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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="change_sp" name="change_sp" version="1.0">
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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2 <description>Change code name to full species name in fasta or phytab</description>
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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3 <command interpreter="perl">
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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4 change_sp.pl $infile $changefile $outfile
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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5 </command>
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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6 <inputs>
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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7 <param name="infile" type="data" format="tabular" label="Input File" help="PHYTAB file to alter" />
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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8 <param name="changefile" type="data" format="tabular" label="Conversion Table" help="Tabular format with column 1=code; column 2=Full species name" />
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9 </inputs>
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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10 <outputs>
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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11 <data format="tabular" name="outfile" label="${tool.name} on ${on_string}: Out file" />
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12 </outputs>
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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13 <help>
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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14 **What it does**
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15
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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16 Many times a dataset will have code names instead of full species names. This will search for a code name and replace with a species name based on a table of input values.
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17
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18 ------
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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19
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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20 **Inputs**
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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21
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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22 PHYTAB with species codes
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23
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24 ------
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25
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26 **Outputs**
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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27
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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28 PHYTAB with full species names replacing codes
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29 ------
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30
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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31 **Additional Information**
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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32
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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33 Please direct questions or comments to ucsb_phylogenetics@lifesci.ucsb.edu or, if you can, enter them on the
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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34 osiris_phylogenetics site at bitbucket.org
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35
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36 ------
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37
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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38 **Citations**
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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39
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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40 This tool is part of the Osiris Phylogenetics Tool Package for Galaxy. If you make extensive use
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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41 of this tool in a publication, please consider citing the following.
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42
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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43 Current Osiris Citation is here
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44
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45 http://osiris-phylogenetics.blogspot.com/2012/10/citation.html
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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46 </help>
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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47 </tool>