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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="phytab_ssr" name="phytab Similar Sequence Remover">
2 <description>Removes redundant sequences</description>
3 <requirements>
4 <requirement type="package">java</requirement>
5 </requirements>
6 <command interpreter="python">phytab_ssr.py -i $in -s $percentage -a $h</command>
7
8 <inputs>
9 <param name="in" type="data" format="fasta,tabular,text" label="Input Sequences" help="Single/multi-gene PHYTAB or single-gene FASTA accepted." />
10 <param name="percentage" type="float" value="0.99" label="Percentage similarity to be considered redundant."/>
11 <param name="h" type="boolean" truevalue="t" falsevalue="f" label="Align first 100 characters instead of entire sequence" />
12 </inputs>
13
14 <outputs>
15 <data from_work_dir="data/results.data" format="input" name="nonredundant seqs" label="${tool.name} on ${on_string}: Nonredundant Sequences"/>
16 </outputs>
17
18 <help>
19 **What it does**
20
21 phytab Similar Sequence Remover will take a set of sequences in either FASTA or phytab format and remove redundant sequences based on the minimum similarity percentage specified.
22
23 ------
24
25 **Inputs**
26
27 FASTA, phytab
28
29 ------
30
31 **Outputs**
32
33 FASTA, phytab
34
35 -------
36
37 **Additional Information**
38
39 Introduction to phytab format: http://osiris-phylogenetics.blogspot.com/2012/09/introduction-to-phytab-format.html
40
41 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
42
43 -------
44
45 **Citations**
46
47 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.
48
49 Current Osiris Citation is here
50
51 http://osiris-phylogenetics.blogspot.com/2012/10/citation.html
52 </help>
53 </tool>