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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="genbankstrip" name="GenBank_strip" version="1.0.0">
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2 <description> Extracts sequences from GenBank files by gene name </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 genbankstrip.pl "-f"$data_file "-g"$gene "-l"$length $sp -op
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5 </command>
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6 <inputs>
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7 <param format="txt" name="data_file" type="data" optional="false" label="GenBank flat file"/>
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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8 <param name="gene" type="text" label="Gene to extract" help="Name must match the GenBank files or be synonymized" />
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9 <param name="length" type="integer" value="75" label="Minimum gene length" help="Does not retain short genes." />
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10 <param name='sp' type='boolean' checked='true' truevalue='-s' falsevalue='' label='Ignore undefined species' help='For example Vargula sp. would be ignored' />
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11 </inputs>
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12 <outputs>
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13 <data format="tabular" name="stripfile" label="Summary ${tool.name} with ${on_string}" from_work_dir="striplist.txt"/>
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14 <data format="tabular" name="phytabfile" label="Phytab Data ${tool.name} with ${on_string}" from_work_dir="osiris_gbs.phytab"/>
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15 </outputs>
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16 <help>
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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17 **What it does**
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18
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19 Extracts sequences from GenBank flat file based on gene name.
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20
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21 ------
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22
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23 **Inputs**
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24
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25 There are two alternative ways to input information.
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26 1. A list of Accession numbers in a text file that is uploaded to the Galaxy history.
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27 2. Optionally, the user can paste in a list of accession numbers separated by spaces.
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28
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29 ------
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30
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31 **Outputs**
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32
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33 The user selects which output format to use for data downloaded from GenBank. Options Include::
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34 1. GenBank format
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35 2. FASTA format
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36 3. phytab format
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37
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38 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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39 family names for all entries. If adding only one gene name, that will be used for all entries.
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40
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41 -------
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42
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43 **Additional Information**
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44
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45 phytab format is described here:
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46 http://osiris-phylogenetics.blogspot.com/2012/09/introduction-to-phytab-format.html
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47
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48 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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50 -------
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51
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52 **Citations**
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53
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54 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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55
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56 Current Osiris Citation is here
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57
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58 http://osiris-phylogenetics.blogspot.com/2012/10/citation.html
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59
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60 </help>
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61 </tool>
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