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author izsam
date Thu, 19 Mar 2015 11:46:50 -0400
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1 <tool id="phylogeny_converter" name="phylogeny_converter">
2 <description></description>
3 <command interpreter="python">
4 converter.py $input $output $filetype.inouttype $filetype.type
5 </command>
6 <inputs>
7 <conditional name="filetype">
8 <param name="type" type="select" label="is this a multi-sequence file?">
9 <option value="multi">Multi sequence</option>
10 <option value="single">Single sequence</option>
11 </param>
12 <when value="single">
13 <param name="input" type="data" label="Original sigle sequence file"/>
14 <param name="inouttype" type="select" label="conversion">
15 <option value="f-g">Fasta to GenBank</option>
16 <option value="g-f">GenBank to Fasta</option>
17 </param>
18 </when>
19 <when value="multi">
20 <param name="input" type="data" label="Original multi sequence file" help="Please note that Phylip and nexus limit sequence names to a maximum of 10 characters"/>
21 <param name="inouttype" type="select" label="conversion">
22 <option value="f-g">Fasta to GenBank</option>
23 <option value="g-f">GenBank to Fasta</option>
24 <option value="f-p">Fasta to Phylip</option>
25 <option value="f-n">Fasta to Nexus</option>
26 <option value="p-f">Phylip to Fasta</option>
27 <option value="p-n">Phylip to Nexus</option>
28 <option value="n-p">Nexus to Phylip</option>
29 <option value="n-f">Nexus to Fasta</option>
30 </param>
31 </when>
32 </conditional>
33 </inputs>
34 <outputs>
35 <data name="output" format="tabular"/>
36 </outputs>
37 <help>
38
39 What it does
40
41 This tool converts different file formats to allow the data-exchange from different philogeny tools.
42
43 Developed by
44 Iolanda Mangone
45
46 </help>
47 </tool>