| Previous changeset 2:2d86d5b112e8 (2011-07-14) |
|
Commit message:
minor updates for v2.6 |
|
modified:
runAssembly.xml runAssembly_cDNA.xml runAssembly_cDNA_wrapper.pl runAssembly_wrapper.pl runMapping.xml runMapping_cDNA.xml runMapping_cDNA_wrapper.pl runMapping_wrapper.pl |
| b |
| diff -r 2d86d5b112e8 -r bf1f8bc4abe6 runAssembly.xml --- a/runAssembly.xml Thu Jul 14 22:14:07 2011 -0400 +++ b/runAssembly.xml Wed Dec 21 19:42:53 2011 -0800 |
| [ |
| b'@@ -1,6 +1,6 @@\n-<tool id="runAssembly" name="runAssembly" version="1.0.0" force_history_refresh=\'True\'>\n+<tool id="runAssembly" name="runAssembly" version="1.0.1" force_history_refresh="True">\n <description>De novo assembly of Roche/454 reads using Newbler</description>\n-<command interpreter=\'perl\'>runAssembly_wrapper.pl\n+<command interpreter="perl">runAssembly_wrapper.pl\n $newbler_metrics.extra_files_path\n $newbler_metrics\n $read_status\n@@ -17,11 +17,13 @@\n $scaffolds_fasta\n $scaffolds_qual\n $scaffolds_agp\n+$contig_scaffolds_agp\n $tag_pair_align\n $trim_status\n $large_contigs_fasta\n $large_contigs_qual\n-$newbler_exe -o $newbler_metrics.extra_files_path\n+runAssembly\n+-o $newbler_metrics.extra_files_path\n -cpu 8 \n $rip \n -e $e \n@@ -63,137 +65,135 @@\n #end for\n </command>\n <inputs>\n- <!-- NEWBLER VERSION -->\n- <param name=\'newbler_exe\' type=\'select\' display=\'radio\' label=\'Newbler version\'>\n- <option value=\'/jgi/tools/454/rig-DataProcessing_2.3/bin/runAssembly\'>2.3</option>\n- <option value=\'/jgi/tools/454/rig-DataProcessing_2.4pre-20091204/bin/runAssembly\'>2.4</option>\n- <option value=\'/home/copeland/local/x86_64/newbler/v2.5p1-internal-10Jun23-1/runAssembly\' selected=\'true\'>2.5</option>\n- </param>\n-\n <!-- READSEQ INFILES -->\n <repeat name="sff_inputs" title="Unpaired Reads Sff Files">\n <param name="sff_input" type="data" format="sff" label="SE Sff file"/>\n </repeat>\n- <repeat name="sanger_inputs" title="Unpaired Reads Fasta Files">\n- <param name="sanger_input" type="data" format="fasta" label="SE Fasta file"/>\n+ <repeat name="sanger_inputs" title="Unpaired Reads Fasta/Fastq Files">\n+ <param name="sanger_input" type="data" format="fasta,fastqsanger" label="SE Fasta/Fastq file"/>\n </repeat>\n <repeat name="sff_paired_inputs" title="Paired Reads Sff Files">\n <param name="sff_paired_input" type="data" format="sff" label="PE Sff file"/>\n </repeat>\n- <repeat name="sanger_paired_inputs" title="Paired Reads Fasta Files">\n- <param name="sanger_paired_input" type="data" format="fasta" label="PE Fasta file"/>\n+ <repeat name="sanger_paired_inputs" title="Paired Reads Fasta/Fastq Files">\n+ <param name="sanger_paired_input" type="data" format="fasta,fastqsanger" label="PE Fasta/Fastq file"/>\n </repeat>\n- <param name=\'paired_reads\' type=\'select\' display=\'radio\' label=\'[-paired_reads] If supplying paired reads (above), do you want paired-read info?\'>\n- <option value=\'false\'>no</option>\n- <option value=\'true\'>[-paired_reads] yes</option>\n+ <param name="paired_reads" type="select" display="radio" label="[-paired_reads] If supplying paired reads (above), do you want paired-read info?">\n+ <option value="false">no</option>\n+ <option value="true">[-paired_reads] yes</option>\n </param>\n- <param name=\'pair\' type=\'select\' display=\'radio\' label=\'[-pair] Output pairwise overlaps\'>\n- <option value=\'\'>no</option>\n- <option value=\'-pair\'>[-pair] yes</option>\n+ <param name="pair" type="select" display="radio" label="[-pair] Output pairwise overlaps">\n+ <option value="">no</option>\n+ <option value="-pair">[-pair] yes</option>\n </param>\n \n- <param name=\'l\' type="integer" value=\'500\' label="[-l] This option sets the minimum length for a contig to appear in the 454LargeContigs.fna file"/>\n+ <param name="l" type="integer" value="500" label="[-l] This option sets the minimum length for a contig to appear in the 454LargeContigs.fna file"/>\n \n <!-- OPTIONAL ARGUMENTS -->\n- <param name=\'mcf\' type=\'data\' format=\'tabular\' optional=\'true\' label=\'[-mcf] Specify non-default MID config file\' />\n- <param name=\'fi\' type=\'data\' format=\'txt\' optional=\'true\' label=\'[-fi] Include filter file to be specified\' />\n- <param name=\'fe\' type=\'data\' format=\'txt\' optional=\'true\' label=\'[-fe] Exclude filter file to be specified\' />\n- <param name=\'vt\' type=\'data\' format=\'fasta\' o'..b' <filter>no != "-no"</filter>\n </data>\n- <data name=\'all_contigs_qual\' format=\'qual454\' label=\'All Contigs (Qual454)\'>\n- <filter>no != \'-no\'</filter>\n+ <data name="all_contigs_qual" format="qual454" label="${tool.name} on $on_string: All Contigs (Qual454)">\n+ <filter>no != "-no"</filter>\n </data>\n- <data name=\'contigs_ace\' format=\'ace\' label=\'Contigs (Ace)\'>\n- <filter>ace == \'-ace\' and no != \'-no\'</filter>\n+ <data name="contigs_ace" format="ace" label="${tool.name} on $on_string: Contigs (Ace)">\n+ <filter>ace == "-ace" and no != "-no"</filter>\n </data>\n- <data name=\'contigs_consed_ace\' format=\'ace\' label=\'Contigs (Consed/Ace)\'>\n- <filter>ace == \'-ace -consed\' and no != \'-no\'</filter>\n+ <data name="contigs_consed_ace" format="ace" label="${tool.name} on $on_string: Contigs (Consed/Ace)">\n+ <filter>ace == "-ace -consed" and no != "-no"</filter>\n </data>\n \n- <data name=\'contig_graph\' format=\'txt\' label=\'Contig Graph\'/>\n- <data name=\'large_contigs_fasta\' format=\'fasta\' label=\'Large Contigs (Fasta)\'>\n- <filter>no != \'-no\'</filter>\n+ <data name="contig_graph" format="txt" label="${tool.name} on $on_string: Contig Graph"/>\n+ <data name="large_contigs_fasta" format="fasta" label="${tool.name} on $on_string: Large Contigs (Fasta)">\n+ <filter>no != "-no"</filter>\n </data>\n- <data name=\'large_contigs_qual\' format=\'qual454\' label=\'Large Contigs (Qual454)\'>\n- <filter>no != \'-no\'</filter>\n+ <data name="large_contigs_qual" format="qual454" label="${tool.name} on $on_string: Large Contigs (Qual454)">\n+ <filter>no != "-no"</filter>\n </data>\n- <data name=\'pair_align\' format=\'txt\' label=\'Pairwise Alignments\'>\n- <filter>pair == \'-pair\' and no != \'-no\'</filter>\n+ <data name="pair_align" format="txt" label="${tool.name} on $on_string: Pairwise Alignments">\n+ <filter>pair == "-pair" and no != "-no"</filter>\n </data>\n- <data name=\'pair_status\' format=\'tabular\' label=\'Paired-End Read Status\'>\n- <filter>paired_reads == \'true\' and no != \'-no\'</filter>\n+ <data name="pair_status" format="tabular" label="${tool.name} on $on_string: Paired-End Read Status">\n+ <filter>paired_reads == "true" and no != "-no"</filter>\n </data>\n- <data name=\'scaffolds_fasta\' format=\'fasta\' label=\'Scaffolds (Fasta)\'>\n- <filter>paired_reads == \'true\' and no != \'-no\'</filter>\n+ <data name="scaffolds_fasta" format="fasta" label="${tool.name} on $on_string: Scaffolds (Fasta)">\n+ <filter>paired_reads == "true" and no != "-no"</filter>\n </data>\n- <data name=\'scaffolds_qual\' format=\'qual454\' label=\'Scaffolds (Qual454)\'>\n- <filter>paired_reads == \'true\' and no != \'-no\'</filter>\n+ <data name="scaffolds_qual" format="qual454" label="${tool.name} on $on_string: Scaffolds (Qual454)">\n+ <filter>paired_reads == "true" and no != "-no"</filter>\n </data>\n- <data name=\'scaffolds_agp\' format=\'tabular\' label=\'Scaffolds (Agp)\'>\n- <filter>paired_reads == \'true\' and no != \'-no\'</filter>\n+ <data name="scaffolds_agp" format="tabular" label="${tool.name} on $on_string: Scaffolds (Agp)">\n+ <filter>paired_reads == "true" and no != "-no"</filter>\n </data>\n- <data name=\'tag_pair_align\' format=\'txt\' label=\'Tag Pair Alignments\'>\n- <filter>pair == \'-pair\' and paired_reads == \'true\' and no != \'-no\'</filter>\n+ <data name="contig_scaffolds_agp" format="tabular" label="${tool.name} on $on_string: Contig Scaffolds(Agp)">\n+ <filter>scaffold is True</filter>\n </data>\n- <data name=\'trim_status\' format=\'tabular\' label=\'Trim Status\'/>\n+ <data name="tag_pair_align" format="txt" label="${tool.name} on $on_string: Tag Pair Alignments">\n+ <filter>pair == "-pair" and paired_reads == "true" and no != "-no"</filter>\n+ </data>\n+ <data name="trim_status" format="tabular" label="${tool.name} on $on_string: Trim Status"/>\n \n </outputs>\n <help>\n' |
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| diff -r 2d86d5b112e8 -r bf1f8bc4abe6 runAssembly_cDNA.xml --- a/runAssembly_cDNA.xml Thu Jul 14 22:14:07 2011 -0400 +++ b/runAssembly_cDNA.xml Wed Dec 21 19:42:53 2011 -0800 |
| [ |
| b'@@ -1,4 +1,4 @@\n-<tool id="runAssembly_cDNA" name="runAssembly cDNA" version="1.0.0" force_history_refresh=\'True\'>\n+<tool id="runAssembly_cDNA" name="runAssembly cDNA" version="1.0.1" force_history_refresh=\'True\'>\n <description>De novo assembly of Roche/454 cDNA reads using Newbler</description>\n <command interpreter=\'perl\'>runAssembly_cDNA_wrapper.pl\n $newbler_metrics.extra_files_path\n@@ -17,6 +17,7 @@\n $scaffolds_fasta\n $scaffolds_qual\n $scaffolds_agp\n+$contig_scaffolds_agp\n $tag_pair_align\n $trim_status\n $isotigs_ace\n@@ -24,7 +25,8 @@\n $isotigs_qual\n $isotigs_agp\n $isotigs_layout\n-$newbler_exe -o $newbler_metrics.extra_files_path\n+runAssembly\n+-o $newbler_metrics.extra_files_path\n -cpu 8 \n $rip \n -e $e \n@@ -70,149 +72,147 @@\n #end for\n </command>\n <inputs>\n- <!-- NEWBLER VERSION -->\n- <param name=\'newbler_exe\' type=\'select\' display=\'radio\' label=\'Newbler version\'>\n- <option value=\'/jgi/tools/454/rig-DataProcessing_2.3/bin/runAssembly\'>2.3</option>\n- <option value=\'/jgi/tools/454/rig-DataProcessing_2.4pre-20091204/bin/runAssembly\'>2.4</option>\n- <option value=\'/home/copeland/local/x86_64/newbler/v2.5p1-internal-10Jun23-1/runAssembly\' selected=\'true\'>2.5</option>\n- </param>\n-\n <!-- READSEQ INFILES -->\n <repeat name="sff_inputs" title="Unpaired Reads Sff Files">\n <param name="sff_input" type="data" format="sff" label="SE Sff file"/>\n </repeat>\n- <repeat name="sanger_inputs" title="Unpaired Reads Fasta Files">\n- <param name="sanger_input" type="data" format="fasta" label="SE Fasta file"/>\n+ <repeat name="sanger_inputs" title="Unpaired Reads Fasta/Fastq Files">\n+ <param name="sanger_input" type="data" format="fasta,fastqsanger" label="SE Fasta/Fastq file"/>\n </repeat>\n <repeat name="sff_paired_inputs" title="Paired Reads Sff Files">\n <param name="sff_paired_input" type="data" format="sff" label="PE Sff file"/>\n </repeat>\n- <repeat name="sanger_paired_inputs" title="Paired Reads Fasta Files">\n- <param name="sanger_paired_input" type="data" format="fasta" label="PE Fasta file"/>\n+ <repeat name="sanger_paired_inputs" title="Paired Reads Fasta/Fastq Files">\n+ <param name="sanger_paired_input" type="data" format="fasta,fastqsanger" label="PE Fasta/Fastq file"/>\n </repeat>\n- <param name=\'paired_reads\' type=\'select\' display=\'radio\' label=\'[-paired_reads] If supplying paired reads (above), do you want paired-read info?\'>\n- <option value=\'false\'>no</option>\n- <option value=\'true\'>[-paired_reads] yes</option>\n+ <param name="paired_reads" type="select" display="radio" label="[-paired_reads] If supplying paired reads (above), do you want paired-read info?">\n+ <option value="false">no</option>\n+ <option value="true">[-paired_reads] yes</option>\n </param>\n- <param name=\'pair\' type=\'select\' display=\'radio\' label=\'[-pair] Output pairwise overlaps\'>\n- <option value=\'\'>no</option>\n- <option value=\'-pair\'>[-pair] yes</option>\n+ <param name="pair" type="select" display="radio" label="[-pair] Output pairwise overlaps">\n+ <option value="">no</option>\n+ <option value="-pair">[-pair] yes</option>\n </param>\n \n- <param name=\'it\' type=\'integer\' value=\'100\' label=\'[-it] Specify the maximum number of isotigs in an isogroup. Maximum is 10,000.\'/>\n- <param name=\'ig\' type=\'integer\' value=\'500\' label=\'[-ig] Specify the maximum number of contigs in an isogroup.\'/>\n- <param name=\'icc\' type=\'integer\' value=\'100\' label=\'[-icc] Specify the maximum number of contigs in an isotig. Maximum is 200 and corresponds to the recursion depth during graph traversal\'/>\n- <param name=\'icl\' type=\'integer\' value=\'3\' label=\'[-icl] Specify the minimum length a contig must be to be part of an isotig. Minimum is 3bp.\'/>\n+ <param name="it" type="integer" value="100" label="[-it] Specify the maximum number of isotigs in an isogroup. Maximum is 10,000."/>\n+ <param name="ig" type'..b'o != \'-no\'</filter>\n+ <data name="contigs_consed_ace" format="ace" label="${tool.name} on $on_string: Contigs (Consed/Ace)">\n+ <filter>ace == "-ace -consed" and no != "-no"</filter>\n </data>\n \n- <data name=\'contig_graph\' format=\'txt\' label=\'Contig Graph\'/>\n- <data name=\'pair_align\' format=\'txt\' label=\'Pairwise Alignments\'>\n- <filter>pair == \'-pair\' and no != \'-no\'</filter>\n+ <data name="contig_graph" format="txt" label="${tool.name} on $on_string: Contig Graph"/>\n+ <data name="pair_align" format="txt" label="${tool.name} on $on_string: Pairwise Alignments">\n+ <filter>pair == "-pair" and no != "-no"</filter>\n </data>\n- <data name=\'pair_status\' format=\'tabular\' label=\'Paired-End Read Status\'>\n- <filter>paired_reads == \'true\' and no != \'-no\'</filter>\n+ <data name="pair_status" format="tabular" label="${tool.name} on $on_string: Paired-End Read Status">\n+ <filter>paired_reads == "true" and no != "-no"</filter>\n </data>\n- <data name=\'scaffolds_fasta\' format=\'fasta\' label=\'Scaffolds (Fasta)\'>\n- <filter>paired_reads == \'true\' and no != \'-no\'</filter>\n+ <data name="scaffolds_fasta" format="fasta" label="${tool.name} on $on_string: Scaffolds (Fasta)">\n+ <filter>paired_reads == "true" and no != "-no"</filter>\n+ </data>\n+ <data name="scaffolds_qual" format="qual454" label="${tool.name} on $on_string: Scaffolds (Qual454)">\n+ <filter>paired_reads == "true" and no != "-no"</filter>\n </data>\n- <data name=\'scaffolds_qual\' format=\'qual454\' label=\'Scaffolds (Qual454)\'>\n- <filter>paired_reads == \'true\' and no != \'-no\'</filter>\n+ <data name="scaffolds_agp" format="tabular" label="${tool.name} on $on_string: Scaffolds (Agp)">\n+ <filter>paired_reads == "true" and no != "-no"</filter>\n </data>\n- <data name=\'scaffolds_agp\' format=\'tabular\' label=\'Scaffolds (Agp)\'>\n- <filter>paired_reads == \'true\' and no != \'-no\'</filter>\n+ <data name="contig_scaffolds_agp" format="tabular" label="${tool.name} on $on_string: Contig Scaffolds(Agp)">\n+ <filter>scaffold is True</filter>\n </data>\n- <data name=\'tag_pair_align\' format=\'txt\' label=\'Tag Pair Alignments\'>\n- <filter>pair == \'-pair\' and paired_reads == \'true\' and no != \'-no\'</filter>\n+ <data name="tag_pair_align" format="txt" label="${tool.name} on $on_string: Tag Pair Alignments">\n+ <filter>pair == "-pair" and paired_reads == "true" and no != "-no"</filter>\n </data>\n- <data name=\'trim_status\' format=\'tabular\' label=\'Trim Status\'/>\n+ <data name="trim_status" format="tabular" label="${tool.name} on $on_string: Trim Status"/>\n \n- <data name=\'isotigs_ace\' format=\'ace\' label=\'Isotigs (Ace)\'>\n- <filter>ace != \'\' and no != \'-no\'</filter>\n+ <data name="isotigs_ace" format="ace" label="${tool.name} on $on_string: Isotigs (Ace)">\n+ <filter>ace != "" and no != "-no"</filter>\n </data>\n- <data name=\'isotigs_fasta\' format=\'fasta\' label=\'Isotigs (Fasta)\'>\n- <filter>no != \'-no\'</filter>\n+ <data name="isotigs_fasta" format="fasta" label="${tool.name} on $on_string: Isotigs (Fasta)">\n+ <filter>no != "-no"</filter>\n </data>\n- <data name=\'isotigs_qual\' format=\'qual454\' label=\'Isotigs (Qual454)\'>\n- <filter>no != \'-no\'</filter>\n+ <data name="isotigs_qual" format="qual454" label="${tool.name} on $on_string: Isotigs (Qual454)">\n+ <filter>no != "-no"</filter>\n </data>\n- <data name=\'isotigs_agp\' format=\'tabular\' label=\'Isotigs (Agp)\'>\n- <filter>no != \'-no\'</filter>\n+ <data name="isotigs_agp" format="tabular" label="${tool.name} on $on_string: Isotigs (Agp)">\n+ <filter>no != "-no"</filter>\n </data>\n- <data name=\'isotigs_layout\' format=\'txt\' label=\'Isotig Layout\'>\n- <filter>no != \'-no\'</filter>\n+ <data name="isotigs_layout" format="txt" label="${tool.name} on $on_string: Isotig Layout">\n+ <filter>no != "-no"</filter>\n </data>\n \n </outputs>\n' |
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| diff -r 2d86d5b112e8 -r bf1f8bc4abe6 runAssembly_cDNA_wrapper.pl --- a/runAssembly_cDNA_wrapper.pl Thu Jul 14 22:14:07 2011 -0400 +++ b/runAssembly_cDNA_wrapper.pl Wed Dec 21 19:42:53 2011 -0800 |
| b |
| @@ -22,6 +22,7 @@ my $scaffolds_fasta=shift @ARGV; my $scaffolds_qual=shift @ARGV; my $scaffolds_agp=shift @ARGV; +my $contig_scaffolds_agp=shift @ARGV; my $tag_pair_align=shift @ARGV; my $trim_status=shift @ARGV; my $isotigs_ace=shift @ARGV; @@ -35,9 +36,8 @@ my @cmd=removeUnusedOptions(@ARGV); # RUN COMMAND -# NOTE: FIRST ARG EXPECTED TO BE EXECUTABLE my $stderr; -eval { $stderr=`@cmd 2>&1`; }; +eval { $stderr=`runAssembly @cmd 2>&1`; }; if ( $@ ) { print STDERR "Newbler ERROR: $stderr\n"; `cat $outdir/assembly/454NewblerProgress.txt 1>&2`; @@ -59,6 +59,7 @@ get_outfile("$outdir/454Scaffolds.fna", $scaffolds_fasta); get_outfile("$outdir/454Scaffolds.qual", $scaffolds_qual); get_outfile("$outdir/454Scaffolds.txt", $scaffolds_agp); +get_outfile("$outdir/454ContigScaffolds.txt", $contig_scaffolds_agp); get_outfile("$outdir/454TagPairAlign.txt", $tag_pair_align); get_outfile("$outdir/454TrimStatus.txt", $trim_status); get_outfile("$outdir/454Isotigs.ace", $isotigs_ace); |
| b |
| diff -r 2d86d5b112e8 -r bf1f8bc4abe6 runAssembly_wrapper.pl --- a/runAssembly_wrapper.pl Thu Jul 14 22:14:07 2011 -0400 +++ b/runAssembly_wrapper.pl Wed Dec 21 19:42:53 2011 -0800 |
| b |
| @@ -22,6 +22,7 @@ my $scaffolds_fasta=shift @ARGV; my $scaffolds_qual=shift @ARGV; my $scaffolds_agp=shift @ARGV; +my $contig_scaffolds_agp=shift @ARGV; my $tag_pair_align=shift @ARGV; my $trim_status=shift @ARGV; my $large_contigs_fasta=shift @ARGV; @@ -32,9 +33,8 @@ my @cmd=removeUnusedOptions(@ARGV); # RUN COMMAND -# NOTE: FIRST ARG EXPECTED TO BE EXECUTABLE my $stderr; -eval { $stderr=`@cmd 2>&1`; }; +eval { $stderr=`runAssembly @cmd 2>&1`; }; if ( $@ ) { print STDERR "Newbler ERROR: $stderr\n"; `cat $outdir/assembly/454NewblerProgress.txt 1>&2`; @@ -56,6 +56,7 @@ get_outfile("$outdir/454Scaffolds.fna", $scaffolds_fasta); get_outfile("$outdir/454Scaffolds.qual", $scaffolds_qual); get_outfile("$outdir/454Scaffolds.txt", $scaffolds_agp); +get_outfile("$outdir/454ContigScaffolds.txt", $contig_scaffolds_agp); get_outfile("$outdir/454TagPairAlign.txt", $tag_pair_align); get_outfile("$outdir/454TrimStatus.txt", $trim_status); get_outfile("$outdir/454LargeContigs.fna", $large_contigs_fasta); |
| b |
| diff -r 2d86d5b112e8 -r bf1f8bc4abe6 runMapping.xml --- a/runMapping.xml Thu Jul 14 22:14:07 2011 -0400 +++ b/runMapping.xml Wed Dec 21 19:42:53 2011 -0800 |
| [ |
| b'@@ -1,4 +1,4 @@\n-<tool id="runMapping" name="runMapping" version="1.0.0">\n+<tool id="runMapping" name="runMapping" version="1.0.1">\n <description>Map Roche/454 reads to a reference using Newbler</description>\n <command interpreter=\'perl\'>runMapping_wrapper.pl\n $newbler_metrics.extra_files_path\n@@ -19,10 +19,12 @@\n $trimmed_reads_fasta\n $trimmed_reads_qual\n $contigs_ace\n+$contigs_bam\n $large_contigs_fasta\n $large_contigs_qual\n $gene_status\n-$newbler_exe -o $newbler_metrics.extra_files_path\n+runAssembly\n+-o $newbler_metrics.extra_files_path\n -cpu 8 \n -a $a\n -e $e \n@@ -34,6 +36,7 @@\n $notrim \n $tr \n $ace \n+$bam\n $no \n $qo \n $nor \n@@ -70,155 +73,152 @@\n #end for\n </command>\n <inputs>\n- <!-- NEWBLER VERSION -->\n- <param name=\'newbler_exe\' type=\'select\' display=\'radio\' label=\'Newbler version\'>\n- <option value=\'/jgi/tools/454/rig-DataProcessing_2.3/bin/runMapping\'>2.3</option>\n- <option value=\'/jgi/tools/454/rig-DataProcessing_2.4pre-20091204/bin/runMapping\'>2.4</option>\n- <option value=\'/home/copeland/local/x86_64/newbler/v2.5p1-internal-10Jun23-1/runMapping\' selected=\'true\'>2.5</option>\n- </param>\n-\n <!-- READSEQ INFILES -->\n <repeat name="sff_inputs" title="Unpaired Reads Sff Files">\n <param name="sff_input" type="data" format="sff" label="SE Sff file"/>\n </repeat>\n- <repeat name="sanger_inputs" title="Unpaired Reads Fasta Files">\n- <param name="sanger_input" type="data" format="fasta" label="SE Fasta file"/>\n+ <repeat name="sanger_inputs" title="Unpaired Reads Fasta/Fastq Files">\n+ <param name="sanger_input" type="data" format="fasta,fastqsanger" label="SE Fasta/Fastq file"/>\n </repeat>\n <repeat name="sff_paired_inputs" title="Paired Reads Sff Files">\n <param name="sff_paired_input" type="data" format="sff" label="PE Sff file"/>\n </repeat>\n- <repeat name="sanger_paired_inputs" title="Paired Reads Fasta Files">\n- <param name="sanger_paired_input" type="data" format="fasta" label="PE Fasta file"/>\n+ <repeat name="sanger_paired_inputs" title="Paired Reads Fasta/Fastq Files">\n+ <param name="sanger_paired_input" type="data" format="fasta,fastqsanger" label="PE Fasta/Fastq file"/>\n </repeat>\n- <param name=\'paired_reads\' type=\'select\' display=\'radio\' label=\'[-paired_reads] If supplying paired reads (above), do you want paired-read info?\'>\n- <option value=\'false\'>no</option>\n- <option value=\'true\'>[-paired_reads] yes</option>\n+ <param name="paired_reads" type="select" display="radio" label="[-paired_reads] If supplying paired reads (above), do you want paired-read info?">\n+ <option value="false">no</option>\n+ <option value="true">[-paired_reads] yes</option>\n </param>\n- <param name=\'pair\' type=\'select\' display=\'radio\' label=\'[-pair] Output pairwise overlaps\'>\n- <option value=\'\'>no</option>\n- <option value=\'-pair\'>[-pair] yes</option>\n+ <param name="pair" type="select" display="radio" label="[-pair] Output pairwise overlaps">\n+ <option value="">no</option>\n+ <option value="-pair">[-pair] yes</option>\n </param>\n \n <!-- SOURCE DNA TYPE -->\n- <param name=\'l\' type="integer" value=\'500\' label="[-l] This option sets the minimum length for a contig to appear in the 454LargeContigs.fna file"/>\n+ <param name="l" type="integer" value="500" label="[-l] This option sets the minimum length for a contig to appear in the 454LargeContigs.fna file"/>\n \n <!-- INPUTS SPECIFIC TO MAPPING -->\n- <repeat name=\'ref_inputs\' title=\'Reference Sequence\'>\n- <param name=\'ref_input\' type=\'data\' format=\'fasta\' label=\'Fasta file\'/>\n+ <repeat name="ref_inputs" title="Reference Sequence">\n+ <param name="ref_input" type="data" format="fasta" label="Fasta file"/>\n </repeat>\n- <param name=\'ref_type\' type=\'select\' display=\'radio\' label=\'Reference type\'>\n- <option value=\'-gref\'>[-gref] Genomic reference sequence</option>\n- <option valu'..b't="bam" label="${tool.name} on $on_string: Contigs (Bam)">\n+ <filter>bam is True and no != "-no"</filter>\n </data>\n- <data name=\'large_contigs_qual\' format=\'qual454\' label=\'Large Contigs (Qual454)\'>\n- <filter>no != \'-no\'</filter>\n+ <data name="large_contigs_fasta" format="fasta" label="${tool.name} on $on_string: Large Contigs (Fasta)">\n+ <filter>no != "-no"</filter>\n+ </data>\n+ <data name="large_contigs_qual" format="qual454" label="${tool.name} on $on_string: Large Contigs (Qual454)">\n+ <filter>no != "-no"</filter>\n </data>\n- <data name=\'pair_align\' format=\'txt\' label=\'Pairwise Alignments\'>\n- <filter>pair == \'-pair\' and no != \'-no\'</filter>\n+ <data name="pair_align" format="txt" label="${tool.name} on $on_string: Pairwise Alignments">\n+ <filter>pair == "-pair" and no != "-no"</filter>\n </data>\n- <data name=\'pair_status\' format=\'tabular\' label=\'Paired-End Read Status\'>\n- <filter>paired_reads == \'true\' and no != \'-no\'</filter>\n+ <data name="pair_status" format="tabular" label="${tool.name} on $on_string: Paired-End Read Status">\n+ <filter>paired_reads == "true" and no != "-no"</filter>\n </data>\n- <data name=\'scaffolds_fasta\' format=\'fasta\' label=\'Scaffolds (Fasta)\'>\n- <filter>paired_reads == \'true\' and no != \'-no\'</filter>\n+ <data name="scaffolds_fasta" format="fasta" label="${tool.name} on $on_string: Scaffolds (Fasta)">\n+ <filter>paired_reads == "true" and no != "-no"</filter>\n </data>\n- <data name=\'scaffolds_qual\' format=\'qual454\' label=\'Scaffolds (Qual454)\'>\n- <filter>paired_reads == \'true\' and no != \'-no\'</filter>\n+ <data name="scaffolds_qual" format="qual454" label="${tool.name} on $on_string: Scaffolds (Qual454)">\n+ <filter>paired_reads == "true" and no != "-no"</filter>\n </data>\n- <data name=\'scaffolds_agp\' format=\'tabular\' label=\'Scaffolds (Agp)\'>\n- <filter>paired_reads == \'true\' and no != \'-no\'</filter>\n+ <data name="scaffolds_agp" format="tabular" label="${tool.name} on $on_string: Scaffolds (Agp)">\n+ <filter>paired_reads == "true" and no != "-no"</filter>\n </data>\n- <data name=\'tag_pair_align\' format=\'txt\' label=\'Tag Pair Alignments\'>\n- <filter>pair == \'-pair\' and paired_reads == \'true\' and no != \'-no\'</filter>\n+ <data name="tag_pair_align" format="txt" label="${tool.name} on $on_string: Tag Pair Alignments">\n+ <filter>pair == "-pair" and paired_reads == "true" and no != "-no"</filter>\n </data>\n- <data name=\'trim_status\' format=\'tabular\' label=\'Trim Status\'/>\n+ <data name="trim_status" format="tabular" label="${tool.name} on $on_string: Trim Status"/>\n \n <!-- THE FOLLOWING ARE LIMITED TO MAPPING -->\n- <data name=\'all_diffs\' format=\'tabular\' label=\'All Diffs\'/>\n- <data name=\'all_struct_vars\' format=\'tabular\' label=\'All Struct Vars\'/>\n- <data name=\'hc_diff\' format=\'tabular\' label=\'High Confidence Diff\'/>\n- <data name=\'hc_struct_vars\' format=\'tabular\' label=\'High Confidence Struct Vars\'/>\n- <data name=\'gene_status\' format=\'tabular\' label=\'Gene Status\'/>\n- <data name=\'mapping_qc\' format=\'xls\' label=\'Mapping QC (Excel)\'/>\n- <data name=\'ref_status\' format=\'tabular\' label=\'Ref Status\'/>\n+ <data name="all_diffs" format="tabular" label="${tool.name} on $on_string: All Diffs"/>\n+ <data name="all_struct_vars" format="tabular" label="${tool.name} on $on_string: All Struct Vars"/>\n+ <data name="hc_diff" format="tabular" label="${tool.name} on $on_string: High Confidence Diff"/>\n+ <data name="hc_struct_vars" format="tabular" label="${tool.name} on $on_string: High Confidence Struct Vars"/>\n+ <data name="gene_status" format="tabular" label="${tool.name} on $on_string: Gene Status"/>\n+ <data name="mapping_qc" format="xls" label="${tool.name} on $on_string: Mapping QC (Excel)"/>\n+ <data name="ref_status" format="tabular" label="${tool.name} on $on_string: Ref Status"/>\n \n </outputs>\n <help>\n' |
| b |
| diff -r 2d86d5b112e8 -r bf1f8bc4abe6 runMapping_cDNA.xml --- a/runMapping_cDNA.xml Thu Jul 14 22:14:07 2011 -0400 +++ b/runMapping_cDNA.xml Wed Dec 21 19:42:53 2011 -0800 |
| [ |
| b'@@ -1,4 +1,4 @@\n-<tool id="runMapping_cDNA" name="runMapping cDNA" version="1.0.0">\n+<tool id="runMapping_cDNA" name="runMapping cDNA" version="1.0.1">\n <description>Map Roche/454 reads to a reference using Newbler</description>\n <command interpreter=\'perl\'>runMapping_cDNA_wrapper.pl\n $newbler_metrics.extra_files_path\n@@ -25,7 +25,8 @@\n $isotigs_qual\n $isotigs_agp\n $isotigs_layout\n-$newbler_exe -o $newbler_metrics.extra_files_path\n+runAssembly\n+-o $newbler_metrics.extra_files_path\n -cpu 8 \n -a $a\n -e $e \n@@ -78,167 +79,160 @@\n #end for\n </command>\n <inputs>\n- <!-- NEWBLER VERSION -->\n- <param name=\'newbler_exe\' type=\'select\' display=\'radio\' label=\'Newbler version\'>\n- <option value=\'/jgi/tools/454/rig-DataProcessing_2.3/bin/runMapping\'>2.3</option>\n- <option value=\'/jgi/tools/454/rig-DataProcessing_2.4pre-20091204/bin/runMapping\'>2.4</option>\n- <option value=\'/home/copeland/local/x86_64/newbler/v2.5p1-internal-10Jun23-1/runMapping\' selected=\'true\'>2.5</option>\n- </param>\n-\n <!-- READSEQ INFILES -->\n <repeat name="sff_inputs" title="Unpaired Reads Sff Files">\n <param name="sff_input" type="data" format="sff" label="SE Sff file"/>\n </repeat>\n- <repeat name="sanger_inputs" title="Unpaired Reads Fasta Files">\n- <param name="sanger_input" type="data" format="fasta" label="SE Fasta file"/>\n+ <repeat name="sanger_inputs" title="Unpaired Reads Fasta/Fastq Files">\n+ <param name="sanger_input" type="data" format="fasta,fastqsanger" label="SE Fasta/Fastq file"/>\n </repeat>\n <repeat name="sff_paired_inputs" title="Paired Reads Sff Files">\n <param name="sff_paired_input" type="data" format="sff" label="PE Sff file"/>\n </repeat>\n- <repeat name="sanger_paired_inputs" title="Paired Reads Fasta Files">\n- <param name="sanger_paired_input" type="data" format="fasta" label="PE Fasta file"/>\n+ <repeat name="sanger_paired_inputs" title="Paired Reads Fasta/Fastq Files">\n+ <param name="sanger_paired_input" type="data" format="fasta,fastqsanger" label="PE Fasta/Fastq file"/>\n </repeat>\n- <param name=\'paired_reads\' type=\'select\' display=\'radio\' label=\'[-paired_reads] If supplying paired reads (above), do you want paired-read info?\'>\n- <option value=\'false\'>no</option>\n- <option value=\'true\'>[-paired_reads] yes</option>\n+ <param name="paired_reads" type="select" display="radio" label="[-paired_reads] If supplying paired reads (above), do you want paired-read info?">\n+ <option value="false">no</option>\n+ <option value="true">[-paired_reads] yes</option>\n </param>\n- <param name=\'pair\' type=\'select\' display=\'radio\' label=\'[-pair] Output pairwise overlaps\'>\n- <option value=\'\'>no</option>\n- <option value=\'-pair\'>[-pair] yes</option>\n+ <param name="pair" type="select" display="radio" label="[-pair] Output pairwise overlaps">\n+ <option value="">no</option>\n+ <option value="-pair">[-pair] yes</option>\n </param>\n \n <!-- SOURCE DNA TYPE -->\n- <param name=\'it\' type=\'integer\' value=\'100\' label=\'[-it] Specify the maximum number of isotigs in an isogroup. Maximum is 10,000.\'/>\n- <param name=\'ig\' type=\'integer\' value=\'500\' label=\'[-ig] Specify the maximum number of contigs in an isogroup.\'/>\n- <param name=\'icc\' type=\'integer\' value=\'100\' label=\'[-icc] Specify the maximum number of contigs in an isotig. Maximum is 200 and corresponds to the recursion depth during graph traversal\'/>\n- <param name=\'icl\' type=\'integer\' value=\'3\' label=\'[-icl] Specify the minimum length a contig must be to be part of an isotig. Minimum is 3bp.\'/>\n+ <param name="it" type="integer" value="100" label="[-it] Specify the maximum number of isotigs in an isogroup. Maximum is 10,000."/>\n+ <param name="ig" type="integer" value="500" label="[-ig] Specify the maximum number of contigs in an isogroup."/>\n+ <param name="icc" type="integer" value="100" label="[-icc] Specify the maximum numbe'..b' \'-no\'</filter>\n+ <data name="scaffolds_fasta" format="fasta" label="${tool.name} on $on_string: Scaffolds (Fasta)">\n+ <filter>paired_reads == "true" and no != "-no"</filter>\n </data>\n- <data name=\'scaffolds_qual\' format=\'qual454\' label=\'Scaffolds (Qual454)\'>\n- <filter>paired_reads == \'true\' and no != \'-no\'</filter>\n+ <data name="scaffolds_qual" format="qual454" label="${tool.name} on $on_string: Scaffolds (Qual454)">\n+ <filter>paired_reads == "true" and no != "-no"</filter>\n </data>\n- <data name=\'scaffolds_agp\' format=\'tabular\' label=\'Scaffolds (Agp)\'>\n- <filter>paired_reads == \'true\' and no != \'-no\'</filter>\n+ <data name="scaffolds_agp" format="tabular" label="${tool.name} on $on_string: Scaffolds (Agp)">\n+ <filter>paired_reads == "true" and no != "-no"</filter>\n </data>\n- <data name=\'tag_pair_align\' format=\'txt\' label=\'Tag Pair Alignments\'>\n- <filter>pair == \'-pair\' and paired_reads == \'true\' and no != \'-no\'</filter>\n+ <data name="tag_pair_align" format="txt" label="${tool.name} on $on_string: Tag Pair Alignments">\n+ <filter>pair == "-pair" and paired_reads == "true" and no != "-no"</filter>\n </data>\n- <data name=\'trim_status\' format=\'tabular\' label=\'Trim Status\'/>\n+ <data name="trim_status" format="tabular" label="${tool.name} on $on_string: Trim Status"/>\n \n <!-- THE FOLLOWING ARE LIMITED TO MAPPING -->\n- <data name=\'all_diffs\' format=\'tabular\' label=\'All Diffs\'/>\n- <data name=\'all_struct_vars\' format=\'tabular\' label=\'All Struct Vars\'/>\n- <data name=\'hc_diff\' format=\'tabular\' label=\'High Confidence Diff\'/>\n- <data name=\'hc_struct_vars\' format=\'tabular\' label=\'High Confidence Struct Vars\'/>\n- <data name=\'gene_status\' format=\'tabular\' label=\'Gene Status\'/>\n- <data name=\'mapping_qc\' format=\'xls\' label=\'Mapping QC (Excel)\'/>\n- <data name=\'ref_status\' format=\'tabular\' label=\'Ref Status\'/>\n+ <data name="all_diffs" format="tabular" label="${tool.name} on $on_string: All Diffs"/>\n+ <data name="all_struct_vars" format="tabular" label="${tool.name} on $on_string: All Struct Vars"/>\n+ <data name="hc_diff" format="tabular" label="${tool.name} on $on_string: High Confidence Diff"/>\n+ <data name="hc_struct_vars" format="tabular" label="${tool.name} on $on_string: High Confidence Struct Vars"/>\n+ <data name="gene_status" format="tabular" label="${tool.name} on $on_string: Gene Status"/>\n+ <data name="mapping_qc" format="xls" label="${tool.name} on $on_string: Mapping QC (Excel)"/>\n+ <data name="ref_status" format="tabular" label="${tool.name} on $on_string: Ref Status"/>\n \n <!-- ISOTIGS -->\n- <data name=\'isotigs_ace\' format=\'ace\' label=\'Isotigs (Ace)\'>\n- <filter>ace != \'\' and no != \'-no\'</filter>\n+ <data name="isotigs_ace" format="ace" label="${tool.name} on $on_string: Isotigs (Ace)">\n+ <filter>ace != "" and no != "-no"</filter>\n </data>\n- <data name=\'isotigs_fasta\' format=\'fasta\' label=\'Isotigs (Fasta)\'>\n- <filter>no != \'-no\'</filter>\n+ <data name="isotigs_fasta" format="fasta" label="${tool.name} on $on_string: Isotigs (Fasta)">\n+ <filter>no != "-no"</filter>\n </data>\n- <data name=\'isotigs_qual\' format=\'qual454\' label=\'Isotigs (Qual454)\'>\n- <filter>no != \'-no\'</filter>\n+ <data name="isotigs_qual" format="qual454" label="${tool.name} on $on_string: Isotigs (Qual454)">\n+ <filter>no != "-no"</filter>\n </data>\n- <data name=\'isotigs_agp\' format=\'tabular\' label=\'Isotigs (Agp)\'>\n- <filter>no != \'-no\'</filter>\n+ <data name="isotigs_agp" format="tabular" label="${tool.name} on $on_string: Isotigs (Agp)">\n+ <filter>no != "-no"</filter>\n </data>\n- <data name=\'isotigs_layout\' format=\'txt\' label=\'Isotig Layout\'>\n- <filter>no != \'-no\'</filter>\n+ <data name="isotigs_layout" format="txt" label="${tool.name} on $on_string: Isotig Layout">\n+ <filter>no != "-no"</filter>\n </data>\n \n </outputs>\n' |
| b |
| diff -r 2d86d5b112e8 -r bf1f8bc4abe6 runMapping_cDNA_wrapper.pl --- a/runMapping_cDNA_wrapper.pl Thu Jul 14 22:14:07 2011 -0400 +++ b/runMapping_cDNA_wrapper.pl Wed Dec 21 19:42:53 2011 -0800 |
| b |
| @@ -36,9 +36,8 @@ my @cmd=removeUnusedOptions(@ARGV); # RUN COMMAND -# NOTE: FIRST ARG EXPECTED TO BE EXECUTABLE my $stderr; -eval { $stderr=`@cmd 2>&1`; }; +eval { $stderr=`runMapping @cmd 2>&1`; }; if ( $@ ) { print STDERR "Newbler ERROR: $stderr\n"; `cat $outdir/assembly/454NewblerProgress.txt 1>&2`; |
| b |
| diff -r 2d86d5b112e8 -r bf1f8bc4abe6 runMapping_wrapper.pl --- a/runMapping_wrapper.pl Thu Jul 14 22:14:07 2011 -0400 +++ b/runMapping_wrapper.pl Wed Dec 21 19:42:53 2011 -0800 |
| b |
| @@ -23,6 +23,7 @@ my $trimmed_reads_fasta=shift @ARGV; my $trimmed_reads_qual=shift @ARGV; my $contigs_ace=shift @ARGV; +my $contigs_bam=shift @ARGV; my $large_contigs_fasta=shift @ARGV; my $large_contigs_qual=shift @ARGV; my $gene_status=shift @ARGV; @@ -32,9 +33,8 @@ my @cmd=removeUnusedOptions(@ARGV); # RUN COMMAND -# NOTE: FIRST ARG EXPECTED TO BE EXECUTABLE my $stderr; -eval { $stderr=`@cmd 2>&1`; }; +eval { $stderr=`runMapping @cmd 2>&1`; }; if ( $@ ) { print STDERR "Newbler ERROR: $stderr\n"; `cat $outdir/assembly/454NewblerProgress.txt 1>&2`; @@ -58,6 +58,7 @@ get_outfile("$outdir/454TrimmedReads.fna", $trimmed_reads_fasta); get_outfile("$outdir/454TrimmedReads.qual", $trimmed_reads_qual); get_outfile("$outdir/454Contigs.ace", $contigs_ace); +get_outfile("$outdir/454Contigs.bam", $contigs_bam); get_outfile("$outdir/454LargeContigs.fna", $large_contigs_fasta); get_outfile("$outdir/454LargeContigs.qual", $large_contigs_qual); get_outfile("$outdir/454GeneStatus.txt", $gene_status); |