Mercurial > repos > mcharles > rapsosnp
changeset 10:0a6c1cfe4dc8 draft
Uploaded
| author | mcharles |
|---|---|
| date | Mon, 19 Jan 2015 04:33:21 -0500 |
| parents | 0e7c6fe60646 |
| children | 0c2743f66e4f |
| files | rapsodyn/CreateMatrix.pl rapsodyn/CreateMatrix.xml rapsodyn/CreateMatrixMultiple.pl rapsodyn/CreateMatrixMultiple.xml rapsodyn/Galaxy-Workflow-rapsosnp_v1.20.ga rapsodyn/Galaxy-Workflow-rapsosnp_v1.20_-_10x_-_sam.ga rapsodyn/MergeLogFiles.pl rapsodyn/MergeLogFiles.xml rapsodyn/ParseBlastForUniqueMatch.pl rapsodyn/ParseBlastForUniqueMatch.xml rapsodyn/PileupVariant.pl rapsodyn/PileupVariant.xml rapsodyn/PrepareFastqLight.pl rapsodyn/PrepareFastqLight.xml rapsodyn/extractseq.pl rapsodyn/extractseq.xml rapsodyn/filtersam_mapped_and_unique.pl rapsodyn/filtersam_mapped_and_unique.xml rapsodyn/repository_dependencies.xml rapsodyn/tool_dependencies.xml |
| diffstat | 20 files changed, 272 insertions(+), 3617 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rapsodyn/CreateMatrix.pl Mon Jan 19 04:33:21 2015 -0500 @@ -0,0 +1,20 @@ +#!/usr/bin/perl +#V1.0.0 +use strict; +use warnings; +use Getopt::Long; + +my $input_pileup_file; +my $input_variant_file; +my $input_variant_unique_file; + +GetOptions ( +"input_pileup_file=s" => \$input_pileup_file, +"input_variant_file=s" => \$input_variant_file, +"input_variant_unique_file=s" => \$input_variant_unique_file +) or die("Error in command line arguments\n"); + + + +print "$input_pileup_file\n$input_variant_file\n$input_variant_unique_file\n"; +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rapsodyn/CreateMatrix.xml Mon Jan 19 04:33:21 2015 -0500 @@ -0,0 +1,21 @@ +<tool id="CreateMatrix" name="CreateMatrix" version="1.00"> +<description>Create Genotyping Matrix</description> +<command interpreter="perl"> + CreateMatrix.pl -input_pileup_file $input_pileup_file -input_variant_file $input_variant_file -input_variant_unique_file $input_variant_unique_file > $output_file +</command> +<inputs> + <param name="input_pileup_file" type="data" format="pileup" label="Select suitable PILEUP files from your history"/> + <param name="input_variant_file" type="data" format="pileup" label="Select suitable VARIANT files from your history"/> + <param name="input_variant_unique_file" type="data" format="pileup" label="Select suitable VARIANT UNIQUE files from your history"/> + +</inputs> +<outputs> + <data name="output_file" format="txt" label="MATRIX on ${on_string}" /> +</outputs> + +<help> + + + +</help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rapsodyn/CreateMatrixMultiple.pl Mon Jan 19 04:33:21 2015 -0500 @@ -0,0 +1,17 @@ +#!/usr/bin/perl +#V1.0.0 +use strict; +use warnings; +use Getopt::Long; + + +my $input_matrix_files; +GetOptions ( +"input_matrix_files=s" => \$input_matrix_files +) or die("Error in command line arguments\n"); + +my @files = split(/,/,$input_matrix_files); +for (my $i=0;$i<=$#files;$i++){ + print $files[$i],"\n"; +} +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rapsodyn/CreateMatrixMultiple.xml Mon Jan 19 04:33:21 2015 -0500 @@ -0,0 +1,18 @@ +<tool id="CreateMatrixMultiple" name="CreateMatrixMultiple" version="1.00"> +<description>Create Global Genotyping Matrix</description> +<command interpreter="perl"> + CreateMatrixMultiple.pl -input_matrix_files $input_matrix_files > $output_file +</command> +<inputs> + <param name="input_matrix_files" type="data" format="txt" multiple="true" label="Select suitable MATRIX files from your history"/> +</inputs> +<outputs> + <data name="output_file" format="txt" label="GLOBAL MATRIX on ${on_string}" /> +</outputs> + +<help> + + + +</help> +</tool>
--- a/rapsodyn/Galaxy-Workflow-rapsosnp_v1.20.ga Mon Oct 20 05:58:31 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,604 +0,0 @@ -{ - "a_galaxy_workflow": "true", - "annotation": "", - "format-version": "0.1", - "name": "rapsosnp v1.20", - "steps": { - "0": { - "annotation": "", - "id": 0, - "input_connections": {}, - "inputs": [ - { - "description": "", - "name": "ASSEMBLY" - } - ], - "name": "Input dataset", - "outputs": [], - "position": { - "left": 200, - "top": 221 - }, - "tool_errors": null, - "tool_id": null, - "tool_state": "{\"name\": \"ASSEMBLY\"}", - "tool_version": null, - "type": "data_input", - "user_outputs": [] - }, - "1": { - "annotation": "", - "id": 1, - "input_connections": {}, - "inputs": [ - { - "description": "", - "name": "READ1" - } - ], - "name": "Input dataset", - "outputs": [], - "position": { - "left": 200, - "top": 306.76666259765625 - }, - "tool_errors": null, - "tool_id": null, - "tool_state": "{\"name\": \"READ1\"}", - "tool_version": null, - 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"tool_version": "1.00", - "type": "tool", - "user_outputs": [] - } - } -} \ No newline at end of file
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"action_arguments": { - "newname": "LOGS" - }, - "action_type": "RenameDatasetAction", - "output_name": "output_file" - } - }, - "tool_errors": null, - "tool_id": "MergeMultiFile", - "tool_state": "{\"out_format\": \"\\\"txt\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_files\": \"null\"}", - "tool_version": "1.00", - "type": "tool", - "user_outputs": [] - } - } -} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rapsodyn/MergeLogFiles.pl Mon Jan 19 04:33:21 2015 -0500 @@ -0,0 +1,16 @@ +#!/usr/bin/perl +#V1.0.0 +use strict; +use warnings; +use Getopt::Long; + + +my $input_log_files; +GetOptions ( +"input_log_files=s" => \$input_log_files +) or die("Error in command line arguments\n"); + +my @files = split(/,/,$input_log_files); +for (my $i=0;$i<=$#files;$i++){ + print $files[$i],"\n"; +} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rapsodyn/MergeLogFiles.xml Mon Jan 19 04:33:21 2015 -0500 @@ -0,0 +1,18 @@ +<tool id="MergeLogFiles" name="MergeLogFiles" version="1.00"> +<description>Merge multiple log files</description> +<command interpreter="perl"> + MergeLogFiles.pl -input_log_files $input_log_files > $output_file +</command> +<inputs> + <param name="input_log_files" type="data" format="txt" multiple="true" label="Select suitable LOG files from your history"/> +</inputs> +<outputs> + <data name="output_file" format="txt" label="MERGE LOG on ${on_string}" /> +</outputs> + +<help> + + + +</help> +</tool>
--- a/rapsodyn/ParseBlastForUniqueMatch.pl Mon Oct 20 05:58:31 2014 -0400 +++ b/rapsodyn/ParseBlastForUniqueMatch.pl Mon Jan 19 04:33:21 2015 -0500 @@ -1,4 +1,5 @@ #!/usr/bin/perl +#V1.1.0 manage empty files #V1.0.1 added log, option parameters use strict; use warnings; @@ -24,6 +25,10 @@ my %hash_name; open(INB, $input_blast_file) or die ("Can't open $input_blast_file\n"); +if ( -z INB){ + exit(0); +} + while (my $line =<INB>){ my @fields = split (/\s+/,$line); # print $#fields,"\n";
--- a/rapsodyn/ParseBlastForUniqueMatch.xml Mon Oct 20 05:58:31 2014 -0400 +++ b/rapsodyn/ParseBlastForUniqueMatch.xml Mon Jan 19 04:33:21 2015 -0500 @@ -1,4 +1,4 @@ -<tool id="ParseBlastForUniqueMatch" name="ParseBlastForUniqueMatch" version="1.01"> +<tool id="ParseBlastForUniqueMatch" name="ParseBlastForUniqueMatch" version="1.10"> <description>Filter mpileup with blast results</description> <command interpreter="perl"> ParseBlastForUniqueMatch.pl -input_variant_file $input_variant_file -input_blast_file $input_blast_file -window_length $window_length -nb_mismatch_max $nb_mismatch_max -log_file $log_file > $output_variant_file
--- a/rapsodyn/PileupVariant.pl Mon Oct 20 05:58:31 2014 -0400 +++ b/rapsodyn/PileupVariant.pl Mon Jan 19 04:33:21 2015 -0500 @@ -3,39 +3,94 @@ use strict; use warnings; use Getopt::Long; +#v1.1.0 choose exclusion file +#v1.0.2 manage empty files +#v1.0.1 bug correction +#V1.0.1 added log, option parameters my $input_pileup_file; my $output_pileup_file; +my $input_exclusion_file; my $log_file; my $nb_base_covered=0; my $nb_variant=0; +my $nb_variant_conserved=0; +my $do_exclusion=0; +my $nb_exclusion=0; +my $nb_excluded=0; +my %exclusion; GetOptions ( "input_pileup_file=s" => \$input_pileup_file, +"input_exclusion_file=s" => \$input_exclusion_file, "log_file=s" => \$log_file ) or die("Error in command line arguments\n"); open(IN, $input_pileup_file) or die ("Can't open $input_pileup_file\n"); +if ( -z IN){ + exit(0); +} + +if ($input_exclusion_file){ + open (EX,$input_exclusion_file) or die ("Can't open $input_exclusion_file\n"); + if ( -z EX){ + + } + else { + $do_exclusion=1; + while (my $line=<EX>){ + $nb_exclusion++; + chomp($line); + my @fields = split(/\s+/,$line); + if (($fields[0])&&($fields[1])){ + $exclusion{"$fields[0]\t$fields[1]"}=1; + } + else { + print STDERR "Error formatting in Exclusion File\nExclusion file lines should be 'chromosome number' TAB 'position'\n$line\n",$fields[0],"\n",$fields[1],"\n"; + } + } + + } + close (EX); +} #Extraction des variants my $nb_line=0; while (my $line=<IN>){ #print $line; - $nb_base_covered++; - $line =~ s/\$//g; #the read start at this position - $line =~ s/\^.//g; #the read end at this position followed by quality char + if ($line !~ /^\s*$/){ + my @fields = split(/\s+/,$line); + if ($fields[4]){ + $nb_base_covered++; + my $pile = $fields[4]; + $pile =~ s/\$//g; #the read start at this position + $pile =~ s/\^.//g; #the read end at this position followed by quality char + if ($fields[4]=~/[ATGCN]/i){ #Indel are +/-\d[ATGCatgc]+ and SNP are [ATGCatgc]+ so [ATGCN]/i detection cover indel and snp + $nb_variant++; + if (($do_exclusion==1)&&($exclusion{"$fields[0]\t$fields[1]"})){ + + } + else { + print $line; + $nb_variant_conserved++; + } + } + } + elsif ($fields[3]==0){ + } + else { + print STDERR "Error in pileup format\nPileup result expected at column 5\n$line\n"; + } + } #print $line; - my @field = split(/\s+/,$line); - if ($field[4]=~/[ATGCN]/i){ - print $line; - $nb_variant++; - } + } close(IN); open (LF,">$log_file") or die("Can't open $log_file\n"); print LF "\n####\t Variant extraction \n"; -print LF "Position covered :\t$nb_base_covered\n"; -print LF "Variant detected :\t$nb_variant\n"; +print LF "Position covered\t:\t$nb_base_covered\n"; +print LF "Variant detected\t:\t$nb_variant\n"; +print LF "Variant conserved\t:\t$nb_variant_conserved\n"; close (LF);
--- a/rapsodyn/PileupVariant.xml Mon Oct 20 05:58:31 2014 -0400 +++ b/rapsodyn/PileupVariant.xml Mon Jan 19 04:33:21 2015 -0500 @@ -1,10 +1,27 @@ -<tool id="PileupVariant" name="PileupVariant" version="1.01"> +<tool id="PileupVariant" name="PileupVariant" version="1.10"> <description>Keep only mpileup line with variant</description> <command interpreter="perl"> - PileupVariant.pl -input_pileup_file $input_pileup_file -log_file $log_file > $output_pileup_file + #if $exclude.do=="YES" + PileupVariant.pl -input_pileup_file $input_pileup_file -input_exclusion_file $input_exclusion_file -log_file $log_file > $output_pileup_file + #else + PileupVariant.pl -input_pileup_file $input_pileup_file -log_file $log_file > $output_pileup_file + #end if + </command> <inputs> <param name="input_pileup_file" type="data" format="pileup" label="Select a suitable input file from your history"/> + <conditional name="exclude"> + <param name="do" type="select" label="Exclude some position"> + <option value="NO">NO</option> + <option value="YES">YES</option> + </param> + <when value="YES"> + <param name="input_exclusion_file" type="data" format="pileup" label="Select a suitable input file from your history"/> + </when> + <when value="NO"> + + </when> + </conditional> </inputs> <outputs> <data name="output_pileup_file" format="pileup" label="${tool.name} on ${on_string}"/>
--- a/rapsodyn/PrepareFastqLight.pl Mon Oct 20 05:58:31 2014 -0400 +++ b/rapsodyn/PrepareFastqLight.pl Mon Jan 19 04:33:21 2015 -0500 @@ -1,4 +1,6 @@ #!/usr/bin/perl +#v1.1.0 manage empty files +#v1.0.4 bug correction, last read not considered #v1.0.3 support rapsodyn header (.... 1:... / .... 2:...) #V1.0.2 added auto type detection #V1.0.1 added log, option parameters @@ -49,6 +51,14 @@ open(OUT2, ">$output2_file") or die ("Can't open $output2_file\n"); open (LF,">$log_file") or die("Can't open $log_file\n"); +if (( -z READ1)&&( -z READ2)){ + exit(0); +} +elsif (( -z READ1)||( -z READ2)){ + print STDERR "One empty File\n"; + exit(0); +} + my $error1=0; my $error2=0; @@ -113,7 +123,7 @@ - +my $compt=0; while (my $ligne1_r1 =<READ1>){ my $ligne2_r1 =<READ1>; my $ligne3_r1 =<READ1>; @@ -122,7 +132,13 @@ my $ligne2_r2 =<READ2>; my $ligne3_r2 =<READ2>; my $ligne4_r2 =<READ2>; - + # chomp($ligne1_r1); + # chomp($ligne2_r1); + # chomp($ligne3_r1); + # chomp($ligne4_r1); + # chomp($ligne2_r1); + + $compt++; $nb_read1++; $nb_read2++; @@ -160,13 +176,13 @@ #@ 1 - 2 sec else { - my $length_seq1 = length($ligne2_r1); - my $length_qual1 =length($ligne4_r1); + my $length_seq1 = length(chomp($ligne2_r1)); + my $length_qual1 =length(chomp($ligne4_r1)); my $seq1; my $qual1; - my $length_seq2 = length($ligne2_r2); - my $length_qual2 =length($ligne4_r2); + my $length_seq2 = length(chomp($ligne2_r2)); + my $length_qual2 =length(chomp($ligne4_r2)); my $seq2; my $qual2; my $header1=""; @@ -210,7 +226,7 @@ } elsif (($TYPE eq "sanger")&&((!$header1)||(!$header2))){ if ($VERBOSE eq "ON"){ - print "Error in header refgsd : empty\n"; + print "Error in header ref : empty\n"; print $ligne1_r1; print $ligne2_r1; print $ligne3_r1; @@ -256,10 +272,12 @@ elsif (($length_seq1 != $length_qual1)||($length_seq2 != $length_qual2)){ if ($VERBOSE eq "ON"){ print "Error in seq/qual length\n"; + print "$length_seq1 / $length_qual1 \t $length_seq2 / $length_qual2\n"; print $ligne1_r1; print $ligne2_r1; print $ligne3_r1; print $ligne4_r1; + print "\n"; print $ligne1_r2; print $ligne2_r2; print $ligne3_r2; @@ -270,6 +288,7 @@ } #@ 1 - 2 sec else { + #print "TEST : $compt\n"; ### Parsing sequence & qualité if ($ligne2_r1 =~ /^([ATGCNX]+)\s*$/i){ $seq1 = $1;
--- a/rapsodyn/PrepareFastqLight.xml Mon Oct 20 05:58:31 2014 -0400 +++ b/rapsodyn/PrepareFastqLight.xml Mon Jan 19 04:33:21 2015 -0500 @@ -1,4 +1,4 @@ -<tool id="PrepareFastqLight" name="PrepareFastqLight" version="1.03"> +<tool id="PrepareFastqLight" name="PrepareFastqLight" version="1.10"> <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
--- a/rapsodyn/extractseq.pl Mon Oct 20 05:58:31 2014 -0400 +++ b/rapsodyn/extractseq.pl Mon Jan 19 04:33:21 2015 -0500 @@ -1,4 +1,6 @@ #!/usr/bin/perl +#V1.10 manage empty files +#V1.02 Trop de pb avec nbci blast+, changment du header des fasta #V1.01 #Ajout d'un _ a la fin du nom pour eviter les problemes avec ncbi blast+ use strict; @@ -16,6 +18,12 @@ ) or die("Error in command line arguments\n"); open(INV, $input_variant_file) or die ("Can't open $input_variant_file\n"); + +if ( -z INV){ + print ">empty\nAAAAA"; + exit(0); +} + open(INA, $input_assembly_file) or die ("Can't open $input_assembly_file\n"); my @variant_list; @@ -89,11 +97,13 @@ } $variant{"desc"}=$descriptor; - print ">",$variant{"ref"},"_",$descriptor,"_","\n",$variant{"SEQ"},"\n"; + #print ">",$variant{"ref"},"_",$descriptor,"_","\n",$variant{"SEQ"},"\n"; + #V1.02 : changement du header #print ">",$variant{"ref"},"_",$variant{"position"},"_",$variant{"depth"},"\n",$variant{"SEQ"},"\n"; + print ">",$variant{"ref"},"_",$variant{"position"},"_",$variant{"depth"},"\n",$variant{"SEQ"},"\n"; push(@variant_list,\%variant); }
--- a/rapsodyn/extractseq.xml Mon Oct 20 05:58:31 2014 -0400 +++ b/rapsodyn/extractseq.xml Mon Jan 19 04:33:21 2015 -0500 @@ -1,4 +1,4 @@ -<tool id="extractseq" name="extractseq" version="1.01"> +<tool id="extractseq" name="extractseq" version="1.10"> <description>Extract Sequence around variant position</description> <command interpreter="perl"> extractseq.pl -input_variant_file $input_variant_file -input_assembly_file $input_assembly_file -window_length $window_length > $output_file
--- a/rapsodyn/filtersam_mapped_and_unique.pl Mon Oct 20 05:58:31 2014 -0400 +++ b/rapsodyn/filtersam_mapped_and_unique.pl Mon Jan 19 04:33:21 2015 -0500 @@ -1,4 +1,5 @@ #!/usr/bin/perl +#V1.1.0 manage empty files #V1.0.1 added log, option parameters use strict; use warnings; @@ -7,6 +8,7 @@ my $input_sam_file; my $output_sam_file; my $log_file; +my $empty_file=1; my %bitscore_all; my %bitscore_selected; @@ -37,6 +39,7 @@ my @fields_selected = split (/\s+/,$line); if (($fields_selected[1]==83)||($fields_selected[1]==163)||($fields_selected[1]==147)||($fields_selected[1]==99)){ print $line; + $empty_file=0; my $bit = $fields_selected[1]; if ($bitscore_selected{$bit}){ $bitscore_selected{$bit}++; @@ -50,29 +53,30 @@ } close (IN); - open (LF,">$log_file") or die("Can't open $log_file\n"); -print LF "\n####\t Sam filtering \n"; -print LF "## Before filtering\n"; -print LF "bitscore\t:\t"; -foreach my $key (sort {$bitscore_all{$b} <=> $bitscore_all{$a}} keys %bitscore_all) { - print LF $key,"\t*\t"; -} -print LF "\n number \t:\t"; -foreach my $key (sort {$bitscore_all{$b} <=> $bitscore_all{$a}} keys %bitscore_all) { - print LF $bitscore_all{$key},"\t*\t"; +if ($empty_file==0){ + print LF "\n####\t Sam filtering \n"; + print LF "## Before filtering\n"; + print LF "bitscore\t:\t"; + foreach my $key (sort {$bitscore_all{$b} <=> $bitscore_all{$a}} keys %bitscore_all) { + print LF $key,"\t*\t"; + } + print LF "\n number \t:\t"; + foreach my $key (sort {$bitscore_all{$b} <=> $bitscore_all{$a}} keys %bitscore_all) { + print LF $bitscore_all{$key},"\t*\t"; + } + print LF "\n"; + print LF "## After filtering\n"; + print LF "bitscore\t:\t"; + foreach my $key (sort {$bitscore_selected{$b} <=> $bitscore_selected{$a}} keys %bitscore_selected) { + print LF $key,"\t*\t"; + } + print LF "\n number \t:\t"; + foreach my $key (sort {$bitscore_selected{$b} <=> $bitscore_selected{$a}} keys %bitscore_selected) { + print LF $bitscore_selected{$key},"\t*\t"; + } + print LF "\n"; } -print LF "\n"; -print LF "## After filtering\n"; -print LF "bitscore\t:\t"; -foreach my $key (sort {$bitscore_selected{$b} <=> $bitscore_selected{$a}} keys %bitscore_selected) { - print LF $key,"\t*\t"; -} -print LF "\n number \t:\t"; -foreach my $key (sort {$bitscore_selected{$b} <=> $bitscore_selected{$a}} keys %bitscore_selected) { - print LF $bitscore_selected{$key},"\t*\t"; -} -print LF "\n"; close (LF);
--- a/rapsodyn/filtersam_mapped_and_unique.xml Mon Oct 20 05:58:31 2014 -0400 +++ b/rapsodyn/filtersam_mapped_and_unique.xml Mon Jan 19 04:33:21 2015 -0500 @@ -1,4 +1,4 @@ -<tool id="filtersam_mapped_and_unique" name="filtersam_mapped_and_unique" version="1.01"> +<tool id="filtersam_mapped_and_unique" name="filtersam_mapped_and_unique" version="1.10"> <description>Filter SAM file for uniq and well mapped pair-end reads</description> <command interpreter="perl"> filtersam_mapped_and_unique.pl -input_sam_file $input_sam_file -log_file $log_file> $output_sam_file
--- a/rapsodyn/repository_dependencies.xml Mon Oct 20 05:58:31 2014 -0400 +++ b/rapsodyn/repository_dependencies.xml Mon Jan 19 04:33:21 2015 -0500 @@ -1,6 +1,6 @@ <?xml version="1.0"?> <repositories description="Rapsodyn worflow needed repository"> - <repository changeset_revision="623f727cdff1" name="ncbi_blast_plus" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="2fe07f50a41e" name="ncbi_blast_plus" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" /> <repository changeset_revision="b4427dbb6ced" name="bwa_wrappers" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" /> <repository changeset_revision="973fea5b4bdf" name="samtools_mpileup" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" /> <repository changeset_revision="8176b2575aa1" name="sam_to_bam" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" />
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rapsodyn/tool_dependencies.xml Mon Jan 19 04:33:21 2015 -0500 @@ -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>