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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="gb_gene_summary" name="GB_gene_summary" version="1.0.0">
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2 <description>Summarizes gene names in a GenBank flatfile</description>
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3 <command interpreter="perl">
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4 genbankstrip.pl "-f"$data_file "-l"$length "-ts"$species $sp > $logfile
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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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8 <param name="length" type="integer" value="75" label="Minimum gene length" help="Does not retain short genes." />
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9 <param name="species" type="integer" value="5" label="Minimum" help="Only shows genes present in >x species." />
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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="txt" name="logfile" label="Screen output from ${tool.name} with ${on_string}" />
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14 <data format="tabular" name="stripfile" label="Summary ${tool.name} with ${on_string}" from_work_dir="striplist.txt"/>
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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 Summarizes gene names in a genbank flatfile.
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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 A genbank flatfile.
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26
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27 ------
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28
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29 **Outputs**
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30
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31 A summary of gene names, and how many species are have data available for each gene.
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32
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33 -------
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34
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35 **Additional Information**
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36
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37 The gene names can be used to pull genes using genbankstrip.
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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38 Often, the same gene will have many names in genbank. These names can be synonymized by altering the genbankstrip.pl script.
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39
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40 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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41
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42 -------
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43
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44 **Citations**
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45
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46 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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47
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48 Current Osiris Citation is here
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49
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50 http://osiris-phylogenetics.blogspot.com/2012/10/citation.html
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51
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52 </help>
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53 </tool>
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