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Commit message:
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removed:
svdetect.zip 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 |
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| diff -r 59b91705b68c -r 657e17d618f3 svdetect.zip |
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| Binary file svdetect.zip has changed |
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| diff -r 59b91705b68c -r 657e17d618f3 svdetect/BAM_preprocessingPairs.pl --- a/svdetect/BAM_preprocessingPairs.pl Tue Nov 06 10:02:27 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,340 +0,0 @@\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 $num;\n-}\n-#------------------------------------------------------------------------------#\n' |
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| diff -r 59b91705b68c -r 657e17d618f3 svdetect/BAM_preprocessingPairs.xml --- a/svdetect/BAM_preprocessingPairs.xml Tue Nov 06 10:02:27 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,77 +0,0 @@ -<tool id="svdetect_preprocessing" name="BAM preprocessing"> - - <description>to get abnormal pairs</description> - - <command interpreter="perl"> BAM_preprocessingPairs.pl -t '$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> |
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| diff -r 59b91705b68c -r 657e17d618f3 svdetect/SVDetect_compare.pl --- a/svdetect/SVDetect_compare.pl Tue Nov 06 10:02:27 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,716 +0,0 @@\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=> $l[1]};\n-\t }\n-\t}\n- }\n- \n- \n-}\n-#------------------------------------------------------------------------------#\n-#::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::#\n' |
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| diff -r 59b91705b68c -r 657e17d618f3 svdetect/SVDetect_compare.xml --- a/svdetect/SVDetect_compare.xml Tue Nov 06 10:02:27 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,218 +0,0 @@ -<tool id="svdetect_compare" name="Compare"> - -<description>structural variants between two samples</description> - -<command interpreter="perl">SVDetect_compare.pl links2compare -conf '$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 $file_conversion.file_conversion_select == "convert" -circos_output=${$file_conversion.links2circos} -bed_output=${$file_conversion.links2bed} -#end if -</compare> - - </configfile> -</configfiles> - - <help> -**What it does** - -SVDetect - Version : 0.8 - -Comparison of clusters between two samples to get common or sample-specific SVs - -This program is designed to compare filtered links between two anomalously mapped mate-pair/paired-end datasets -and to identify common and sample-specific SVs (like the usual sample/reference design). -Overlaps between coordinates of clusters and types of SVs are used as parameters of comparison. - -Manual documentation available at the http://svdetect.sourceforge.net/Site/Manual.html - ------ - -.. class:: infomark - -Contact Bruno Zeitouni (svdetect@curie.fr) for any questions or concerns about the Galaxy implementation of SVDetect. - </help> - -</tool> |
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| diff -r 59b91705b68c -r 657e17d618f3 svdetect/SVDetect_import.sh --- a/svdetect/SVDetect_import.sh Tue Nov 06 10:02:27 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,15 +0,0 @@ -#!/bin/bash - - -while getopts "i:o:" optionName; do -case "$optionName" in - -i) INPUT="$OPTARG";; -o) OUTPUT="$OPTARG";; - -esac -done - -rm $OUTPUT - -ln -s $INPUT $OUTPUT |
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| diff -r 59b91705b68c -r 657e17d618f3 svdetect/SVDetect_import.xml --- a/svdetect/SVDetect_import.xml Tue Nov 06 10:02:27 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,85 +0,0 @@ -<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 59b91705b68c -r 657e17d618f3 svdetect/SVDetect_run_parallel.pl --- a/svdetect/SVDetect_run_parallel.pl Tue Nov 06 10:02:27 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,3537 +0,0 @@\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 59b91705b68c -r 657e17d618f3 svdetect/SVDetect_run_parallel.xml --- a/svdetect/SVDetect_run_parallel.xml Tue Nov 06 10:02:27 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,324 +0,0 @@\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=${color_repeat.interval}\n-#end if\n-#end for\n-</colorcode>\n-</bed>\n-#end if\n-#end if\n-#end if\t\n-\t</configfile>\n-</configfiles>\n-\n- <help>\n-**What it does**\n-\n-SVDetect - Version : 0.8\n-\n-Parallel version (nCPU=8)\n-\n-SVDetect is a application for the isolation and the type prediction of intra- and inter-chromosomal rearrangements from paired-end/mate-pair sequencing data provided by the high-throughput sequencing technologies\n-\n-This tool aims to identifying structural variations (SVs) with both clustering and sliding-window strategies, and helping in their visualization at the genome scale.\n-SVDetect is compatible with SOLiD and Illumina (>=1.3) reads.\n-\n-Manual documentation available at the http://svdetect.sourceforge.net/Site/Manual.html\n-\n------\n-\n-.. class:: infomark\n-\n-Contact Bruno Zeitouni (svdetect@curie.fr) for any questions or concerns about the Galaxy implementation of SVDetect.\n-\n- </help>\n-\n-</tool>\n' |
| b |
| diff -r 59b91705b68c -r 657e17d618f3 svdetect/circos_graph.xml --- a/svdetect/circos_graph.xml Tue Nov 06 10:02:27 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,289 +0,0 @@ -<tool id="circos_graph" name="Circos"> - -<description>plots</description> - -<command interpreter="perl">circos/bin/circos - --conf '$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> |