Repository 'svdetect'
hg clone https://toolshed.g2.bx.psu.edu/repos/bzeitouni/svdetect

Changeset 17:f3202b943f88 (2012-07-12)
Previous changeset 16:fc601c7fa886 (2012-07-12) Next changeset 18:e2a28ab2af2e (2012-07-12)
Commit message:
Deleted selected files
removed:
SVDetect_toolshed_version.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/SVDetect_toolshed_version.zip
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diff -r fc601c7fa886 -r f3202b943f88 SVDetect_toolshed_version.zip
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Binary file SVDetect_toolshed_version.zip has changed
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diff -r fc601c7fa886 -r f3202b943f88 svdetect/BAM_preprocessingPairs.pl
--- a/svdetect/BAM_preprocessingPairs.pl Thu Jul 12 12:03:16 2012 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
[
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 $num;\n-}\n-#------------------------------------------------------------------------------#\n'
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diff -r fc601c7fa886 -r f3202b943f88 svdetect/BAM_preprocessingPairs.xml
--- a/svdetect/BAM_preprocessingPairs.xml Thu Jul 12 12:03:16 2012 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
[
@@ -1,77 +0,0 @@
-<tool id="svdetect_preprocessing" name="BAM preprocessing">
-
-  <description>to get abnormal pairs</description>
-
-  <command interpreter="perl"> BAM_preprocessingPairs.pl -t '$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 (bruno.zeitouni@curie.fr) for any questions or concerns about the Galaxy implementation of SVDetect.
-
-  </help>
-
-</tool>
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diff -r fc601c7fa886 -r f3202b943f88 svdetect/SVDetect_compare.pl
--- a/svdetect/SVDetect_compare.pl Thu Jul 12 12:03:16 2012 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
[
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=> $l[1]};\n-\t    }\n-\t}\n-    }\n-   \n-    \n-}\n-#------------------------------------------------------------------------------#\n-#::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::#\n'
b
diff -r fc601c7fa886 -r f3202b943f88 svdetect/SVDetect_compare.xml
--- a/svdetect/SVDetect_compare.xml Thu Jul 12 12:03:16 2012 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
[
@@ -1,218 +0,0 @@
-<tool id="svdetect_compare" name="Compare">
-
-<description>structural variants between two samples</description>
-
-<command interpreter="perl">SVDetect_compare.pl links2compare -conf '$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">
-&lt;general&gt;
-output_dir=$__new_file_path__/svdetect
-&lt;/general&gt; 
-
-#if $file_conversion.file_conversion_select == "convert"
-#if $file_conversion.links2circos
-&lt;circos&gt;
-organism_id=${file_conversion.organism_id}
-&lt;colorcode&gt;
-#for $color_repeat in $file_conversion.color_code
-${color_repeat.color}=${color_repeat.interval}
-#end for
-&lt;/colorcode&gt;
-&lt;/circos&gt;
-#end if
-#if $file_conversion.links2bed
-&lt;bed&gt;
-&lt;colorcode&gt;
-#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=${color_repeat.interval}
-#end if
-#end for
-&lt;/colorcode&gt;
-&lt;/bed&gt;
-#end if
-#end if
-
-&lt;compare&gt;
-list_samples=${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 $file_conversion.file_conversion_select == "convert"
-circos_output=${$file_conversion.links2circos}
-bed_output=${$file_conversion.links2bed}
-#end if
-&lt;/compare&gt; 
-
- </configfile>
-</configfiles>
-
-  <help>
-**What it does**
-
-SVDetect - Version : 0.8
-
-Comparison of clusters between two samples to get common or sample-specific SVs
-
-This program is designed to compare filtered links between two anomalously mapped mate-pair/paired-end datasets
-and to identify common and sample-specific SVs (like the usual sample/reference design).
-Overlaps between coordinates of clusters and types of SVs are used as parameters of comparison.
-
-Manual documentation available at the http://svdetect.sourceforge.net/Site/Manual.html
-
------
-
-.. class:: infomark
-
-Contact Bruno Zeitouni (bruno.zeitouni@curie.fr) for any questions or concerns about the Galaxy implementation of SVDetect.
-  </help>
-
-</tool>
b
diff -r fc601c7fa886 -r f3202b943f88 svdetect/SVDetect_import.sh
--- a/svdetect/SVDetect_import.sh Thu Jul 12 12:03:16 2012 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
b
@@ -1,15 +0,0 @@
-#!/bin/bash
-
-
-while getopts "i:o:" optionName; do
-case "$optionName" in
-
-i) INPUT="$OPTARG";;
-o) OUTPUT="$OPTARG";;
-
-esac
-done
-
-rm $OUTPUT
-
-ln -s $INPUT $OUTPUT
b
diff -r fc601c7fa886 -r f3202b943f88 svdetect/SVDetect_import.xml
--- a/svdetect/SVDetect_import.xml Thu Jul 12 12:03:16 2012 -0400
+++ /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 (bruno.zeitouni@curie.fr) for any questions or concerns about the Galaxy implementation of SVDetect.
-  </help>
-
-</tool>
b
diff -r fc601c7fa886 -r f3202b943f88 svdetect/SVDetect_run_parallel.pl
--- a/svdetect/SVDetect_run_parallel.pl Thu Jul 12 12:03:16 2012 -0400
+++ /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 fc601c7fa886 -r f3202b943f88 svdetect/SVDetect_run_parallel.xml
--- a/svdetect/SVDetect_run_parallel.xml Thu Jul 12 12:03:16 2012 -0400
+++ /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'lt;general&gt;\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-&lt;/general&gt; \n-\n-#if $getLinks.linking == "linking"\n-&lt;detection&gt;\n-#if str($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-&lt;/detection&gt; \n-#end if\n-\n-#if $getFilteredLinks.filtering == "filtering"\n-&lt;filtering&gt;\n-#if str($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-&lt;/filtering&gt; \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-&lt;circos&gt;\n-organism_id=${getFilteredLinks.file_conversion.organism_id}\n-&lt;colorcode&gt;\n-#for $color_repeat in $getFilteredLinks.file_conversion.color_code\n-${color_repeat.color}=${color_repeat.interval}\n-#end for\n-&lt;/colorcode&gt;\n-&lt;/circos&gt;\n-#end if\n-#if str($getFilteredLinks.file_conversion.links2bed) == "create"\n-&lt;bed&gt;\n-&lt;colorcode&gt;\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-&lt;/colorcode&gt;\n-&lt;/bed&gt;\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 (bruno.zeitouni@curie.fr) for any questions or concerns about the Galaxy implementation of SVDetect.\n-\n-  </help>\n-\n-</tool>\n'
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diff -r fc601c7fa886 -r f3202b943f88 svdetect/SVDetect_toolshed_version.zip
b
Binary file svdetect/SVDetect_toolshed_version.zip has changed