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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="phylota_with_taxid" name="PhyLoTA_with_taxID" version="1.0">
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2 <description>Pull all genetic data from phylota using a GenBank Taxonomy ID</description>
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3 <requirements>
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4 <requirement type="perl-module">Bio</requirement>
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5 <requirement type="perl-module">LWP</requirement>
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6 </requirements>
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7 <command interpreter="perl">
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8 phylota_with_taxid.pl $input $outfile $phytabfile
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9 </command>
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10 <inputs>
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11 <param name="input" type="integer" value="0" label="Taxon ID" help="GenBank TaxonID" />
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12 </inputs>
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13 <outputs>
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14 <data format="fasta" name="outfile" label="fasta file from ${tool.name} on ${on_string}: Out file" />
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15 <data format="tabular" name="phytabfile" label="phytab from ${tool.name} on ${on_string}: Out file" />
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16 </outputs>
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17 <help>
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18 **What it does**
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19
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20 PhyLoTA_with_taxID pulls pre-calculated trees and corresponding raw data from the PhyLoTA browser. The PhyLoTA browser groups GenBank
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21 data into gene clusters by similarity, and uses those clusters for phylogenetic analysis.
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22
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23 ------
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24
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25 **Inputs**
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26
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27 1. A GenBank Taxon ID.
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28 Search Here for ID of a taxon
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29 http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/
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30
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31 ------
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32
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33 **Outputs**
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34
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35 1. All raw sequence data in fasta format for the trees in #2.
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36 2. All raw sequence data in PHYTAB format. http://osiris-phylogenetics.blogspot.com/2012/09/introduction-to-phytab-format.html
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37
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38 -------
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39
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40 **Additional Information**
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41
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42 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
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43
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44 ------
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45
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46 **Citations**
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47
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48 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.
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49
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50 Current Osiris Citation is here
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51
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52 http://osiris-phylogenetics.blogspot.com/2012/10/citation.html
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53
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54 Additional Citations for this tool
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55
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56 Sanderson, M. J., D. Boss, D. Chen, K. A. Cranston, and A. Wehe. 2008. The PhyLoTA Browser: processing GenBank for molecular phylogenetics research. Syst. Biol. 57:335-346.
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57
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58 </help>
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59 </tool>
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