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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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-1:000000000000 0:5b9a38ec4a39
1 <tool id="change_sp" name="change_sp" version="1.0">
2 <description>Change code name to full species name in fasta or phytab</description>
3 <command interpreter="perl">
4 change_sp.pl $infile $changefile $outfile
5 </command>
6 <inputs>
7 <param name="infile" type="data" format="tabular" label="Input File" help="PHYTAB file to alter" />
8 <param name="changefile" type="data" format="tabular" label="Conversion Table" help="Tabular format with column 1=code; column 2=Full species name" />
9 </inputs>
10 <outputs>
11 <data format="tabular" name="outfile" label="${tool.name} on ${on_string}: Out file" />
12 </outputs>
13 <help>
14 **What it does**
15
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.
17
18 ------
19
20 **Inputs**
21
22 PHYTAB with species codes
23
24 ------
25
26 **Outputs**
27
28 PHYTAB with full species names replacing codes
29 ------
30
31 **Additional Information**
32
33 Please direct questions or comments to ucsb_phylogenetics@lifesci.ucsb.edu or, if you can, enter them on the
34 osiris_phylogenetics site at bitbucket.org
35
36 ------
37
38 **Citations**
39
40 This tool is part of the Osiris Phylogenetics Tool Package for Galaxy. If you make extensive use
41 of this tool in a publication, please consider citing the following.
42
43 Current Osiris Citation is here
44
45 http://osiris-phylogenetics.blogspot.com/2012/10/citation.html
46 </help>
47 </tool>