Mercurial > repos > mcharles > rapsodyn
changeset 33:193b8462b80c draft default tip
Uploaded
| author | mcharles |
|---|---|
| date | Fri, 10 Oct 2014 04:46:10 -0400 |
| parents | a86903ab5266 |
| children | |
| files | rapsodyn/Galaxy-Workflow-rapsosnp_v1.20.ga rapsodyn/Galaxy-Workflow-rapsosnp_v1.20_-_10x_-_bam.ga rapsodyn/Galaxy-Workflow-rapsosnp_v1.20_-_10x_-_sam.ga rapsodyn/Galaxy-Workflow-rapsosnp_v1.20_-_1x_-_sam.ga rapsodyn/Galaxy-Workflow-rapsosnp_v1.20_-_4x_-_bam.ga rapsodyn/PrepareFastqLight.pl~ rapsodyn/PrepareFastqLight.xml~ rapsodyn/merge_bam.xml rapsodyn/tool_dependencies.xml |
| diffstat | 9 files changed, 5597 insertions(+), 1248 deletions(-) [+] |
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--- a/rapsodyn/Galaxy-Workflow-rapsosnp_v1.20_-_10x_-_sam.ga Thu Oct 09 08:28:22 2014 -0400 +++ b/rapsodyn/Galaxy-Workflow-rapsosnp_v1.20_-_10x_-_sam.ga Fri Oct 10 04:46:10 2014 -0400 @@ -285,14 +285,14 @@ } ], "position": { - "left": 936.93310546875, + "left": 936.933349609375, "top": 338.43333435058594 }, "post_job_actions": {}, "tool_errors": null, "tool_id": "PrepareFastqLight", - "tool_state": "{\"__page__\": 0, \"quality_type\": \"\\\"illumina\\\"\", \"min_length\": \"\\\"30\\\"\", \"__rerun_remap_job_id__\": null, \"min_quality\": \"\\\"30\\\"\", \"input_read1_file\": \"null\", \"input_read2_file\": \"null\"}", - "tool_version": "1.01", + "tool_state": "{\"__page__\": 0, \"quality_type\": \"\\\"auto\\\"\", \"min_length\": \"\\\"30\\\"\", \"__rerun_remap_job_id__\": null, \"min_quality\": \"\\\"30\\\"\", \"input_read1_file\": \"null\", \"input_read2_file\": \"null\"}", + "tool_version": "1.03", "type": "tool", "user_outputs": [] }, @@ -326,14 +326,14 @@ } ], "position": { - "left": 943.93310546875, + "left": 943.933349609375, "top": 585.4333343505859 }, "post_job_actions": {}, "tool_errors": null, "tool_id": "PrepareFastqLight", - 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"id": 65, + "id": 15, "output_name": "log_file" }, { - "id": 66, + "id": 13, "output_name": "log_file" }, { - "id": 67, + "id": 11, "output_name": "log_file" }, { - "id": 68, - "output_name": "log_file" - }, - { - "id": 70, + "id": 10, "output_name": "log_file" }, { - "id": 71, + "id": 14, "output_name": "log_file" }, { - "id": 72, + "id": 12, "output_name": "log_file" }, { - "id": 73, + "id": 9, "output_name": "log_file" }, { - "id": 69, + "id": 8, "output_name": "log_file" }, { - "id": 75, + "id": 7, "output_name": "log_file" } ]
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--- a/rapsodyn/PrepareFastqLight.pl~ Thu Oct 09 08:28:22 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,512 +0,0 @@ -#!/usr/bin/perl -#V1.0.2 added auto type detection -#V1.0.1 added log, option parameters -use strict; -use warnings; -use Getopt::Long; - -my $read1_file; -my $read2_file; -my $log_file; -my $output1_file; -my $output2_file; - -my $TYPE="sanger"; -my $MIN_LENGTH=30; -my $MIN_QUALITY=30; - -my $VERBOSE = "OFF"; - -GetOptions ( -"read1_file=s" => \$read1_file, -"read2_file=s" => \$read2_file, -"log_file=s" => \$log_file, -"output1_file=s" => \$output1_file, -"output2_file=s" => \$output2_file, -"type=s" => \$TYPE, -"min_length=i" => \$MIN_LENGTH, -"min_quality=i" => \$MIN_QUALITY, -"verbose=s" => \$VERBOSE -) or die("Error in command line arguments\n"); - - -my $nb_read1=0; -my $nb_base_read1=0; -my $nb_read2=0; -my $nb_base_read2=0; - -my $nb_read1_t=0; -my $nb_base_read1_t=0; -my $nb_read2_t=0; -my $nb_base_read2_t=0; - -my $nb_base_current_t=0; - -open(READ1, $read1_file) or die ("Can't open $read1_file\n"); -open(READ2, $read2_file) or die ("Can't open $read2_file\n"); -open(OUT1, ">$output1_file") or die ("Can't open $output1_file\n"); -open(OUT2, ">$output2_file") or die ("Can't open $output2_file\n"); -open (LF,">$log_file") or die("Can't open $log_file\n"); - - -my $error1=0; -my $error2=0; -my $error3=0; -my $error4=0; -my $error5=0; -my $error6=0; -my $error7=0; -my $error8=0; -my $error9=0; -my $error10=0; - -my $auto_type=""; -my %qual; -if ($TYPE eq "auto"){ - my $compt=0; - open(DETECT, $read1_file) or die ("Can't open $read1_file\n"); - while (my $ligne1_r1 =<DETECT>){ - my $ligne2_r1 =<DETECT>; - my $ligne3_r1 =<DETECT>; - my $ligne4_r1 =<DETECT>; - $compt++; - if ($ligne4_r1 =~ /^(.*)\s*$/i){ - my $qual = $1; - my @q = split(//,$qual); - for (my $i=0;$i<=$#q;$i++){ - my $num = ord($q[$i]); - if ($qual{$num}){ - $qual{$num}++; - } - else { - $qual{$num} = 1; - } - #range sanger / illumina 1.8+ : 33->94 - #range illumina 1.3->1.7 : 64->105 - if ($num > 94){$auto_type = "illumina";last;} - if ($num < 64){$auto_type = "sanger";last;} - } - } - else { - print STDERR "Error in format detection : quality not recognized\n$ligne4_r1"; - exit(0); - } - - if ($auto_type ne ""){ - last; - } - - } - close (DETECT); - if ($auto_type eq ""){ - print STDERR "Error in format detection : type not recognized parsing read1\n"; - foreach my $key (sort {$a <=> $b} keys %qual){ - print "$key\t:\t",$qual{$key},"\n"; - } - exit(0); - } - else { - $TYPE = $auto_type; - } -} - - - - -while (my $ligne1_r1 =<READ1>){ - my $ligne2_r1 =<READ1>; - my $ligne3_r1 =<READ1>; - my $ligne4_r1 =<READ1>; - my $ligne1_r2 =<READ2>; - my $ligne2_r2 =<READ2>; - my $ligne3_r2 =<READ2>; - my $ligne4_r2 =<READ2>; - - $nb_read1++; - $nb_read2++; - -#@ 1 sec - if ((!$ligne1_r1)||(!$ligne2_r1)||(!$ligne3_r1)||(!$ligne4_r1)||(!$ligne1_r2)||(!$ligne2_r2)||(!$ligne3_r2)||(!$ligne4_r2)){ - if ($VERBOSE eq "ON"){ - print "Error in file format"; - if ($ligne1_r1){print $ligne1_r1;} - if ($ligne2_r1){print $ligne2_r1;} - if ($ligne3_r1){print $ligne3_r1;} - if ($ligne4_r1){print $ligne4_r1;} - if ($ligne1_r2){print $ligne1_r2;} - if ($ligne2_r2){print $ligne2_r2;} - if ($ligne3_r2){print $ligne3_r2;} - if ($ligne4_r2){print $ligne4_r2;} - print "\n"; - } - $error1++; - } - elsif(($ligne1_r1 !~/^\@/)||($ligne1_r2 !~/^\@/)||($ligne3_r1 !~/^\+/)||($ligne3_r2 !~/^\+/)){ - if ($VERBOSE eq "ON"){ - print "Error in header : format\n"; - print $ligne1_r1; - print $ligne2_r1; - print $ligne3_r1; - print $ligne4_r1; - print $ligne1_r2; - print $ligne2_r2; - print $ligne3_r2; - print $ligne4_r2; - print "\n"; - } - $error2++; - } -#@ 1 - 2 sec - else { - - my $length_seq1 = length($ligne2_r1); - my $length_qual1 =length($ligne4_r1); - my $seq1; - my $qual1; - - my $length_seq2 = length($ligne2_r2); - my $length_qual2 =length($ligne4_r2); - my $seq2; - my $qual2; - my $header1=""; - my $header2=""; - my $repheader1=""; - my $repheader2=""; - - - if ($ligne1_r1 =~/^\@(.*?)[\s\/]/){ - $header1 = $1; - } - - if ($ligne3_r1 =~/^\+(.*?)[\s\/]/){ - $repheader1 = $1; - } - - if ($ligne1_r2 =~/^\@(.*?)[\s\/]/){ - $header2 = $1; - } - - if ($ligne3_r2 =~/^\+(.*?)[\s\/]/){ - $repheader2 = $1; - } -#@ 2 sec - - ### Verification de la coherence sequence /qualité @ 1 sec - if (($TYPE eq "illumina")&&((!$header1)||(!$header2)||(!$repheader1)||(!$repheader2))){ - if ($VERBOSE eq "ON"){ - print "Error in header : empty\n"; - print $ligne1_r1; - print $ligne2_r1; - print $ligne3_r1; - print $ligne4_r1; - print $ligne1_r2; - print $ligne2_r2; - print $ligne3_r2; - print $ligne4_r2; - print "\n"; - } - $error3++; - } - elsif (($TYPE eq "sanger")&&((!$header1)||(!$header2))){ - if ($VERBOSE eq "ON"){ - print "Error in header refgsd : empty\n"; - print $ligne1_r1; - print $ligne2_r1; - print $ligne3_r1; - print $ligne4_r1; - print $ligne1_r2; - print $ligne2_r2; - print $ligne3_r2; - print $ligne4_r2; - print "\n"; - } - $error3++; - } - elsif (($TYPE eq "illumina")&&(($header1 ne $repheader1)||($header2 ne $repheader2)||($header1 ne $header2))){ - if ($VERBOSE eq "ON"){ - print "Error in header : different\n"; - print $ligne1_r1; - print $ligne2_r1; - print $ligne3_r1; - print $ligne4_r1; - print $ligne1_r2; - print $ligne2_r2; - print $ligne3_r2; - print $ligne4_r2; - print "\n"; - } - $error4++; - } - elsif (($TYPE eq "sanger")&&($header1 ne $header2)){ - if ($VERBOSE eq "ON"){ - print "Error in header : different\n"; - print $ligne1_r1; - print $ligne2_r1; - print $ligne3_r1; - print $ligne4_r1; - print $ligne1_r2; - print $ligne2_r2; - print $ligne3_r2; - print $ligne4_r2; - print "\n"; - } - $error4++; - } - elsif (($length_seq1 != $length_qual1)||($length_seq2 != $length_qual2)){ - if ($VERBOSE eq "ON"){ - print "Error in seq/qual length\n"; - print $ligne1_r1; - print $ligne2_r1; - print $ligne3_r1; - print $ligne4_r1; - print $ligne1_r2; - print $ligne2_r2; - print $ligne3_r2; - print $ligne4_r2; - print "\n"; - } - $error5++; - } -#@ 1 - 2 sec - else { - ### Parsing sequence & qualité - if ($ligne2_r1 =~ /^([ATGCNX]+)\s*$/i){ - $seq1 = $1; - $nb_base_read1 += length($seq1); - } - if ($ligne2_r2 =~ /^([ATGCNX]+)\s*$/i){ - $seq2 = $1; - $nb_base_read2 += length($seq2); - } - if ($ligne4_r1 =~ /^(.*)\s*$/i){ - $qual1 = $1; - } - if ($ligne4_r2 =~ /^(.*)\s*$/i){ - $qual2 = $1; - } -#@ 2 sec - ### Verification du parsing et de la coherence sequence /qualité (n°2) - if ((!$seq1)||(!$seq2)||(!$qual1)||(!$qual2)){ - if ($VERBOSE eq "ON"){ - print "Error parsing seq / quality \n"; - print $ligne1_r1; - print $ligne2_r1; - print $ligne3_r1; - print $ligne4_r1; - print $ligne1_r2; - print $ligne2_r2; - print $ligne3_r2; - print $ligne4_r2; - print "\n"; - } - $error6++; - } - elsif ((length($seq1) != length($qual1))||(length($seq2) != length($qual2))){ - if ($VERBOSE eq "ON"){ - print "Error in seq/qual length after parsing\n"; - print $ligne1_r1; - print $ligne2_r1; - print $ligne3_r1; - print $ligne4_r1; - print $ligne1_r2; - print $ligne2_r2; - print $ligne3_r2; - print $ligne4_r2; - print "\n"; - } - $error7++; - } -#@ <1 sec - else { - my $fastq_lines_r1=""; - my $fastq_lines_r2=""; - my $nb_base_current_read1_t = 0; - my $nb_base_current_read2_t = 0; - - $fastq_lines_r1 = &grooming_and_trimming($ligne1_r1,$seq1,$qual1); - $nb_base_current_read1_t = $nb_base_current_t; - if ($fastq_lines_r1){ - $fastq_lines_r2 = &grooming_and_trimming($ligne1_r2,$seq2,$qual2); - $nb_base_current_read2_t = $nb_base_current_t; - } - if ($fastq_lines_r2){ - print OUT1 $fastq_lines_r1; - print OUT2 $fastq_lines_r2; - - $nb_read1_t++; - $nb_read2_t++; - $nb_base_read1_t += $nb_base_current_read1_t; - $nb_base_read2_t += $nb_base_current_read2_t; - - - } - } - } - - -#@ 7 sec - } -} - -close (READ1); -close (READ2); -close (OUT1); -close (OUT2); - -print LF "\n####\t Fastq preparation \n"; -print LF "Fastq format : $TYPE\n"; -print LF "## Before preparation\n"; -print LF "#Read1 :\t$nb_read1\t#Base :\t$nb_base_read1\n"; -print LF "#Read2 :\t$nb_read2\t#Base :\t$nb_base_read2\n"; -print LF "## After preparation\n"; -print LF "#Read1 :\t$nb_read1_t\t#Base :\t$nb_base_read1_t\n"; -print LF "#Read2 :\t$nb_read2_t\t#Base :\t$nb_base_read2_t\n"; -close (LF); - - -sub grooming_and_trimming{ - my $header = shift; - my $seq = shift; - my $quality = shift; - my $quality_converted=""; - my $quality_ori=$quality; - - my $lengthseq = length($seq); - my $startTrim = 0; - my $stopTrim = length($quality)-1; - my $startnoN = $startTrim; - my $stopnoN = $stopTrim; - - - my $chercheN = $seq; - my @bad_position_N; - my @bad_position_Q; - my $current_index = index($chercheN,"N"); - my $abs_index = $current_index; - while ($current_index >=0){ - push (@bad_position_N,$abs_index); - - if ($current_index<length($seq)){ - $chercheN = substr($chercheN,$current_index+1); - $current_index = index($chercheN,"N"); - $abs_index = $current_index + $bad_position_N[$#bad_position_N]+1; - } - else { - last; - } - } - - my @q = split(//,$quality); - for (my $i=0;$i<=$#q;$i++){ - my $chr = $q[$i]; - my $num = ord($q[$i]); - if ($TYPE eq "illumina"){ - $num = $num - 31; # 31 comme la difference entre la plage sanger (33-> 93 / 0->60) et illumina (64->104 / 0->40) - $quality_converted .= chr($num); - } - - if ($num < $MIN_QUALITY + 33){ #33 comme le départ de la plage sanger - push(@bad_position_Q,$i); - } - } - if ($quality_converted){$quality = $quality_converted;} - - my @bad_position = (@bad_position_N, @bad_position_Q); - - if ($#bad_position>=0){ - @bad_position = sort {$a <=> $b} @bad_position; - my %coord=%{&extract_longer_string_coordinates_from_bad_position(0,$stopTrim,\@bad_position)}; - $startTrim = $coord{"start"}; - $stopTrim = $coord{"stop"}; -#print "$startTrim .. $stopTrim\n"; - - } - my $lengthTrim = $stopTrim - $startTrim +1; - - #if ($stats_length{$lengthTrim}){ - # $stats_length{$lengthTrim} = 1; - #} - #else { - # $stats_length{$lengthTrim}++; - #} - my $fastq_lines=""; - -# if ($header =~ /GA8\-EAS671_0005\:3\:1\:1043\:4432/){ -# print "HEAD:\t$header"; -# print "SEQ:\n$seq\n"; -# print "$quality_ori\n"; -# print "$quality\n"; -# for (my $i=0;$i<=$#bad_position;$i++){ -# print $bad_position[$i]."(".$q[$bad_position[$i]]." : ".ord($q[$bad_position[$i]]).")"."\t"; -# } -# print "\n"; -# print "$startTrim .. $stopTrim / $lengthTrim \n"; -# print $fastq_lines; -# print "\n"; -# } - - #for (my $i=$startTrim;$i<=$stopTrim;$i++){ - # if ($stats_quality{ord($q{$i])}){ - # $stats_quality{ord($q{$i])}=1; - # } - # else { - # $stats_quality{ord($q{$i])}++; - # } - #} - - if ($lengthTrim >= $MIN_LENGTH){ - $fastq_lines .= $header; - my $new_seq = substr($seq,$startTrim,$lengthTrim); - $nb_base_current_t = length($new_seq); - $fastq_lines .= $new_seq."\n"; - $fastq_lines .= "+\n"; - my $new_q = substr($quality,$startTrim,$lengthTrim); - $fastq_lines .= $new_q."\n"; - return $fastq_lines; - - } - else { - #print "Insufficient length after trimming\n"; - return ""; - } -} - -sub extract_longer_string_coordinates_from_bad_position{ - my $start=shift; - my $stop =shift; - my $refbad = shift; - my @bad_position = @$refbad; - my %coord; - - my $current_start = $start; - my $current_stop = $bad_position[0]-1; - if ($current_stop < $start){$current_stop = $start;} - - - #debut -> premier N - my $current_length = $current_stop - $current_start +1; - my $test_length; - - #entre les N - for (my $i=1;$i<=$#bad_position;$i++){ - $test_length = $bad_position[$i]+1-$bad_position[$i-1]-1; - if ( $test_length > $current_length){ - $current_start = $bad_position[$i-1]+1; - $current_stop = $bad_position[$i]-1; - $current_length = $current_stop - $current_start +1; - } - } - - #dernier N -> fin - $test_length = $stop-$bad_position[$#bad_position]+1; - if ( $test_length > $current_length){ - $current_start = $bad_position[$#bad_position]+1; - if ($current_start > $stop){$current_start=$stop;} - $current_stop = $stop; - } - $coord{"start"}=$current_start; - $coord{"stop"}= $current_stop; - $coord{"lenght"}=$current_stop-$current_start+1; - - return \%coord; -}
--- a/rapsodyn/PrepareFastqLight.xml~ Thu Oct 09 08:28:22 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,28 +0,0 @@ -<tool id="PrepareFastqLight" name="PrepareFastqLight" version="1.02"> -<description>Fastq preparation</description> -<command interpreter="perl"> - PrepareFastqLight.pl -read1_file $input_read1_file -read2_file $input_read2_file -output1 $output_read1_file -output2 $output_read2_file -log_file $log_file -type $quality_type -min_quality $min_quality -min_length $min_length -</command> -<inputs> - <param name="input_read1_file" type="data" format="txt,fastq" label="Select a suitable FASTQ READ 1 file from your history"/> - <param name="input_read2_file" type="data" format="txt,fastq" label="Select a suitable FASTQ READ 2 file from your history"/> - <param name="quality_type" type="select" label="Select input quality format"> - <option value="auto" selected="true">Auto-detect</option> - <option value="sanger">Sanger</option> - <option value="illumina">Illumina 1.3-1.7</option> - </param> - <param name="min_quality" type="integer" value="30" label="Minimum quality for 5' and 3' trimming "/> - <param name="min_length" type="integer" value="30" label="Minimum sequence length after trimming"/> -</inputs> -<outputs> - <data name="output_read1_file" format="fastqsanger" label="${tool.name} on ${on_string}"/> - <data name="output_read2_file" format="fastqsanger" label="${tool.name} on ${on_string}"/> - <data name="log_file" format="txt" label="${tool.name} LOG on ${on_string}"/> -</outputs> - -<help> - - - -</help> -</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rapsodyn/merge_bam.xml Fri Oct 10 04:46:10 2014 -0400 @@ -0,0 +1,41 @@ +<tool id="merge_bam" name="Merge BAM Files" version="1.0.0"> + <description>merges BAM files together</description> + <requirements> + <requirement type="package" version="1.56.0">picard</requirement> + </requirements> + <command> +java -Xmx2G -jar \$JAVA_JAR_PATH/MergeSamFiles.jar MSD=$mergeSD VALIDATION_STRINGENCY=LENIENT O=$output1 I=$input1 I=$input2 TMP_DIR=$__new_file_path__ + #for $i in $inputs + I=${i.input} + #end for + 2> $outlog + || echo "Error running Picard MergeSamFiles" >&2 + </command> + <inputs> + <param name="title" label="Name for the output merged bam file" type="text" default="Merged.bam" + help="This name will appear in your history so use it to remember what the new file in your history contains" /> + <param name="mergeSD" value="true" type="boolean" label="Merge all component bam file headers into the merged bam file" + truevalue="true" falsevalue="false" checked="yes" + help="Control the MERGE_SEQUENCE_DICTIONARIES flag for Picard MergeSamFiles. Default (true) correctly propagates read groups and other important metadata" /> + <param name="input1" label="First file" type="data" format="bam,sam" /> + <param name="input2" label="with file" type="data" format="bam,sam" help="Need to add more files? Use controls below." /> + <repeat name="inputs" title="Input Files"> + <param name="input" label="Add file" type="data" format="bam,sam" /> + </repeat> + </inputs> + <outputs> + <data format="bam" name="output1" label="${title}.bam" /> + <data format="txt" name="outlog" label="${title}_${tool.name}.log" /> + </outputs> + + <help> + +**What it does** + +This tool uses the Picard_ merge command to merge any number of BAM files together into one BAM file while preserving the BAM +metadata such as read groups + +.. _Picard: http://picard.sourceforge.net/command-line-overview.shtml#MergeSamFiles + + </help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rapsodyn/tool_dependencies.xml Fri Oct 10 04:46:10 2014 -0400 @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="picard" version="1.56.0"> + <repository changeset_revision="61e41d21cb6f" name="package_picard_1_56_0" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency>