# HG changeset patch
# User edward-kirton
# Date 1307483432 14400
# Node ID f036c7107601f5baf299287ae12b2cb3e8c4ca24
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
diff -r 000000000000 -r f036c7107601 roche454/README
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/roche454/README Tue Jun 07 17:50:32 2011 -0400
@@ -0,0 +1,6 @@
+- Newbler requires a license and the executables are not included here
+- the Newbler tool config files include options to support multiple versions of Newbler; you'll need to add the paths to
+the XML file if you wish to use this feature. Or, just remove this parameter entirely. Note the wrapper is expecting the
+executable as the first argument.
+- the SFF->Fastq converter requires the executable "fasta_qual_to_fastq" is installed; replace with whatever converter
+you have installed in the perl script.
diff -r 000000000000 -r f036c7107601 roche454/runAssembly.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/roche454/runAssembly.xml Tue Jun 07 17:50:32 2011 -0400
@@ -0,0 +1,215 @@
+
+De novo assembly of Roche/454 reads using Newbler
+runAssembly_wrapper.pl
+$newbler_metrics.extra_files_path
+$newbler_metrics
+$read_status
+$trimmed_reads_fasta
+$trimmed_reads_qual
+$alignment_info
+$all_contigs_fasta
+$all_contigs_qual
+$contigs_ace
+$contigs_consed_ace
+$contig_graph
+$pair_align
+$pair_status
+$scaffolds_fasta
+$scaffolds_qual
+$scaffolds_agp
+$tag_pair_align
+$trim_status
+$large_contigs_fasta
+$large_contigs_qual
+$newbler_exe -o $newbler_metrics.extra_files_path
+-cpu 8
+$rip
+-e $e
+-mi $mi
+-ml $ml
+-minlen $minlen
+$large
+$pair
+$info
+$notrim
+$tr
+$ace
+$no
+$qo
+$nor
+$ud
+-ss $ss
+-sl $sl
+-sc $sc
+-ais $ais
+-a $a
+-mcf $mcf
+-vs $vs
+-vt $vt
+-fi $fi
+-fe $fe
+-l $l
+#for $i in $sff_paired_inputs
+-p ${i.sff_paired_input}
+#end for
+#for $i in $sanger_paired_inputs
+-p ${i.sanger_paired_input}
+#end for
+#for $i in $sff_inputs
+${i.sff_input}
+#end for
+#for $i in $sanger_inputs
+${i.sanger_input}
+#end for
+
+
+
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+
+
+
+
+
+
+
+
+
+
+
+
+ tr == '-tr'
+
+
+ tr == '-tr'
+
+
+
+ no != '-no'
+
+
+ no != '-no'
+
+
+ no != '-no'
+
+
+ ace == '-ace' and no != '-no'
+
+
+ ace == '-ace -consed' and no != '-no'
+
+
+
+
+ no != '-no'
+
+
+ no != '-no'
+
+
+ pair == '-pair' and no != '-no'
+
+
+ paired_reads == 'true' and no != '-no'
+
+
+ paired_reads == 'true' and no != '-no'
+
+
+ paired_reads == 'true' and no != '-no'
+
+
+ paired_reads == 'true' and no != '-no'
+
+
+ pair == '-pair' and paired_reads == 'true' and no != '-no'
+
+
+
+
+
+
+**What it does**
+
+Assemble (Roche/454) reads using Newbler.
+
+Download the manual here: http://galaxy.jgi-psf.org/static/manuals/GSFLXSystemSoftwareManual_PartC_Assembler-Mapper-SFFTools.pdf
+
+.. class:: warningmark
+
+**Fasta Header Format** Fasta input must provide any pairing information in the header using the expected key=value format. Use the 'Sanger tab to Newbler Fasta' tool.
+
+
+
diff -r 000000000000 -r f036c7107601 roche454/runAssembly_cDNA.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/roche454/runAssembly_cDNA.xml Tue Jun 07 17:50:32 2011 -0400
@@ -0,0 +1,235 @@
+
+De novo assembly of Roche/454 cDNA reads using Newbler
+runAssembly_cDNA_wrapper.pl
+$newbler_metrics.extra_files_path
+$newbler_metrics
+$read_status
+$trimmed_reads_fasta
+$trimmed_reads_qual
+$alignment_info
+$all_contigs_fasta
+$all_contigs_qual
+$contigs_ace
+$contigs_consed_ace
+$contig_graph
+$pair_align
+$pair_status
+$scaffolds_fasta
+$scaffolds_qual
+$scaffolds_agp
+$tag_pair_align
+$trim_status
+$isotigs_ace
+$isotigs_fasta
+$isotigs_qual
+$isotigs_agp
+$isotigs_layout
+$newbler_exe -o $newbler_metrics.extra_files_path
+-cpu 8
+$rip
+-e $e
+-mi $mi
+-ml $ml
+-minlen $minlen
+$large
+$pair
+$info
+$notrim
+$tr
+$ace
+$no
+$qo
+$nor
+$ud
+-ss $ss
+-sl $sl
+-sc $sc
+-ais $ais
+-a $a
+-mcf $mcf
+-vs $vs
+-vt $vt
+-fi $fi
+-fe $fe
+-cdna
+-ig $ig
+-it $it
+-icc $icc
+-icl $icl
+#for $i in $sff_paired_inputs
+-p ${i.sff_paired_input}
+#end for
+#for $i in $sanger_paired_inputs
+-p ${i.sanger_paired_input}
+#end for
+#for $i in $sff_inputs
+${i.sff_input}
+#end for
+#for $i in $sanger_inputs
+${i.sanger_input}
+#end for
+
+
+
+
+
+
+
+
+
+
+
+
+
+
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+
+
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+
+
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+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ tr == '-tr'
+
+
+ tr == '-tr'
+
+
+
+ no != '-no'
+
+
+ no != '-no'
+
+
+ no != '-no'
+
+
+ ace == '-ace' and no != '-no'
+
+
+ ace == '-ace -consed' and no != '-no'
+
+
+
+
+ pair == '-pair' and no != '-no'
+
+
+ paired_reads == 'true' and no != '-no'
+
+
+ paired_reads == 'true' and no != '-no'
+
+
+ paired_reads == 'true' and no != '-no'
+
+
+ paired_reads == 'true' and no != '-no'
+
+
+ pair == '-pair' and paired_reads == 'true' and no != '-no'
+
+
+
+
+ ace != '' and no != '-no'
+
+
+ no != '-no'
+
+
+ no != '-no'
+
+
+ no != '-no'
+
+
+ no != '-no'
+
+
+
+
+
+**What it does**
+
+Assemble (Roche/454) reads using Newbler.
+
+Download the manual here: http://galaxy.jgi-psf.org/static/manuals/GSFLXSystemSoftwareManual_PartC_Assembler-Mapper-SFFTools.pdf
+
+.. class:: warningmark
+
+**Fasta Header Format** Fasta input must provide any pairing information in the header using the expected key=value format. Use the 'Sanger tab to Newbler Fasta' tool.
+
+
+
diff -r 000000000000 -r f036c7107601 roche454/runAssembly_cDNA_wrapper.pl
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/roche454/runAssembly_cDNA_wrapper.pl Tue Jun 07 17:50:32 2011 -0400
@@ -0,0 +1,94 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+use File::Copy;
+
+# EXPECT 23 FILE HANDLES, SOME OF WHICH MAY BE 'None'
+my $outdir=shift @ARGV;
+my $newbler_metrics=shift @ARGV;
+my $read_status=shift @ARGV;
+my $trimmed_reads_fasta=shift @ARGV;
+my $trimmed_reads_qual=shift @ARGV;
+my $alignment_info=shift @ARGV;
+my $all_contigs_fasta=shift @ARGV;
+my $all_contigs_qual=shift @ARGV;
+my $contigs_ace=shift @ARGV;
+my $contigs_consed_ace=shift @ARGV;
+my $contig_graph=shift @ARGV;
+my $pair_align=shift @ARGV;
+my $pair_status=shift @ARGV;
+my $scaffolds_fasta=shift @ARGV;
+my $scaffolds_qual=shift @ARGV;
+my $scaffolds_agp=shift @ARGV;
+my $tag_pair_align=shift @ARGV;
+my $trim_status=shift @ARGV;
+my $isotigs_ace=shift @ARGV;
+my $isotigs_fasta=shift @ARGV;
+my $isotigs_qual=shift @ARGV;
+my $isotigs_agp=shift @ARGV;
+my $isotigs_layout=shift @ARGV;
+
+# REMOVE PARAMETERS FOR OPTIONAL FILES WHICH WERE NOT PROVIDED
+
+my @cmd=removeUnusedOptions(@ARGV);
+
+# RUN COMMAND
+# NOTE: FIRST ARG EXPECTED TO BE EXECUTABLE
+my $stderr;
+eval { $stderr=`@cmd 2>&1`; };
+if ( $@ ) {
+ print STDERR "Newbler ERROR: $stderr\n";
+ `cat $outdir/assembly/454NewblerProgress.txt 1>&2`;
+ die($@);
+}
+
+get_outfile("$outdir/454NewblerMetrics.txt", $newbler_metrics);
+get_outfile("$outdir/454ReadStatus.txt", $read_status);
+get_outfile("$outdir/454TrimmedReads.fna", $trimmed_reads_fasta);
+get_outfile("$outdir/454TrimmedReads.qual", $trimmed_reads_qual);
+get_outfile("$outdir/454AlignmentInfo.tsv", $alignment_info);
+get_outfile("$outdir/454AllContigs.fna", $all_contigs_fasta);
+get_outfile("$outdir/454AllContigs.qual", $all_contigs_qual);
+get_outfile("$outdir/454Contigs.ace", $contigs_ace);
+get_outfile("$outdir/consed/edit_dir/454Contigs.ace.1", $contigs_consed_ace);
+get_outfile("$outdir/454ContigGraph.txt", $contig_graph);
+get_outfile("$outdir/454PairAlign.txt", $pair_align);
+get_outfile("$outdir/454PairStatus.txt", $pair_status);
+get_outfile("$outdir/454Scaffolds.fna", $scaffolds_fasta);
+get_outfile("$outdir/454Scaffolds.qual", $scaffolds_qual);
+get_outfile("$outdir/454Scaffolds.txt", $scaffolds_agp);
+get_outfile("$outdir/454TagPairAlign.txt", $tag_pair_align);
+get_outfile("$outdir/454TrimStatus.txt", $trim_status);
+get_outfile("$outdir/454Isotigs.ace", $isotigs_ace);
+get_outfile("$outdir/454Isotigs.fna", $isotigs_fasta);
+get_outfile("$outdir/454Isotigs.qual", $isotigs_qual);
+get_outfile("$outdir/454Isotigs.txt", $isotigs_agp);
+get_outfile("$outdir/454IsotigsLayout.txt", $isotigs_layout);
+exit;
+
+# EVERY 'None' ARG AND IT'S PRECEEDING OPTION TAG ARE DISCARDED
+sub removeUnusedOptions {
+ my @cmd=();
+ my $prev;
+ foreach (@_) {
+ unless ($_ eq 'None') {
+ push @cmd, $prev if defined($prev);
+ $prev=$_;
+ } else {
+ $prev=undef;
+ }
+ }
+ push @cmd, $prev if defined($prev);
+ return @cmd;
+}
+
+sub get_outfile {
+ my ($src, $dest)=@_;
+ # make sure dest defined and src exist; skip if dest is 'None'
+ if ( $dest and $dest ne 'None' and $src and -f $src ) {
+ move($src,$dest);
+ }
+}
+
+__END__
diff -r 000000000000 -r f036c7107601 roche454/runAssembly_wrapper.pl
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/roche454/runAssembly_wrapper.pl Tue Jun 07 17:50:32 2011 -0400
@@ -0,0 +1,88 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+use File::Copy;
+
+# EXPECT 20 FILE HANDLES, SOME OF WHICH MAY BE 'None'
+my $outdir=shift @ARGV;
+my $newbler_metrics=shift @ARGV;
+my $read_status=shift @ARGV;
+my $trimmed_reads_fasta=shift @ARGV;
+my $trimmed_reads_qual=shift @ARGV;
+my $alignment_info=shift @ARGV;
+my $all_contigs_fasta=shift @ARGV;
+my $all_contigs_qual=shift @ARGV;
+my $contigs_ace=shift @ARGV;
+my $contigs_consed_ace=shift @ARGV;
+my $contig_graph=shift @ARGV;
+my $pair_align=shift @ARGV;
+my $pair_status=shift @ARGV;
+my $scaffolds_fasta=shift @ARGV;
+my $scaffolds_qual=shift @ARGV;
+my $scaffolds_agp=shift @ARGV;
+my $tag_pair_align=shift @ARGV;
+my $trim_status=shift @ARGV;
+my $large_contigs_fasta=shift @ARGV;
+my $large_contigs_qual=shift @ARGV;
+
+# REMOVE PARAMETERS FOR OPTIONAL FILES WHICH WERE NOT PROVIDED
+
+my @cmd=removeUnusedOptions(@ARGV);
+
+# RUN COMMAND
+# NOTE: FIRST ARG EXPECTED TO BE EXECUTABLE
+my $stderr;
+eval { $stderr=`@cmd 2>&1`; };
+if ( $@ ) {
+ print STDERR "Newbler ERROR: $stderr\n";
+ `cat $outdir/assembly/454NewblerProgress.txt 1>&2`;
+ die($@);
+}
+
+get_outfile("$outdir/454NewblerMetrics.txt", $newbler_metrics);
+get_outfile("$outdir/454ReadStatus.txt", $read_status);
+get_outfile("$outdir/454TrimmedReads.fna", $trimmed_reads_fasta);
+get_outfile("$outdir/454TrimmedReads.qual", $trimmed_reads_qual);
+get_outfile("$outdir/454AlignmentInfo.tsv", $alignment_info);
+get_outfile("$outdir/454AllContigs.fna", $all_contigs_fasta);
+get_outfile("$outdir/454AllContigs.qual", $all_contigs_qual);
+get_outfile("$outdir/454Contigs.ace", $contigs_ace);
+get_outfile("$outdir/consed/edit_dir/454Contigs.ace.1", $contigs_consed_ace);
+get_outfile("$outdir/454ContigGraph.txt", $contig_graph);
+get_outfile("$outdir/454PairAlign.txt", $pair_align);
+get_outfile("$outdir/454PairStatus.txt", $pair_status);
+get_outfile("$outdir/454Scaffolds.fna", $scaffolds_fasta);
+get_outfile("$outdir/454Scaffolds.qual", $scaffolds_qual);
+get_outfile("$outdir/454Scaffolds.txt", $scaffolds_agp);
+get_outfile("$outdir/454TagPairAlign.txt", $tag_pair_align);
+get_outfile("$outdir/454TrimStatus.txt", $trim_status);
+get_outfile("$outdir/454LargeContigs.fna", $large_contigs_fasta);
+get_outfile("$outdir/454LargeContigs.qual", $large_contigs_qual);
+exit;
+
+# EVERY 'None' ARG AND IT'S PRECEEDING OPTION TAG ARE DISCARDED
+sub removeUnusedOptions {
+ my @cmd=();
+ my $prev;
+ foreach (@_) {
+ unless ($_ eq 'None') {
+ push @cmd, $prev if defined($prev);
+ $prev=$_;
+ } else {
+ $prev=undef;
+ }
+ }
+ push @cmd, $prev if defined($prev);
+ return @cmd;
+}
+
+sub get_outfile {
+ my ($src, $dest)=@_;
+ # make sure dest defined and src exist; skip if dest is 'None'
+ if ( $dest and $dest ne 'None' and $src and -f $src ) {
+ move($src,$dest);
+ }
+}
+
+__END__
diff -r 000000000000 -r f036c7107601 roche454/runMapping.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/roche454/runMapping.xml Tue Jun 07 17:50:32 2011 -0400
@@ -0,0 +1,240 @@
+
+Map Roche/454 reads to a reference using Newbler
+runMapping_wrapper.pl
+$newbler_metrics.extra_files_path
+$alignment_info
+$all_contigs_fasta
+$all_contigs_qual
+$all_diffs
+$all_struct_vars
+$hc_diff
+$hc_struct_vars
+$mapping_qc
+$newbler_metrics
+$pair_align
+$read_status
+$ref_status
+$tag_pair_align
+$trim_status
+$trimmed_reads_fasta
+$trimmed_reads_qual
+$contigs_ace
+$large_contigs_fasta
+$large_contigs_qual
+$gene_status
+$newbler_exe -o $newbler_metrics.extra_files_path
+-cpu 8
+-a $a
+-e $e
+-mi $mi
+-ml $ml
+-minlen $minlen
+$pair
+$info
+$notrim
+$tr
+$ace
+$no
+$qo
+$nor
+$ud
+-ss $ss
+-sl $sl
+-sc $sc
+-ais $ais
+-rst $rst
+-hsl $hsl
+-mcf $mcf
+-vs $vs
+-vt $vt
+-fi $fi
+-fe $fe
+-l $l
+$ref_type
+-ref
+#for $i in $ref_inputs
+${i.ref_input}
+#end for
+-read
+#for $i in $sff_paired_inputs
+-p ${i.sff_paired_input}
+#end for
+#for $i in $sanger_paired_inputs
+-p ${i.sanger_paired_input}
+#end for
+#for $i in $sff_inputs
+${i.sff_input}
+#end for
+#for $i in $sanger_inputs
+${i.sanger_input}
+#end for
+
+
+
+
+
+
+
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+
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+
+
+
+
+
+
+
+
+
+
+
+
+ tr == '-tr'
+
+
+ tr == '-tr'
+
+
+
+
+ no != '-no'
+
+
+ no != '-no'
+
+
+ ace == '-ace' and no != '-no'
+
+
+ no != '-no'
+
+
+ no != '-no'
+
+
+ pair == '-pair' and no != '-no'
+
+
+ paired_reads == 'true' and no != '-no'
+
+
+ paired_reads == 'true' and no != '-no'
+
+
+ paired_reads == 'true' and no != '-no'
+
+
+ paired_reads == 'true' and no != '-no'
+
+
+ pair == '-pair' and paired_reads == 'true' and no != '-no'
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+**What it does**
+
+Map (Roche/454) reads to a reference using Newbler.
+
+Download the manual here: http://galaxy.jgi-psf.org/static/manuals/GSFLXSystemSoftwareManual_PartC_Assembler-Mapper-SFFTools.pdf
+
+.. class:: warningmark
+
+**Fasta Header Format** Fasta input must provide any pairing information in the header using the expected key=value format. Use the 'Sanger tab to Newbler Fasta' tool.
+
+
+
diff -r 000000000000 -r f036c7107601 roche454/runMapping_cDNA.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/roche454/runMapping_cDNA.xml Tue Jun 07 17:50:32 2011 -0400
@@ -0,0 +1,261 @@
+
+Map Roche/454 reads to a reference using Newbler
+runMapping_cDNA_wrapper.pl
+$newbler_metrics.extra_files_path
+$alignment_info
+$all_contigs_fasta
+$all_contigs_qual
+$all_diffs
+$all_struct_vars
+$hc_diff
+$hc_struct_vars
+$mapping_qc
+$newbler_metrics
+$pair_align
+$read_status
+$ref_status
+$tag_pair_align
+$trim_status
+$trimmed_reads_fasta
+$trimmed_reads_qual
+$contigs_ace
+$gene_status
+$isotigs_ace
+$isotigs_fasta
+$isotigs_qual
+$isotigs_agp
+$isotigs_layout
+$newbler_exe -o $newbler_metrics.extra_files_path
+-cpu 8
+-a $a
+-e $e
+-mi $mi
+-ml $ml
+-minlen $minlen
+$pair
+$info
+$notrim
+$tr
+$ace
+$no
+$qo
+$nor
+$ud
+-ss $ss
+-sl $sl
+-sc $sc
+-ais $ais
+-rst $rst
+-hsl $hsl
+-mcf $mcf
+-vs $vs
+-vt $vt
+-fi $fi
+-fe $fe
+-cdna
+$srv
+-ig $ig
+-it $it
+-icc $icc
+-icl $icl
+$ref_type
+-ref
+#for $i in $ref_inputs
+${i.ref_input}
+#end for
+-read
+#for $i in $sff_paired_inputs
+-p ${i.sff_paired_input}
+#end for
+#for $i in $sanger_paired_inputs
+-p ${i.sanger_paired_input}
+#end for
+#for $i in $sff_inputs
+${i.sff_input}
+#end for
+#for $i in $sanger_inputs
+${i.sanger_input}
+#end for
+
+
+
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+
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+
+
+
+
+
+
+
+
+
+
+ tr == '-tr'
+
+
+ tr == '-tr'
+
+
+
+
+ no != '-no'
+
+
+ no != '-no'
+
+
+ ace == '-ace' and no != '-no'
+
+
+ pair == '-pair' and no != '-no'
+
+
+ paired_reads == 'true' and no != '-no'
+
+
+ paired_reads == 'true' and no != '-no'
+
+
+ paired_reads == 'true' and no != '-no'
+
+
+ paired_reads == 'true' and no != '-no'
+
+
+ pair == '-pair' and paired_reads == 'true' and no != '-no'
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ ace != '' and no != '-no'
+
+
+ no != '-no'
+
+
+ no != '-no'
+
+
+ no != '-no'
+
+
+ no != '-no'
+
+
+
+
+
+**What it does**
+
+Map (Roche/454) reads to a reference using Newbler.
+
+Download the manual here: http://galaxy.jgi-psf.org/static/manuals/GSFLXSystemSoftwareManual_PartC_Assembler-Mapper-SFFTools.pdf
+
+.. class:: warningmark
+
+**Fasta Header Format** Fasta input must provide any pairing information in the header using the expected key=value format. Use the 'Sanger tab to Newbler Fasta' tool.
+
+
+
diff -r 000000000000 -r f036c7107601 roche454/runMapping_cDNA_wrapper.pl
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/roche454/runMapping_cDNA_wrapper.pl Tue Jun 07 17:50:32 2011 -0400
@@ -0,0 +1,96 @@
+#!/usr/bin/env/perl
+
+use warnings;
+use strict;
+use File::Copy;
+
+# EXPECT 21 FILE HANDLES, SOME OF WHICH MAY BE 'None'
+my $outdir=shift @ARGV;
+my $alignment_info=shift @ARGV;
+my $all_contigs_fasta=shift @ARGV;
+my $all_contigs_qual=shift @ARGV;
+my $all_diffs=shift @ARGV
+my $all_struct_vars=shift @ARGV
+my $hc_diff=shift @ARGV
+my $hc_struct_vars=shift @ARGV
+my $mapping_qc=shift @ARGV
+my $newbler_metrics=shift @ARGV;
+my $pair_align=shift @ARGV;
+my $read_status=shift @ARGV;
+my $ref_status=shift @ARGV;
+my $tag_pair_align=shift @ARGV;
+my $trim_status=shift @ARGV;
+my $trimmed_reads_fasta=shift @ARGV;
+my $trimmed_reads_qual=shift @ARGV;
+my $contigs_ace=shift @ARGV;
+my $gene_status=shift @ARGV;
+my $isotigs_ace=shift @ARGV;
+my $isotigs_fasta=shift @ARGV;
+my $isotigs_qual=shift @ARGV;
+my $isotigs_agp=shift @ARGV;
+my $isotigs_layout=shift @ARGV;
+
+# REMOVE PARAMETERS FOR OPTIONAL FILES WHICH WERE NOT PROVIDED
+
+my @cmd=removeUnusedOptions(@ARGV);
+
+# RUN COMMAND
+# NOTE: FIRST ARG EXPECTED TO BE EXECUTABLE
+my $stderr;
+eval { $stderr=`@cmd 2>&1`; };
+if ( $@ ) {
+ print STDERR "Newbler ERROR: $stderr\n";
+ `cat $outdir/assembly/454NewblerProgress.txt 1>&2`;
+ die($@);
+}
+
+get_outfile("$outdir/454AlignmentInfo.tsv", $alignment_info);
+get_outfile("$outdir/454AllContigs.fna", $all_contigs_fasta);
+get_outfile("$outdir/454AllContigs.qual", $all_contigs_qual);
+get_outfile("$outdir/454AllDiffs.txt", $all_diffs);
+get_outfile("$outdir/454AllStructVars.txt", $all_struct_vars);
+get_outfile("$outdir/454HCDiff.txt", $hc_diff);
+get_outfile("$outdir/454HCStructVars.txt", $hc_struct_vars);
+get_outfile("$outdir/454MappingQC.xls", $mapping_qc);
+get_outfile("$outdir/454NewblerMetrics.txt", $newbler_metrics);
+get_outfile("$outdir/454PairAlign.txt", $pair_align);
+get_outfile("$outdir/454ReadStatus.txt", $read_status);
+get_outfile("$outdir/454RefStatus.txt", $ref_status);
+get_outfile("$outdir/454TagPairAlign.txt", $tag_pair_align);
+get_outfile("$outdir/454TrimStatus.txt", $trim_status);
+get_outfile("$outdir/454TrimmedReads.fna", $trimmed_reads_fasta);
+get_outfile("$outdir/454TrimmedReads.qual", $trimmed_reads_qual);
+get_outfile("$outdir/454Contigs.ace", $contigs_ace);
+get_outfile("$outdir/454GeneStatus.txt", $gene_status);
+get_outfile("$outdir/454Isotigs.ace", $isotigs_ace);
+get_outfile("$outdir/454Isotigs.fna", $isotigs_fasta);
+get_outfile("$outdir/454Isotigs.qual", $isotigs_qual);
+get_outfile("$outdir/454Isotigs.txt", $isotigs_agp);
+get_outfile("$outdir/454IsotigsLayout.txt", $isotigs_layout);
+exit;
+
+# EVERY 'None' ARG AND IT'S PRECEEDING OPTION TAG ARE DISCARDED
+sub removeUnusedOptions {
+ my @cmd=();
+ my $prev;
+ foreach (@_) {
+ unless ($_ eq 'None') {
+ push @cmd, $prev if defined($prev);
+ $prev=$_;
+ } else {
+ $prev=undef;
+ }
+ }
+ push @cmd, $prev if defined($prev);
+ return @cmd;
+}
+
+sub get_outfile {
+ my ($src, $dest)=@_;
+ # make sure dest defined and src exist; skip if dest is 'None'
+ if ( $dest and $dest ne 'None' and $src and -f $src ) {
+ move($src,$dest);
+ }
+}
+
+__END__
diff -r 000000000000 -r f036c7107601 roche454/runMapping_wrapper.pl
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/roche454/runMapping_wrapper.pl Tue Jun 07 17:50:32 2011 -0400
@@ -0,0 +1,89 @@
+#!/jgi/tools/bin/perl -w
+
+use strict;
+use File::Copy;
+
+# EXPECT 21 FILE HANDLES, SOME OF WHICH MAY BE 'None'
+my $outdir=shift @ARGV;
+my $alignment_info=shift @ARGV;
+my $all_contigs_fasta=shift @ARGV;
+my $all_contigs_qual=shift @ARGV;
+my $all_diffs=shift @ARGV
+my $all_struct_vars=shift @ARGV
+my $hc_diff=shift @ARGV
+my $hc_struct_vars=shift @ARGV
+my $mapping_qc=shift @ARGV
+my $newbler_metrics=shift @ARGV;
+my $pair_align=shift @ARGV;
+my $read_status=shift @ARGV;
+my $ref_status=shift @ARGV;
+my $tag_pair_align=shift @ARGV;
+my $trim_status=shift @ARGV;
+my $trimmed_reads_fasta=shift @ARGV;
+my $trimmed_reads_qual=shift @ARGV;
+my $contigs_ace=shift @ARGV;
+my $large_contigs_fasta=shift @ARGV;
+my $large_contigs_qual=shift @ARGV;
+my $gene_status=shift @ARGV;
+
+# REMOVE PARAMETERS FOR OPTIONAL FILES WHICH WERE NOT PROVIDED
+
+my @cmd=removeUnusedOptions(@ARGV);
+
+# RUN COMMAND
+# NOTE: FIRST ARG EXPECTED TO BE EXECUTABLE
+my $stderr;
+eval { $stderr=`@cmd 2>&1`; };
+if ( $@ ) {
+ print STDERR "Newbler ERROR: $stderr\n";
+ `cat $outdir/assembly/454NewblerProgress.txt 1>&2`;
+ die($@);
+}
+
+get_outfile("$outdir/454AlignmentInfo.tsv", $alignment_info);
+get_outfile("$outdir/454AllContigs.fna", $all_contigs_fasta);
+get_outfile("$outdir/454AllContigs.qual", $all_contigs_qual);
+get_outfile("$outdir/454AllDiffs.txt", $all_diffs);
+get_outfile("$outdir/454AllStructVars.txt", $all_struct_vars);
+get_outfile("$outdir/454HCDiff.txt", $hc_diff);
+get_outfile("$outdir/454HCStructVars.txt", $hc_struct_vars);
+get_outfile("$outdir/454MappingQC.xls", $mapping_qc);
+get_outfile("$outdir/454NewblerMetrics.txt", $newbler_metrics);
+get_outfile("$outdir/454PairAlign.txt", $pair_align);
+get_outfile("$outdir/454ReadStatus.txt", $read_status);
+get_outfile("$outdir/454RefStatus.txt", $ref_status);
+get_outfile("$outdir/454TagPairAlign.txt", $tag_pair_align);
+get_outfile("$outdir/454TrimStatus.txt", $trim_status);
+get_outfile("$outdir/454TrimmedReads.fna", $trimmed_reads_fasta);
+get_outfile("$outdir/454TrimmedReads.qual", $trimmed_reads_qual);
+get_outfile("$outdir/454Contigs.ace", $contigs_ace);
+get_outfile("$outdir/454LargeContigs.fna", $large_contigs_fasta);
+get_outfile("$outdir/454LargeContigs.qual", $large_contigs_qual);
+get_outfile("$outdir/454GeneStatus.txt", $gene_status);
+exit;
+
+# EVERY 'None' ARG AND IT'S PRECEEDING OPTION TAG ARE DISCARDED
+sub removeUnusedOptions {
+ my @cmd=();
+ my $prev;
+ foreach (@_) {
+ unless ($_ eq 'None') {
+ push @cmd, $prev if defined($prev);
+ $prev=$_;
+ } else {
+ $prev=undef;
+ }
+ }
+ push @cmd, $prev if defined($prev);
+ return @cmd;
+}
+
+sub get_outfile {
+ my ($src, $dest)=@_;
+ # make sure dest defined and src exist; skip if dest is 'None'
+ if ( $dest and $dest ne 'None' and $src and -f $src ) {
+ move($src,$dest);
+ }
+}
+
+__END__
diff -r 000000000000 -r f036c7107601 roche454/sff_to_fastq.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/roche454/sff_to_fastq.xml Tue Jun 07 17:50:32 2011 -0400
@@ -0,0 +1,11 @@
+
+ Convert SFF to Fastq
+ sff_to_fastq_converter.pl $input $output.extra_files_path $output
+
+
+
+
+
+
+ Convert Sff to Fastq
+
diff -r 000000000000 -r f036c7107601 roche454/sff_to_fastq_converter.pl
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/roche454/sff_to_fastq_converter.pl Tue Jun 07 17:50:32 2011 -0400
@@ -0,0 +1,31 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+use Getopt::Long;
+use File::Basename;
+
+# VALIDATE INPUT
+die("Expected 3 args") unless @ARGV == 3;
+my ($sff, $extra_files_path, $fastq) = @ARGV;
+
+# DEFINE PATHS
+mkdir($extra_files_path) unless -d $extra_files_path;
+my $base = basename($sff);
+my $fasta = "$extra_files_path/$base.fasta";
+my $qual = "$extra_files_path/$base.qual";
+
+# GENERATE FASTA, QUAL, FASTQ
+my $outf;
+my $out;
+eval { $out=`sffinfo -seq $sff > $fasta` };
+die("ERROR: $out") if $@;
+print $out;
+eval { $out=`sffinfo -qual $sff > $qual` };
+die("ERROR: $out") if $@;
+print $out;
+eval { $out=`fasta_qual_to_fastq $fasta $qual $fastq` };
+die("ERROR: $out") if $@;
+print $out;
+unlink($fasta, $qual);
+exit 0;
diff -r 000000000000 -r f036c7107601 roche454/sfffile.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/roche454/sfffile.xml Tue Jun 07 17:50:32 2011 -0400
@@ -0,0 +1,29 @@
+
+Select reads to include or exclude from one or more input Sff files
+sfffile -$include_or_exclude $list_file -o $output
+#for $i in $inputs
+${i.input}
+#end for
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+**What it does**
+
+This tool creates an Sff file, either including or excluding named reads.
+
+
diff -r 000000000000 -r f036c7107601 roche454/suite_config.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/roche454/suite_config.xml Tue Jun 07 17:50:32 2011 -0400
@@ -0,0 +1,21 @@
+
+ This suite contains Roche/454's Newbler and sff-fastq converter
+
+ Assemble 454 gDNA reads
+
+
+ Assemble 454 cDNA reads
+
+
+ Map 454 cDNA reads to reference
+
+
+ Map 454 cDNA reads to reference
+
+
+ Convert SFF to Fastq
+
+
+ Utility to make Sff files
+
+