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First commit of old repositories
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" name="Get_GB" version="1.0">
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2 <description> Grab GenBank Data from a text list of accession numbers </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 #if $outtypeconditional.outtype == "phytab":
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8 get_gb.pl $data_file $database $outtypeconditional.outtype $outfile '$manual' '$mannames' '$outtypeconditional.genenames'
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9 #else:
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10 get_gb.pl $data_file $database $outtypeconditional.outtype $outfile '$manual' '$mannames' None
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11 #end if
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12 </command>
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13 <inputs>
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14 <param format="txt" name="data_file" type="data" optional="true" label="Text list of accession numbers" help="One Accession number per line"/>
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15 <param name="manual" type="text" label="Paste in accession numbers (optional)" help="You can optionally list the Accession numbers here (spaces between) The name of one, which will ignore the text list above"/>
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16 <param name="mannames" type="text" label="Paste in new names for sequences (optional)" help="You can optionally list Custom Names (with spaces between) for the sequences in the same order as the Accession Numbers"/>
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17
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18 <param name="database" type="select" label="Protein or Nucleotide Data">
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19 <option value="nucleotide">Nucleotide</option>
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20 <option value="protein">Protein</option>
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21 </param>
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22
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23 <conditional name="outtypeconditional">
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24 <param name="outtype" type="select" label="Output File Format">
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25 <option value="fasta">Fasta</option>
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26 <option value="genbank">GenBank</option>
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27 <option value="phytab">phytab</option>
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28 </param>
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29 <when value="phytab">
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30 <param name="genenames" type="text" label="Gene Names (C3) for phytab format" />
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31 </when>
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32 </conditional>
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33
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34
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35 </inputs>
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36 <outputs>
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37 <data format="txt" name="outfile" label="Sequence Data from ${tool.name} with ${on_string}" />
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38 </outputs>
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39 <help>
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40 **What it does**
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41
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42 Downloads data from GenBank based on Accession numbers.
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43
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44 ------
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45
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46 **Inputs**
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47
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48 There are two alternative ways to input information.
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49 1. A list of Accession numbers in a text file that is uploaded to the Galaxy history.
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50 2. Optionally, the user can paste in a list of accession numbers separated by spaces.
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51
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52 ------
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53
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54 **Outputs**
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55
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56 The user selects which output format to use for data downloaded from GenBank. Options Include::
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57 1. GenBank format
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58 2. Fasta format
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59 3. phytab format
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60
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61 phytab format includes a gene name, which is not standardized in GenBank format, so the user must add manually the gene
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62 family names for all entries. If adding only one gene name, that will be used for all entries.
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63
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64 -------
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65
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66 **Additional Information**
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67
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68 phytab format is described here:
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69 http://osiris-phylogenetics.blogspot.com/2012/09/introduction-to-phytab-format.html
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70
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71 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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72
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73 -------
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74
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75 **Citations**
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76
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77 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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78
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79 Current Osiris Citation is here
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80
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81 http://osiris-phylogenetics.blogspot.com/2012/10/citation.html
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82
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83 </help>
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84 </tool>