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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 <tool id="fasta2phytab" name="FASTA2PHYTAB" version="1.1">
2 <description>Converts FASTA file with sequences from same gene family to PHYTAB format</description>
3 <command interpreter="perl">
4 #if $sp_opts.sp_opts_selector=="fasta"
5 fasta2phytab.pl $infile 'from fasta' $partition $convert > $outfile
6 #else
7 fasta2phytab.pl $infile $sp_opts.species $partition $convert > $outfile
8 #end if
9 </command>
10 <inputs>
11 <param name="infile" type="data" format="fasta" label="Input File" help="fasta file to convert" />
12 <conditional name="sp_opts">
13 <param name="sp_opts_selector" type="select" label="Species Name Source">
14 <option value="fasta" selected="True">Take from fasta header</option>
15 <option value="user">user input</option>
16 </param>
17 <when value="fasta">
18 <param name="species" type="hidden" value="from fasta" label="Species" help="" />
19 </when>
20 <when value="user">
21 <param name="species" type="text" format="tabular" label="Input name of species" help="" />
22 </when>
23 </conditional>
24 <param name="partition" type="text" format="tabular" label="Name of partition" help="" />
25 <param name="convert" type='boolean' checked='false' truevalue='yes' falsevalue='no' label='Replace pipes with underscores' />
26 </inputs>
27 <outputs>
28 <data format="tabular" name="outfile" label="${tool.name} on ${on_string}: Out file" />
29 </outputs>
30 <help>
31 **What it does**
32
33 FASTA2PHYTAB takes an input FASTA file with sequences from the same gene family, and adds species name - either from the fasta header or from a single text entry - and
34 partition (gene family) name that will apply for all sequences. The output is a PHYTAB tabular format file.
35
36 ------
37
38 **Inputs**
39
40 A FASTA file with all sequences from the same gene family.
41
42 ------
43
44 **Outputs**
45
46 PHYTAB file format: http://osiris-phylogenetics.blogspot.com/2012/09/introduction-to-phytab-format.html
47
48 -------
49
50 **Additional Information**
51
52 Please direct questions or comments to ucsb_phylogenetics@lifesci.ucsb.edu or, if you can, enter them on the
53 osiris_phylogenetics site at bitbucket.org
54
55 ------
56
57 **Citations**
58
59 This tool is part of the Osiris Phylogenetics Tool Package for Galaxy. If you make extensive use of this tool in a
60 publication, please consider citing the following.
61
62 Current Osiris Citation is here
63
64 http://osiris-phylogenetics.blogspot.com/2012/10/citation.html
65 </help>
66 </tool>