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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="get_gb_sp" name="Get_GB_sp" version="1.0">
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2 <description> Grab All GenBank Data from a text list of species </description>
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3 <requirements>
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4 <requirement type="perl-module">Bio</requirement>
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5 </requirements>
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6 <command interpreter="perl">
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7 get_gb_sp.pl $data_file $database $outtype $outfile $nffile 2> error.log
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8 </command>
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9 <inputs>
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10 <param format="txt" name="data_file" type="data" optional="false" label="Text list of species" help="One species per line"/>
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11
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12 <param name="database" type="select" label="Protein or Nucleotide Data">
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13 <option value="nucleotide">Nucleotide</option>
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14 <option value="protein">Protein</option>
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15 </param>
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16
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17 <param name="outtype" type="select" label="Output File Format">
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18 <option value="fasta">Fasta</option>
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19 <option value="genbank">GenBank</option>
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20 </param>
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21 </inputs>
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22 <outputs>
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23 <data format="txt" name="nffile" label="No genbank data ${tool.name} with ${on_string}" />
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24 <data format="txt" name="outfile" label="Sequence Data from ${tool.name} with ${on_string}" />
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25 </outputs>
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26 <help>
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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27 **What it does**
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28
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29 Downloads ALL data from GenBank based on species names.
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30
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31 ------
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32
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33 **Inputs**
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34
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35 A text list of species names (or genus names will retrieve all data for a genus.)
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36
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37 ------
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38
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39 **Outputs**
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40
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41 The user selects which output format to use for data downloaded from GenBank. Options Include::
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42 1. GenBank format
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43 2. FASTA format
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44
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45 -------
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46
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47 **Additional Information**
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48
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49 GenBank format can be converted to phytab or other formats using GenBankstrip.
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50
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51 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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52
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53 -------
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54
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55 **Citations**
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56
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57 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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58
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59 Current Osiris Citation is here
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60
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61 http://osiris-phylogenetics.blogspot.com/2012/10/citation.html
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62
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63 </help>
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64 </tool>