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