NCLconverter 2.1 A file format transformation tool Paul Lewis, Mark Holder, Brian O'Meara Nucleic Acid Sequence, Protein Sequence, Phylogeny / Alignment nclconverter intiation_string perl "/expanse/projects/ngbt/opt/expanse/nclconverter/build/example/normalizer/NCLconverter" 0 scheduler_input scheduler.conf perl "ChargeFactor=1.0\\n" . "nodes=1\\n" . "node_exclusive=0\\n" . "threads_per_process=1\\n" infile Input Data perl "input.sequence" input.sequence 10 runtime 1 scheduler.conf Maximum Hours to Run (click here for help setting this correctly) 1.0 Estimate the maximum time your job will need to run (up to 72 hrs). Your job will be killed if it doesn't finish within the time you specify, however jobs with shorter maximum run times are often scheduled sooner than longer jobs. Maximum Hours to Run must be between 0.1 - 72.0. perl $runtime < 0.1 || $runtime > 72.0 Please set a value for the runtime perl !defined $runtime perl "runhours=$value\\n" format_type Choose the Input Format nexus nexus fasta phylip phylipt clustal nexml Clustal files must begin with the text Clustal on the first line. If you create .aln files using other programs, you may need to edit them manually, or (as with Muscle) you might be able to use a command line option to print Clustal on the first line. Depending on its composition, the input may be converted to multiple output files. This is because NEXUS can have multiple characters blocks; NCLconverter currently writes each one to a separate file in the chosen format. data_type Specify the Data Type (Mixed data types are not supported) perl "" perl $format_type eq "fasta" || $format_type eq "clustal" || $format_type eq "phylip" || $format_type eq "rphylip" dna dna rna protein discrete Sorry, Clustal format does not use discrete characters perl $value eq "discrete" & $format_type eq "clustal" Sorry, Fasta format does not use discrete characters perl $value eq "discrete" & $format_type eq "fasta" 5 relaxed_type My data is in a relaxed Phylip format perl "" perl $format_type eq "phylip" 0 Relaxed Phylip format is used by progams such as RAxML. It differs from strict Phlylip in allowing taxon names more than 10 characters long. interleaved_type My data is interleaved perl "" perl $format_type eq "phylip" 0 format_nexus_comline perl "-fnexus" perl $format_type eq "nexus" 5 0 format_nexml_comline perl "-fnexml" perl $format_type eq "nexml" 5 0 format_aafasta_comline perl "-faafasta" perl $format_type eq "fasta" & $data_type eq "protein" 5 format_dnafasta_comline perl "-fdnafasta" perl $format_type eq "fasta" &$data_type eq "dna" 5 format_rnafasta_comline perl "-frnafasta" perl $format_type eq "fasta" & $data_type eq "rna" 5 format_raaphylip_comline perl "-faarelaxedphylip" perl $format_type eq "phylip" & $data_type eq "protein" & $relaxed_type & !$interleaved_type 5 format_rdnaphylip_comline perl "-fdnarelaxedphylip" perl $format_type eq "phylip" & $data_type eq "dna" & $relaxed_type & !$interleaved_type 5 format_rrnaphylip_comline perl "-frnarelaxedphylip" perl $format_type eq "phylip" & $data_type eq "rna" & $relaxed_type & !$interleaved_type 5 format_rdiscphylip_comline perl "-fdiscreterelaxedphylip" perl $format_type eq "phylip" & $data_type eq "discrete" & $relaxed_type & !$interleaved_type 5 format_riaaaphylip_comline perl "-faarelaxedphylipinterleaved" perl $format_type eq "phylip" & $data_type eq "protein" & $relaxed_type & $interleaved_type 5 format_ridnaphylip_comline perl "-fdnarelaxedphylipinterleaved" perl $format_type eq "phylip" & $data_type eq "dna" & $relaxed_type & $interleaved_type 5 format_ridnaphylip_comline perl "-frnarelaxedphylipinterleaved" perl $format_type eq "phylip" & $data_type eq "rna" & $relaxed_type & $interleaved_type 5 format_ridiscphylip_comline perl "-fdiscreterelaxedphylipinterleaved" perl $format_type eq "phylip" & $data_type eq "discrete" & $relaxed_type & $interleaved_type 5 format_saaphylip_comline perl "-faaphylip" perl $format_type eq "phylip" & $data_type eq "protein" & !$relaxed_type & !$interleaved_type 5 format_sdnaphylip_comline perl "-fdnaphylip" perl $format_type eq "phylip" & $data_type eq "dna" & !$relaxed_type & !$interleaved_type 5 format_srnaphylip_comline perl "-frnaphylip" perl $format_type eq "phylip" & $data_type eq "rna" & !$relaxed_type & !$interleaved_type 5 format_sdiscphylip_comline perl "-fdiscretephylip" perl $format_type eq "phylip" & $data_type eq "discrete" & !$relaxed_type & !$interleaved_type 5 format_siaaphylip_comline perl "-faaphylipinterleaved" perl $format_type eq "phylip" & $data_type eq "protein" & !$relaxed_type & $interleaved_type 5 format_sidnaphylip_comline perl "-fdnaphylipinterleaved" perl $format_type eq "phylip" & $data_type eq "dna" & !$relaxed_type & $interleaved_type 5 format_sirnaphylip_comline perl "-frnaphylipinterleaved" perl $format_type eq "phylip" & $data_type eq "rna" & !$relaxed_type & $interleaved_type 5 format_sidiscphylip_comline perl "-fdiscretephylipinterleaved" perl $format_type eq "phylip" & $data_type eq "discrete" & !$relaxed_type & $interleaved_type 5 format_aaaln_comline perl "-faaaln" perl $format_type eq "clustal" & $data_type eq "protein" 5 format_dnaaln_comline perl "-fdnaaln" perl $format_type eq "clustal" & $data_type eq "dna" 5 format_rnaaln_comline perl "-frnaaln" perl $format_type eq "clustal" & $data_type eq "rna" 5 format_phylipt_comline perl "-fphyliptree" perl $format_type eq "phylip" & $data_type eq "phylipt" & !$relaxed_type 5 format_rphylipt_comline perl "-frelaxedphyliptree" perl $format_type eq "phylip" & $data_type eq "phylipt" & $relaxed_type 5 nexus_strictness Set the NEXUS strictness level (-s) perl $format_type eq "nexus" perl "-s$value" 2 5 The default level is 2. Invoking the program with 3 or a higher number will convert some warnings into fatal errors. Running with 1 will cause the parser to accept dangerous constructs, and running with 0 will cause the parser make every attempt to finish parsing the file (warning about very serious errors). Note that when 0 strictness level is used, and the parser fails to finish, it is often the result of an earlier error that occurred prior to the error reported in the last message. output_type Choose the Output format (* values could produce multiple output files) perl "$value" -enexus -enexus -efasta -ephylip -erelaxedphylip -enexml 15 WE MAY HAVE TO MODIFY YOUR TAXON NAMES TO SATISFY THE FORMAT REQUIREMENTS! If taxon names had to be translated, then a NameTranslationFile (in a somewhat ad-hoc xml format) will also be produced. This file shows how the names are remapped. A back-translation service is planned. Mixed data are not supported for NEXML output. outfile_nexus Please enter a prefix for your output file (default is "out") perl " -o$value" 20 all_output *