +<colorcode> +#for $color_repeat in $file_conversion.color_code +${color_repeat.color}=${color_repeat.interval} +#end for +</colorcode> +</circos> +#end if +#if $file_conversion.links2bed +<bed> +<colorcode> +#for $color_repeat in $file_conversion.color_code +#if str($color_repeat.color)== "grey" +190,190,190=${color_repeat.interval} +#end if +#if str($color_repeat.color)== "black" +0,0,0=${color_repeat.interval} +#end if +#if str($color_repeat.color)== "blue" +0,0,255=${color_repeat.interval} +#end if +#if str($color_repeat.color)== "green" +0,255,0=${color_repeat.interval} +#end if +#if str($color_repeat.color)== "purple" +153,50,205=${color_repeat.interval} +#end if +#if str($color_repeat.color)== "orange" +255,140,0=${color_repeat.interval} +#end if +#if str($color_repeat.color)== "red" +255,0,0=${color_repeat.interval} +#end if +#end for +</colorcode> +</bed> +#end if +#end if + +<compare> +list_samples=${sample_name},${reference_name} +list_read_lengths=${sample_read1_length}-${sample_read2_length},${reference_read1_length}-${reference_read2_length} +sample_link_file=${sample_mates_file} +reference_link_file=${reference_mates_file} +min_overlap=${min_overlap} +same_sv_type=${same_sv_type} +sv_output=${links2SV} +#if $file_conversion.file_conversion_select == "convert" +circos_output=${$file_conversion.links2circos} +bed_output=${$file_conversion.links2bed} +#end if +</compare> + + </configfile> +</configfiles> + + <help> +**What it does** + +SVDetect - Version : 0.8 + +Comparison of clusters between two samples to get common or sample-specific SVs + +This program is designed to compare filtered links between two anomalously mapped mate-pair/paired-end datasets +and to identify common and sample-specific SVs (like the usual sample/reference design). +Overlaps between coordinates of clusters and types of SVs are used as parameters of comparison. + +Manual documentation available at the http://svdetect.sourceforge.net/Site/Manual.html + +----- + +.. class:: infomark + +Contact Bruno Zeitouni (svdetect@curie.fr) for any questions or concerns about the Galaxy implementation of SVDetect. + </help> + +</tool> |
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| diff -r 105e78d03f35 -r eb65c0fa5542 svdetect/SVDetect_import.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/svdetect/SVDetect_import.sh Thu Jul 12 12:19:40 2012 -0400 |
| b |
| @@ -0,0 +1,15 @@ +#!/bin/bash + + +while getopts "i:o:" optionName; do +case "$optionName" in + +i) INPUT="$OPTARG";; +o) OUTPUT="$OPTARG";; + +esac +done + +rm $OUTPUT + +ln -s $INPUT $OUTPUT |
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| diff -r 105e78d03f35 -r eb65c0fa5542 svdetect/SVDetect_import.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/svdetect/SVDetect_import.xml Thu Jul 12 12:19:40 2012 -0400 |
| [ |
| @@ -0,0 +1,85 @@ +<tool id="svdetect_import" name="Import data"> + <description>BAM, chromosome info or sv files</description> + <command interpreter="bash">SVDetect_import.sh -i $file_path + #if str($type.file_type)=="bam" + -o $outbamfile + #elif str($type.file_type)=="len" + -o $outlenfile + #elif str($type.file_type)=="sv" + -o $outsvfile + #end if + </command> + <inputs> + <param name="file_name" type="text" value="file1" label="File Name"/> + <conditional name="type"> + <param name="file_type" type="select" label="Select the file type to import" help="BAM file (BAM) or text file (SAM, chromosome list or a SV tabulated text file)"> + <option value="bam">BAM file (.bam)</option> + <option value="len">Chromosome info file (.len)</option> + <option value="sv">SVDetect output file (.sv)</option> + </param> + <when value="bam"> + <!-- do nothing here --> + </when> + <when value="len"> + <!-- do nothing here --> + </when> + <when value="sv"> + <!-- do nothing here --> + </when> + </conditional> + <param name="file_path" type="text" size="150" label="Path to file"/> + </inputs> + <outputs> + <data format="bam" name="outbamfile" label="${file_name}.bam"> + <filter>type['file_type']=="bam"</filter> + </data> + <data format="len" name="outlenfile" label="${file_name}.len"> + <filter>type['file_type']=="len"</filter> + </data> + <data format="sv" name="outsvfile" label="${file_name}.sv"> + <filter>type['file_type']=="sv"</filter> + </data> + </outputs> + <help> +**What it does** + +This tool allows you to import quickly a BAM file, a chromosome info file or a SVDetect output file from you computer as inputs for SVDetect. + + +**Example of chromosome file** + +Input len file:: + + 1 chr1 247249719 + 2 chr2 242951149 + 3 chr3 199501827 + 4 chr4 191273063 + 5 chr5 180857866 + 6 chr6 170899992 + 7 chr7 158821424 + 8 chr8 146274826 + 9 chr9 140273252 + 10 chr10 135374737 + 11 chr11 134452384 + 12 chr12 132349534 + 13 chr13 114142980 + 14 chr14 106368585 + 15 chr15 100338915 + 16 chr16 88827254 + 17 chr17 78774742 + 18 chr18 76117153 + 19 chr19 63811651 + 20 chr20 62435964 + 21 chr21 46944323 + 22 chr22 49691432 + 23 chrX 154913754 + 24 chrY 57772954 + +----- + +.. class:: infomark + +Contact Bruno Zeitouni (svdetect@curie.fr) for any questions or concerns about the Galaxy implementation of SVDetect. + </help> + +</tool> |
| b |
| diff -r 105e78d03f35 -r eb65c0fa5542 svdetect/SVDetect_run_parallel.pl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/svdetect/SVDetect_run_parallel.pl Thu Jul 12 12:19:40 2012 -0400 |
| [ |
| b'@@ -0,0 +1,3537 @@\n+#!/usr/bin/perl -w\n+\n+=pod\n+\n+=head1 NAME\n+\n+SVDetect - Program designed to the detection of structural variations\n+from paired-end/mate-pair sequencing data, compatible with SOLiD and Illumina (>=1.3) reads\n+\n+Version: 0.8 for Galaxy\n+\n+=head1 SYNOPSIS\n+\n+SVDetect <command> -conf <configuration_file> [-help] [-man]\n+ \n+ Command:\n+\n+ \tlinking\t\tdetection and isolation of links\n+ filtering\tfiltering of links according different parameters\n+ links2circos\tlinks conversion to circos format\n+\tlinks2bed \tpaired-ends of links converted to bed format (UCSC)\n+\tlinks2SV\tformatted output to show most significant SVs\n+\tcnv\t\tcalculate copy-number profiles\n+\tratio2circos\tratio conversion to circos density format\n+\tratio2bedgraph\tratio conversion to bedGraph density format (UCSC)\n+ \n+=head1 DESCRIPTION\n+\n+This is a command-line interface to SVDetect.\n+\n+\n+=head1 AUTHORS\n+\n+Bruno Zeitouni E<lt>bruno.zeitouni@curie.frE<gt>,\n+Valentina Boeva E<lt>valentina.boeva@curie.frE<gt>\n+\n+=cut\n+\n+# -------------------------------------------------------------------\n+\n+use strict;\n+use warnings;\n+\n+use Pod::Usage;\n+use Getopt::Long;\n+\n+use Config::General;\n+use Tie::IxHash;\n+use FileHandle;\n+use Parallel::ForkManager;\n+\n+#::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::#\n+#PARSE THE COMMAND LINE\n+my %OPT;\n+GetOptions(\\%OPT,\n+\t \'conf=s\',\n+\t \'out1=s\', #GALAXY\n+\t \'out2=s\', #GALAXY\n+\t \'out3=s\', #GALAXY\n+\t \'out4=s\', #GALAXY\n+\t \'out5=s\', #GALAXY\n+\t \'l=s\', #GALAXY\n+\t \'N=s\',#GALAXY\n+\t \'help\',#GALAXY\n+ \'man\'\n+\t );\n+\n+pod2usage() if $OPT{help};\n+pod2usage(-verbose=>2) if $OPT{man};\n+pod2usage(-message=> "$!", -exitval => 2) if (!defined $OPT{conf});\n+\n+pod2usage() if(@ARGV<1);\n+\n+tie (my %func, \'Tie::IxHash\',linking=>\\&createlinks,\n+\t\t\t filtering=>\\&filterlinks,\n+\t\t\t links2circos=>\\&links2circos,\n+\t\t\t links2bed=>\\&links2bed,\n+\t\t\t links2compare=>\\&links2compare,\n+\t\t\t links2SV=>\\&links2SV,\n+\t\t\t cnv=>\\&cnv,\n+\t\t\t ratio2circos=>\\&ratio2circos,\n+\t\t\t ratio2bedgraph=>\\&ratio2bedgraph);\n+\n+foreach my $command (@ARGV){\n+ pod2usage(-message=> "Unknown command \\"$command\\"", -exitval => 2) if (!defined($func{$command}));\n+}\n+#::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::#\n+\n+\n+#::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::#\n+#READ THE CONFIGURATION FILE\n+my $conf=Config::General->new( -ConfigFile => $OPT{conf},\n+ -Tie => "Tie::IxHash",\n+ -AllowMultiOptions => 1,\n+\t\t\t\t -LowerCaseNames => 1,\n+\t\t\t\t -AutoTrue => 1);\n+my %CONF= $conf->getall;\n+validateconfiguration(\\%CONF);\t\t\t\t\t\t\t#validation of the configuration parameters\n+\n+my $SAMTOOLS_BIN_DIR="/bioinfo/local/samtools"; #GALAXY\n+\n+my $pt_log_file=$OPT{l}; #GALAXY\n+my $pt_links_file=$OPT{out1} if($OPT{out1}); #GALAXY\n+my $pt_flinks_file=$OPT{out2} if($OPT{out2}); #GALAXY\n+my $pt_sv_file=$OPT{out3} if($OPT{out3}); #GALAXY\n+my $pt_circos_file=$OPT{out4} if($OPT{out4}); #GALAXY\n+my $pt_bed_file=$OPT{out5} if($OPT{out5}); #GALAXY\n+\n+$CONF{general}{mates_file}=readlink($CONF{general}{mates_file});#GALAXY\n+$CONF{general}{cmap_file}=readlink($CONF{general}{cmap_file});#GALAXY\n+\n+my $log_file=$CONF{general}{output_dir}.$OPT{N}.".svdetect_run.log"; #GALAXY\n+open LOG,">$log_file" or die "$0: can\'t open ".$log_file.":$!\\n";#GALAXY\n+#::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::#\n+\n+#::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::#\n+#COMMAND EXECUTION\n+foreach my $command (@ARGV){\n+ &{$func{$command}}();\n+}\n+print LOG "-- end\\n";#GALAXY\n+\n+close LOG;#GALAXY\n+system "rm $pt_log_file ; ln -s $log_file $pt_log_file"; #GALAXY\n+exit'..b'y $chrName (@chrs){\n+\t \n+\t\tdie("Error Config : The filtering parameter \\"chromosomes\\" is not valid\\n")\n+\t\tif(($chrName!~/^\\-/ && $exclude) || ($chrName=~/^\\-/ && !$exclude));\n+\t\t\n+\t }\n+\t}\n+\t\n+\tif (( $conf{filtering}{order_filtering} )&& !$conf{filtering}{strand_filtering}) {\n+\t die("Error Config : The parameter strand_filtering is set to \\"0\\" while order_filtering is selected".\n+\t\t"\\nChange strand_filtering to \\"1\\" if you want to use the order filtering\\n");\n+\t}\n+\tif (( !defined($conf{filtering}{mu_length}) || !defined($conf{filtering}{sigma_length}) )&& $conf{filtering}{order_filtering}) {\n+\t die("Error Config : You should set parameters \\"mu_length\\" and \\"sigma_length\\" to use order filtering\\n");\n+\t}\n+\tif (( $conf{filtering}{insert_size_filtering} )&& !$conf{filtering}{strand_filtering}) {\n+\t die("Error Config : The parameter strand_filtering is set to \\"0\\" while insert_size_filtering is selected".\n+\t\t"\\nChange strand_filtering to \\"1\\" if you want to use the insert size filtering\\n");\n+\t}\n+\tif (( !defined($conf{filtering}{mu_length}) || !defined($conf{filtering}{sigma_length}) )&& $conf{filtering}{insert_size_filtering}) {\n+\t die("Error Config : You should set parameters \\"mu_length\\" and \\"sigma_length\\" to use discriminate insertions from deletions\\n");\n+\t}\n+\t\n+\tif (!defined($conf{filtering}{indel_sigma_threshold})) {\n+\t $conf{filtering}{indel_sigma_threshold} = 2;\n+\t}\n+\tif (!defined($conf{filtering}{dup_sigma_threshold})) {\n+\t $conf{filtering}{dup_sigma_threshold} = 2;\n+\t}\n+\tif (!defined($conf{filtering}{singleton_sigma_threshold})) {\n+\t $conf{filtering}{singleton_sigma_threshold} = 4;\n+\t}\n+\t\n+\tif (!defined($conf{filtering}{nb_pairs_order_threshold})) {\n+\t $conf{filtering}{nb_pairs_order_threshold} = 1;\n+\t}\n+\t\n+\tif (!defined($conf{filtering}{final_score_threshold})) {\n+\t $conf{filtering}{final_score_threshold} = 0.8;\n+\t}\n+\t\n+\tif ($conf{filtering}{nb_pairs_order_threshold}>$conf{filtering}{nb_pairs_threshold}) {\n+\t die("Error Config : Parameter \\"nb_pairs_order_threshold\\" should not exceed \\"nb_pairs_threshold\\"\\n");\n+\t}\n+\t\n+ }\n+ \n+ if($list_prgs=~/2circos$/){\n+\tforeach my $p (@circos_params) {\n+\t next if($list_prgs=~/^ratio/ && $p eq "colorcode");\n+\t die("Error Config : The circos parameter \\"$p\\" is not defined\\n") if (!defined $conf{circos}{$p});\n+\t}\n+ }\n+ \n+ if($list_prgs=~/2bed$/){\n+\tforeach my $p (@bed_params) {\n+\t die("Error Config : The bed parameter \\"$p\\" is not defined\\n") if (!defined $conf{bed}{$p});\n+\t}\n+ }\n+ \n+ if($list_prgs=~/links2compare/){\n+\tforeach my $p (@compare_params) {\n+\t die("Error Config : The compare parameter \\"$p\\" is not defined\\n") if (!defined $conf{compare}{$p});\n+\t}\n+\t\n+\tunless (defined($conf{compare}{same_sv_type})) {\n+\t $conf{compare}{same_sv_type} = 0;\n+\t}\n+\t\n+\tunless (defined($conf{compare}{min_overlap})) {\n+\t $conf{compare}{min_overlap} = 1E-9;\n+\t}\n+\t\n+\tif($conf{compare}{circos_output}){\n+\t foreach my $p (@circos_params) {\n+\t\tnext if($list_prgs=~/^ratio/ && $p eq "colorcode");\n+\t\tdie("Error Config : The circos parameter \\"$p\\" is not defined\\n") if (!defined $conf{circos}{$p});\n+\t }\n+\t}\n+\tif($conf{compare}{bed_output}){\n+\t foreach my $p (@bed_params) {\n+\t\tdie("Error Config : The bed parameter \\"$p\\" is not defined\\n") if (!defined $conf{bed}{$p});\n+\t }\n+\t die("Error Config : The compare parameter \\"list_read_lengths\\" is not defined\\n") if (!defined $conf{compare}{list_read_lengths});\n+\n+\t my @samples=split(",",$conf{compare}{list_samples});\n+\t my @read_lengths=split(",",$conf{compare}{list_read_lengths});\n+\t for my $i (0..$#samples){\n+\t\tmy @l=split("-",$read_lengths[$i]);\n+\t\t$conf{compare}{read_lengths}{$samples[$i]}={ 1=> $l[0], 2=> $l[1]};\n+\t }\n+\t}\n+ }\n+ \n+ \n+}\n+#------------------------------------------------------------------------------#\n+#::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::#\n' |
| b |
| diff -r 105e78d03f35 -r eb65c0fa5542 svdetect/SVDetect_run_parallel.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/svdetect/SVDetect_run_parallel.xml Thu Jul 12 12:19:40 2012 -0400 |
| b |
| b'@@ -0,0 +1,324 @@\n+<tool id="svdetect_run_parallel" name="Detect clusters of anomalously mapped pairs">\n+\n+<description>and identify structural variants</description>\n+\n+<command interpreter="perl">SVDetect_run_parallel.pl\n+\n+#if $getLinks.linking == "linking"\n+linking\n+<!-- -out1 \'$links_file\' -->\n+#end if\n+#if $getFilteredLinks.filtering == "filtering"\n+filtering\n+<!--- out2 \'$flinks_file\' -->\n+#if str($getFilteredLinks.links2SV) == "create"\n+links2SV\n+-out3 \'$sv_file\'\n+#end if\n+#if $getFilteredLinks.file_conversion.file_conversion_select=="convert" and str($getFilteredLinks.file_conversion.links2circos) == "create"\n+links2circos\n+-out4 \'$circos_file\'\n+#end if\n+#if $getFilteredLinks.file_conversion.file_conversion_select=="convert" and str($getFilteredLinks.file_conversion.links2bed) == "create"\n+links2bed\n+-out5 \'$bed_file\'\n+#end if\n+#end if\n+-conf \'$config_file\'\n+-l \'$log_file\'\n+-N \'$sample_name\'\n+\n+</command>\n+\n+<inputs>\n+\t<param name="sample_name" type="text" value="sample" label="Sample Name"/>\n+\t<param name="mates_file" format="bam" type="data" label="Input BAM file (.ab.bam)"/>\n+ \t<param name="cmap_file" format="len" type="data" label="Chromosomes list file (.len)" help="Tabulated file format with Chromosome ID (integer from 1), name and length"/>\n+ \t<param name="mates_orientation" type="select" format="txt" label="Type of sequencing technology and libraries">\n+\t\t<option value="FR">Illumina paired-ends</option>\n+\t\t<option value="RF">Illumina mate-pairs</option>\n+\t\t<option value="FR">SOLiD paired-ends</option>\n+\t\t<option value="RR">SOLiD mate-pairs</option>\n+ \t</param>\n+\t<param name="read1_length" type="integer" size="10" value="50" label="Read 1 length (bp)" help="Length of the first read in a pair (left read)"/>\n+\t<param name="read2_length" type="integer" size="10" value="50" label="Read 2 length (bp)" help="Length of the second read in a pair (right read)"/>\n+\t<param name="sv_type" type="select" format="txt" label="Type of SV to detect">\n+\t\t<option value="all">all types of SVs</option>\n+\t\t<option value="intra">intrachromosomal SVs only</option>\n+\t\t<option value="inter">interchromosomal SVs only</option>\n+ \t</param>\n+ \t\n+ \t<conditional name="getLinks">\n+ \t\t<param name="linking" type="select" label="Linking procedure" help="Detection and isolation of links">\n+\t\t\t<option value="linking">Yes</option>\n+\t\t\t<option value="">No, already done</option>\n+ \t\t</param>\n+\t\t<when value="">\n+ \t\t\t<!-- do nothing here -->\n+ \t\t</when>\n+ \t\t<when value="linking">\n+\t\t\t<param name="splitmate" label="Do you want to split the original mate file per chromosome for parallel computing?" type="boolean" truevalue="split" falsevalue="do_not_split" checked="True" help="Untick it if already done"/>\n+ \t\t\t<param name="window_size" type="integer" size="20" value="3000" label="Window size (bp)" help="Equal to at least \xe2\x80\x9c2\xc2\xb5+2\xe2\x88\x9a2\xcf\x83"/>\n+\t\t\t<param name="step_length" type="integer" size="20" value="250" label="Step length size (bp)" help="Equal to 1/2 or 1/4 of the window size"/>\n+ \t\t</when>\n+ \t</conditional>\n+\n+ \t<conditional name="getFilteredLinks">\n+\t \t<param name="filtering" type="select" label="Filtering procedure" help="Filtering of links according different parameters and thresholds">\n+\t\t\t<option value="filtering">Yes</option>\n+ <option value="">No</option>\n+\t \t</param>\n+\t\t<when value="">\n+\t \t\t<!-- do nothing here -->\n+\t \t</when>\n+\t \t<when value="filtering">\n+\t\t\t\n+\t\t\t<param name="splitlink" label="Do you want to split the original link file per chromosome for parallel computing?" type="boolean" truevalue="split" falsevalue="do_not_split" checked="False" help="Untick it if (the linking is) already done"/>\n+\t\t\t<param name="chromosomes" type="text" size="20" label="List of chromosome names to keep or exclude"/>\n+\t\t\t<param name="nb_pairs_threshold" type="integer" size="20" value="5" label="Minimum number of pairs in a cluster"/>\n+\t\t\n+\t\t\t<conditional name="filter1">\n+\t \t\t\t<param name='..b'e">\n+<general>\n+input_format = bam\n+sv_type = ${sv_type}\n+mates_orientation=${mates_orientation}\n+read1_length=${read1_length}\n+read2_length=${read2_length}\n+mates_file=${mates_file}\n+cmap_file=${cmap_file}\n+tmp_dir=$__new_file_path__/svdetect/tmp\n+output_dir=$__new_file_path__/svdetect\n+num_threads=8\n+</general> \n+\n+#if $getLinks.linking == "linking"\n+<detection>\n+#if str($getLinks.splitmate) == "split"\n+split_mate_file=1\n+#else\n+split_mate_file=0\n+#end if\n+window_size=${getLinks.window_size}\n+step_length=${getLinks.step_length}\n+</detection> \n+#end if\n+\n+#if $getFilteredLinks.filtering == "filtering"\n+<filtering>\n+#if str($getFilteredLinks.splitlink) == "split"\n+split_link_file=1\n+#else\n+split_link_file=0\n+#end if\n+#if str($getFilteredLinks.chromosomes) != ""\n+chromosomes=${getFilteredLinks.chromosomes}\n+#end if\n+nb_pairs_threshold=${getFilteredLinks.nb_pairs_threshold}\n+#if $getFilteredLinks.filter1.strand_filtering == "strand"\n+strand_filtering=1\n+final_score_threshold=${getFilteredLinks.filter1.final_score_threshold}\n+#if $getFilteredLinks.filter1.filter2.order_filtering == "order"\n+order_filtering=1\n+mu_length=${getFilteredLinks.filter1.filter2.mu_length}\n+sigma_length=${getFilteredLinks.filter1.filter2.sigma_length}\n+nb_pairs_order_threshold=${getFilteredLinks.filter1.filter2.nb_pairs_order_threshold}\n+#if $getFilteredLinks.filter1.filter2.filter3.insert_size_filtering == "insert"\n+insert_size_filtering=1\n+indel_sigma_threshold=${getFilteredLinks.filter1.filter2.filter3.indel_sigma_threshold}\n+dup_sigma_threshold=${getFilteredLinks.filter1.filter2.filter3.dup_sigma_threshold}\n+singleton_sigma_threshold=${getFilteredLinks.filter1.filter2.filter3.singleton_sigma_threshold}\n+#else\n+insert_size_filtering=0\n+#end if\n+#else\n+order_filtering=0\n+#end if\n+#else\n+strand_filtering=0\n+#end if\n+</filtering> \n+#end if\n+\n+#if $getFilteredLinks.filtering == "filtering"\n+#if $getFilteredLinks.file_conversion.file_conversion_select == "convert"\n+#if str($getFilteredLinks.file_conversion.links2circos) == "create"\n+<circos>\n+organism_id=${getFilteredLinks.file_conversion.organism_id}\n+<colorcode>\n+#for $color_repeat in $getFilteredLinks.file_conversion.color_code\n+${color_repeat.color}=${color_repeat.interval}\n+#end for\n+</colorcode>\n+</circos>\n+#end if\n+#if str($getFilteredLinks.file_conversion.links2bed) == "create"\n+<bed>\n+<colorcode>\n+#for $color_repeat in $getFilteredLinks.file_conversion.color_code\n+#if str($color_repeat.color)== "grey"\n+190,190,190=${color_repeat.interval}\n+#end if\n+#if str($color_repeat.color)== "black"\n+0,0,0=${color_repeat.interval}\n+#end if\n+#if str($color_repeat.color)== "blue"\n+0,0,255=${color_repeat.interval}\n+#end if\n+#if str($color_repeat.color)== "green"\n+0,255,0=${color_repeat.interval}\n+#end if\n+#if str($color_repeat.color)== "purple"\n+153,50,205=${color_repeat.interval}\n+#end if\n+#if str($color_repeat.color)== "orange"\n+255,140,0=${color_repeat.interval}\n+#end if\n+#if str($color_repeat.color)== "red"\n+255,0,0=${color_repeat.interval}\n+#end if\n+#end for\n+</colorcode>\n+</bed>\n+#end if\n+#end if\n+#end if\t\n+\t</configfile>\n+</configfiles>\n+\n+ <help>\n+**What it does**\n+\n+SVDetect - Version : 0.8\n+\n+Parallel version (nCPU=8)\n+\n+SVDetect is a application for the isolation and the type prediction of intra- and inter-chromosomal rearrangements from paired-end/mate-pair sequencing data provided by the high-throughput sequencing technologies\n+\n+This tool aims to identifying structural variations (SVs) with both clustering and sliding-window strategies, and helping in their visualization at the genome scale.\n+SVDetect is compatible with SOLiD and Illumina (>=1.3) reads.\n+\n+Manual documentation available at the http://svdetect.sourceforge.net/Site/Manual.html\n+\n+-----\n+\n+.. class:: infomark\n+\n+Contact Bruno Zeitouni (svdetect@curie.fr) for any questions or concerns about the Galaxy implementation of SVDetect.\n+\n+ </help>\n+\n+</tool>\n' |
| b |
| diff -r 105e78d03f35 -r eb65c0fa5542 svdetect/circos_graph.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/svdetect/circos_graph.xml Thu Jul 12 12:19:40 2012 -0400 |
| b |
| @@ -0,0 +1,289 @@ +<tool id="circos_graph" name="Circos"> + +<description>plots</description> + +<command interpreter="perl">circos/bin/circos + +-conf '$circos_config_file' +-outputdir $__new_file_path__/svdetect +-outputfile '$outputfile' +-png +-out1 '$out1_png' + +> '$log_file' + +</command> + + +<inputs> + <param name="graph_name" type="text" size="20" value="graph1" label="Graph name"/> + + <param name="karyotype" type="select" format="txt" label="Type of model organism"> + <option value="data/karyotype.human_hg19.txt">Human (homo sapiens, hs) -hg19-</option> + <option value="data/karyotype.human.txt">Human (homo sapiens, hs) -hg18-</option> + <option value="data/2/karyotype.mouse.txt">Mouse (Mus Musculus, mm)</option> + <option value="data/2/karyotype.dog.txt">Dog (Canis familiaris, cf)</option> + <option value="data/2/karyotype.rt.txt">Rat (Rattus norvegicus, rn)</option> + <option value="data/karyotype.yeast.txt">Yeast (Saccharomyces Cerevisiae, sc) -SGD-</option> + + </param> + <param name="chromosomes_units" type="integer" size="50" value="1000000" label="Chromosomes units"/> + <param name="chromosomes" type="text" size="100" value="" label="List of chromosome names to keep or exclude" help="ex: hs2;hs3 or -hsX;-hsY"> + <sanitizer> + <valid initial="string.printable"> + <add value=";"/> + </valid> + </sanitizer> + </param> + <param name="link_file" format="segdup" type="data" label="Input link file (.segdup)"/> + <param name="outputfile" type="text" size="50" value="graph1.circos.png" label="Output image name file (png)"/> +</inputs> + +<outputs> + <data format="txt" name="log_file" label="${graph_name}.circos.log"/> + <data format="png" name="out1_png" label="${outputfile}"/> +</outputs> + + + +<configfiles> + <configfile name="ideogram_config_file"> + +<ideogram> + +<spacing> + +default = 5u +break = 1u + +axis_break_at_edge = yes +axis_break = yes +axis_break_style = 2 + +<break_style 1> +stroke_color = black +fill_color = blue +thickness = 0.25r +stroke_thickness = 2 +</break> + +<break_style 2> +stroke_color = black +stroke_thickness = 3p +thickness = 1.5r +</break> + +</spacing> + +## thickness (px) of chromosome ideogram +thickness = 100p +stroke_thickness = 2 +## ideogram border color +stroke_color = black +fill = yes +## the default chromosome color is set here and any value +## defined in the karyotype file overrides it +fill_color = black + +## fractional radius position of chromosome ideogram within image +radius = 0.85r +show_label = yes +label_with_tag = yes +label_font = condensedbold +label_radius = dims(ideogram,radius) + 0.075r +label_size = 60p + +## cytogenetic bands +band_stroke_thickness = 2 + +## show_bands determines whether the outline of cytogenetic bands +## will be seen +show_bands = yes +## in order to fill the bands with the color defined in the karyotype +## file you must set fill_bands +fill_bands = yes + +</ideogram> + + </configfile> + + <configfile name="ticks_config_file"> + +show_ticks = yes +show_tick_labels = yes + +<ticks> +radius = dims(ideogram,radius_outer) +multiplier = 1e-6 + +<tick> +spacing = 0.5u +size = 2p +thickness = 2p +color = grey +show_label = no +label_size = 12p +label_offset = 0p +format = %.2f +</tick> + +<tick> +spacing = 1u +size = 3p +thickness = 2p +color = dgrey +show_label = no +label_size = 12p +label_offset = 0p +format = %.2f +</tick> + +<tick> +spacing = 5u +size = 5p +thickness = 2p +color = black +show_label = yes +label_size = 16p +label_offset = 0p +format = %d +</tick> + +<tick> +spacing = 10u +size = 8p +thickness = 2p +color = black +show_label = yes +label_size = 20p +label_offset = 5p +format = %d +</tick> +</ticks> + </configfile> + + + <configfile name="circos_config_file"> +<colors> +<<include etc/colors.conf>> +</colors> + +<fonts> +<<include etc/fonts.conf>> +</fonts> + +<<include $ideogram_config_file>> +<<include $ticks_config_file>> + +karyotype = $karyotype + +<image> +24bit = yes +##png = yes +##svg = no +## radius of inscribed circle in image +radius = 1500p +background = white +## by default angle=0 is at 3 o'clock position +angle_offset = -90 +#angle_orientation = counterclockwise + +auto_alpha_colors = yes +auto_alpha_steps = 5 +</image> + +chromosomes_units= $chromosomes_units + +#if str($chromosomes)=="" +chromosomes_display_default = yes +#else +chromosomes_display_default = no +chromosomes = $chromosomes +#end if + +<links> + +z = 0 +radius = 0.95r +bezier_radius = 0.2r + +<link segdup> +show = yes +color = dgrey_a5 +thickness = 2 +file = $link_file +record_limit = 1000 +</link> + +</links> + + +anglestep = 0.5 +minslicestep = 10 +beziersamples = 40 +debug = no +warnings = no +imagemap = no + +units_ok = bupr +units_nounit = n + </configfile> +</configfiles> + + <help> +**What it does** + +Circos + +Manual documentation available at the http://circos.ca/ + + +**Example of link segdup file** + +segdup file:: + + 1 hs1 1077096 1078746 color=red + 1 hs1 1080923 1082805 color=red + 2 hs1 1137684 1137961 color=red + 2 hs3 1138138 1138423 color=red + 3 hs11 1169417 1170000 color=red + 3 hs11 1170025 1170975 color=red + 4 hs11 1222480 1224271 color=green + 4 hs11 1223328 1225675 color=green + 5 hs12 1223336 1225812 color=grey + 5 hs13 1224709 1227633 color=grey + 6 hs11 1223621 1226460 color=red + 6 hs11 1224918 1227633 color=red + 7 hs11 1399510 1401513 color=white + 7 hs11 1401628 1403697 color=white + 8 hs15 1652045 1653746 color=red + 8 hs15 1657167 1658940 color=red + 9 hs11 165333 165887 color=white + 9 hs11 165981 168016 color=white + 10 hs11 1702700 1702841 color=red + 10 hs11 1702903 1703057 color=red + 11 hs11 1912272 1915186 color=white + 11 hs11 1937111 1939824 color=white + 12 hs11 1983211 1983355 color=red + 12 hs11 1983591 1983748 color=red + 13 hs11 2913657 2913898 color=white + 13 hs11 2914048 2914341 color=white + 14 hs11 3090593 3090749 color=purple + 14 hs11 3090709 3090864 color=purple + 15 hs21 3466365 3466434 color=red + 15 hs21 3466554 3466620 color=red + 16 hsX 3603073 3603321 color=white + 16 hsX 3603295 3603520 color=white + + + +----- + +.. class:: infomark + +Contact Bruno Zeitouni (svdetect@curie.fr) for any questions or concerns about the Galaxy implementation of Circos. + + + </help> + +</tool> |