Mercurial > repos > ucsb-phylogenetics > osiris_phylogenetics
comparison phyloconversion/phylip2fasta.xml @ 0:5b9a38ec4a39 draft default tip
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| author | osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> |
|---|---|
| date | Tue, 11 Mar 2014 12:19:13 -0700 |
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| -1:000000000000 | 0:5b9a38ec4a39 |
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| 1 <tool id="phylip2fasta" name="phylip2fasta" version="1.0"> | |
| 2 <description>Converts phylip file to fasta format</description> | |
| 3 <command interpreter="perl"> | |
| 4 phylip2fasta.pl $infile $interlv $idlen > $outfile | |
| 5 </command> | |
| 6 <inputs> | |
| 7 <param name="infile" type="data" format="phylip" label="Input File" help="file to convert" /> | |
| 8 <param name='interlv' type='boolean' checked='false' truevalue='1' falsevalue='0' label='Interleaved' help='Check if input file is interleaved'/> | |
| 9 <param name="idlen" type="integer" value="10" label="Specify Number characters in sequence IDs" /> | |
| 10 </inputs> | |
| 11 <outputs> | |
| 12 <data format="fasta" name="outfile" label="${tool.name} on ${on_string}: FASTA file" /> | |
| 13 </outputs> | |
| 14 <help> **What it does** | |
| 15 | |
| 16 phylip2fasta takes an input phylip file and converts it to a fasta file | |
| 17 | |
| 18 ------ | |
| 19 | |
| 20 **Inputs** | |
| 21 | |
| 22 A phylip file with sequences from the same species and gene family. The user must choose if the file | |
| 23 is interleaved, and specifiy the number of characters in the ID's of the sequences (default phylip | |
| 24 format is 10). ------ | |
| 25 | |
| 26 **Outputs** | |
| 27 | |
| 28 FASTA file | |
| 29 | |
| 30 ------- | |
| 31 | |
| 32 **Additional Information** | |
| 33 | |
| 34 Please direct questions or comments to ucsb_phylogenetics@lifesci.ucsb.edu or preferably, if you | |
| 35 can, enter them on the osiris_phylogenetics repository site at bitbucket.org | |
| 36 | |
| 37 ------ | |
| 38 | |
| 39 **Citations** | |
| 40 | |
| 41 This tool is part of the Osiris Phylogenetics Tool Package for Galaxy. If you make extensive use of | |
| 42 this tool in a publication, please consider citing the following. | |
| 43 | |
| 44 Current Osiris Citation is here | |
| 45 | |
| 46 http://osiris-phylogenetics.blogspot.com/2012/10/citation.html | |
| 47 </help> </tool> | |
| 48 |