Mercurial > repos > ucsb-phylogenetics > osiris_phylogenetics
diff alignment/prank.xml @ 0:5b9a38ec4a39 draft default tip
First commit of old repositories
author | osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> |
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date | Tue, 11 Mar 2014 12:19:13 -0700 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/alignment/prank.xml Tue Mar 11 12:19:13 2014 -0700 @@ -0,0 +1,68 @@ +<tool id="prank" name="PRANK" version="1.0" force_history_refresh='True'> + <description> Phylogeny Aware Multiple Sequence Alignment </description> + <requirements> + <requirement type="package">prank</requirement> + </requirements> + <command interpreter="perl"> + prank.pl $input1 $format $missing + </command> + <inputs> + <param format="fasta" name="input1" type="data" label="Sequences in FASTA format" help=""/> + <param name="format" type="select" label="Output format"> + <option value="fasta">fasta</option> + </param> + <param name='missing' type='boolean' checked='false' truevalue='yes' falsevalue='no' label='-F +option when sequences have terminal missing data'/> + </inputs> + <outputs> + <data from_work_dir="output.1.fas" format="fasta" name="seqs_aligned" label="${tool.name} on ${on_string}: Alignment" /> + <data from_work_dir="output.2.fas" format="fasta" name="seqs_aligned2" label="${tool.name} on ${on_string}: Alignment" /> + </outputs> + <tests> + </tests> + <help> +**What it does** + +"PRANK is a probabilistic multiple alignment program for DNA, codon and amino-acid sequences. It's based on a novel +algorithm that treats insertions correctly and avoids over-estimation of the number of deletion events. In addition, +PRANK borrows ideas from maximum likelihood methods used in phylogenetics and correctly takes into account the +evolutionary distances between sequences. Lastly, PRANK allows for defining a potential structure for sequences to be +aligned and then, simultaneously with the alignment, predicts the locations of structural units in the sequences." +From the PRANK website: http://code.google.com/p/prank-msa/wiki/PRANK?tm=6 + +------ + +**Inputs** + +FASTA + +------ + +**Outputs** + +FASTA + +------- + +**Additional Information** + +Please direct questions or comments to ucsb_phylogenetics@lifesci.ucsb.edu or, if you can, enter them on the osiris_phylogenetics site at bitbucket.org + +------- + +**Citations** + +This tool is part of the Osiris Phylogenetics Tool Package for Galaxy. If you make extensive use of this tool in a publication, please consider citing the following. + +Current Osiris Citation is here + +http://osiris-phylogenetics.blogspot.com/2012/10/citation.html + +Additional Citations for this tool + +PRANK was developed by Ari Löytynoja and Nick Goldman and is maintained at http://code.google.com/p/prank-msa/ + +The WebCite online citation for PRANK is available here: +http://www.webcitation.org/query.php?url=http://tinyurl.com/prank-msa&refdoi=10.1186/1471-2105-11-579 + </help> +</tool>