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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_1_gb" name="Get_1_GB" version="1.0">
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2 <description> Grab one sequence from GenBank using accession number query </description>
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3 <requirements>
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4 <requirement type="package">bioperl</requirement>
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5 </requirements>
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6 <command interpreter="perl">
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7 get_1_gb.pl $acc $database $outtype $outfile 2>&amp;1
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8 </command>
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9 <inputs>
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10 <param name="acc" type="text" label="Accession Number" />
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11 <param name="database" type="select" label="Protein or Nucleotide Data">
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12 <option value="nucleotide">Nucleotide</option>
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13 <option value="protein">Protein</option>
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14 </param>
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15 <param name="outtype" type="select" label="File Format">
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16 <option value="fasta">Fasta</option>
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17 <option value="genbank">GenBank</option>
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18 </param>
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19 </inputs>
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20 <outputs>
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21 <data format="txt" name="outfile" label="Sequence data from ${tool.name} with ${on_string}" />
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22 </outputs>
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23 <help>
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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24 **What it does**
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25
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26 Get_1_GB grabs one sequence from GenBank using accession number query.
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27
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28 ------
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29
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30 **Inputs**
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31
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32 GenBank accession number
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33
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34 ------
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35
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36 **Outputs**
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37
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38 FASTA or GenBank
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39
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40 -------
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41
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42 **Additional Information**
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43
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44 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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45
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46 -------
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47
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48 **Citations**
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49
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50 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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51
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52 Current Osiris Citation is here
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53
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54 http://osiris-phylogenetics.blogspot.com/2012/10/citation.html
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55
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56 Additional Citations for this tool
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57
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58 Link to Genbank: http://www.ncbi.nlm.nih.gov/genbank/
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59 </help>
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60 </tool>