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