# HG changeset patch
# User edward-kirton
# Date 1310696047 14400
# Node ID 2d86d5b112e89117f5bda7a7df0f784a157b278d
# Parent 368a6ebebddeb275a9a88b192cac9176cd102e59
Uploaded
diff -r 368a6ebebdde -r 2d86d5b112e8 roche454/README
--- a/roche454/README Tue Jun 07 17:51:04 2011 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-- 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 368a6ebebdde -r 2d86d5b112e8 roche454/runAssembly.xml
--- a/roche454/runAssembly.xml Tue Jun 07 17:51:04 2011 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,215 +0,0 @@
-
-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'
-
-
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- no != '-no'
-
-
- no != '-no'
-
-
- no != '-no'
-
-
- ace == '-ace' and no != '-no'
-
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- ace == '-ace -consed' and no != '-no'
-
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- no != '-no'
-
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- no != '-no'
-
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- pair == '-pair' and no != '-no'
-
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- 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 368a6ebebdde -r 2d86d5b112e8 roche454/runAssembly_cDNA.xml
--- a/roche454/runAssembly_cDNA.xml Tue Jun 07 17:51:04 2011 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,235 +0,0 @@
-
-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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- tr == '-tr'
-
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- 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 368a6ebebdde -r 2d86d5b112e8 roche454/runAssembly_cDNA_wrapper.pl
--- a/roche454/runAssembly_cDNA_wrapper.pl Tue Jun 07 17:51:04 2011 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,94 +0,0 @@
-#!/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 368a6ebebdde -r 2d86d5b112e8 roche454/runAssembly_wrapper.pl
--- a/roche454/runAssembly_wrapper.pl Tue Jun 07 17:51:04 2011 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,88 +0,0 @@
-#!/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,$dest);
- }
-}
-
-__END__
diff -r 368a6ebebdde -r 2d86d5b112e8 roche454/runMapping.xml
--- a/roche454/runMapping.xml Tue Jun 07 17:51:04 2011 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,240 +0,0 @@
-
-Map Roche/454 reads to a reference using Newbler
-runMapping_wrapper.pl
-$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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- tr == '-tr'
-
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- 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 368a6ebebdde -r 2d86d5b112e8 roche454/runMapping_cDNA.xml
--- a/roche454/runMapping_cDNA.xml Tue Jun 07 17:51:04 2011 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,261 +0,0 @@
-
-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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- tr == '-tr'
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- tr == '-tr'
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- no != '-no'
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- 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 368a6ebebdde -r 2d86d5b112e8 roche454/runMapping_cDNA_wrapper.pl
--- a/roche454/runMapping_cDNA_wrapper.pl Tue Jun 07 17:51:04 2011 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,96 +0,0 @@
-#!/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 368a6ebebdde -r 2d86d5b112e8 roche454/runMapping_wrapper.pl
--- a/roche454/runMapping_wrapper.pl Tue Jun 07 17:51:04 2011 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,89 +0,0 @@
-#!/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 368a6ebebdde -r 2d86d5b112e8 roche454/sff_to_fastq.xml
--- a/roche454/sff_to_fastq.xml Tue Jun 07 17:51:04 2011 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,11 +0,0 @@
-
- Convert SFF to Fastq
- sff_to_fastq_converter.pl $input $output.extra_files_path $output
-
-
-
-
-
-
- Convert Sff to Fastq
-
diff -r 368a6ebebdde -r 2d86d5b112e8 roche454/sff_to_fastq_converter.pl
--- a/roche454/sff_to_fastq_converter.pl Tue Jun 07 17:51:04 2011 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,31 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-use Getopt::Long;
-use File::Basename;
-
-# VALIDATE INPUT
-die("Expected 3 args") unless @ARGV == 3;
-my ($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, $qual);
-exit 0;
diff -r 368a6ebebdde -r 2d86d5b112e8 roche454/sfffile.xml
--- a/roche454/sfffile.xml Tue Jun 07 17:51:04 2011 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,29 +0,0 @@
-
-Select reads to include or exclude from one or more input Sff files
-sfffile -$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 368a6ebebdde -r 2d86d5b112e8 roche454/suite_config.xml
--- a/roche454/suite_config.xml Tue Jun 07 17:51:04 2011 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,21 +0,0 @@
-
- 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
-
-
diff -r 368a6ebebdde -r 2d86d5b112e8 runAssembly.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/runAssembly.xml Thu Jul 14 22:14:07 2011 -0400
@@ -0,0 +1,212 @@
+
+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
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ 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 368a6ebebdde -r 2d86d5b112e8 runAssembly_cDNA.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/runAssembly_cDNA.xml Thu Jul 14 22:14:07 2011 -0400
@@ -0,0 +1,232 @@
+
+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
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ 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 368a6ebebdde -r 2d86d5b112e8 runAssembly_cDNA_wrapper.pl
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/runAssembly_cDNA_wrapper.pl Thu Jul 14 22:14:07 2011 -0400
@@ -0,0 +1,95 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+use File::Copy;
+
+# EXPECT 23 FILE HANDLES, SOME OF WHICH MAY BE 'None'
+die("Missing arguments; expected at least 23, got ".scalar(@ARGV)."\n") unless @ARGV >= 23;
+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 368a6ebebdde -r 2d86d5b112e8 runAssembly_wrapper.pl
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/runAssembly_wrapper.pl Thu Jul 14 22:14:07 2011 -0400
@@ -0,0 +1,89 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+use File::Copy;
+
+# EXPECT 20 FILE HANDLES, SOME OF WHICH MAY BE 'None'
+die("Missing arguments; expected at least 20, got ".scalar(@ARGV)."\n") unless @ARGV >= 20;
+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,$dest);
+ }
+}
+
+__END__
diff -r 368a6ebebdde -r 2d86d5b112e8 runMapping.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/runMapping.xml Thu Jul 14 22:14:07 2011 -0400
@@ -0,0 +1,237 @@
+
+Map Roche/454 reads to a reference using Newbler
+runMapping_wrapper.pl
+$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
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ 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 368a6ebebdde -r 2d86d5b112e8 runMapping_cDNA.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/runMapping_cDNA.xml Thu Jul 14 22:14:07 2011 -0400
@@ -0,0 +1,258 @@
+
+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
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ 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 368a6ebebdde -r 2d86d5b112e8 runMapping_cDNA_wrapper.pl
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/runMapping_cDNA_wrapper.pl Thu Jul 14 22:14:07 2011 -0400
@@ -0,0 +1,97 @@
+#!/usr/bin/env/perl
+
+use warnings;
+use strict;
+use File::Copy;
+
+# EXPECT 24 FILE HANDLES, SOME OF WHICH MAY BE 'None'
+die("Missing arguments; expected at least 24, got ".scalar(@ARGV)."\n") unless @ARGV >= 24;
+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 368a6ebebdde -r 2d86d5b112e8 runMapping_wrapper.pl
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/runMapping_wrapper.pl Thu Jul 14 22:14:07 2011 -0400
@@ -0,0 +1,90 @@
+#!/jgi/tools/bin/perl -w
+
+use strict;
+use File::Copy;
+
+# EXPECT 21 FILE HANDLES, SOME OF WHICH MAY BE 'None'
+die("Missing arguments; expected at least 21, got ".scalar(@ARGV)."\n") unless @ARGV >= 21;
+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 368a6ebebdde -r 2d86d5b112e8 sff_to_fastq.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/sff_to_fastq.xml Thu Jul 14 22:14:07 2011 -0400
@@ -0,0 +1,11 @@
+
+
+ sff_to_fastq_converter.pl $input $output.extra_files_path $output
+
+
+
+
+
+
+ Convert Sff to Fastq
+
diff -r 368a6ebebdde -r 2d86d5b112e8 sff_to_fastq_converter.pl
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/sff_to_fastq_converter.pl Thu Jul 14 22:14:07 2011 -0400
@@ -0,0 +1,31 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+use Getopt::Long;
+use File::Basename;
+
+# VALIDATE INPUT
+die("Expected 3 args") unless @ARGV == 3;
+my ($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, $qual);
+exit 0;
diff -r 368a6ebebdde -r 2d86d5b112e8 sfffile.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/sfffile.xml Thu Jul 14 22:14:07 2011 -0400
@@ -0,0 +1,29 @@
+
+Select reads to include or exclude from one or more input Sff files
+sfffile -$include_or_exclude $list_file -o $output
+#for $i in $inputs
+${i.input}
+#end for
+
+
+
+
+
+
+
+
+
+
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+**What it does**
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+This tool creates an Sff file, either including or excluding named reads.
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