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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_clearcut" name="phytab clearcut" version="1.0.0">
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2 <description>clearcut: Generate Neighbor Joining phylogeny. Input can be aligned fasta or phytab format.</description>
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3 <requirements>
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4 <requirement type="package">clearcut</requirement>
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5 </requirements>
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6 <command interpreter="python">
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7 phytab_clearcut.py -i $data -t $datatype > $clearcut_stdout 2>&amp;1
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8 </command>
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9 <inputs>
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10 <param format="tabular" name="data" type="data" label="Sequence data" help="This should be sequence data in phytab or fasta"/>
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11 <param name="datatype" type="select" format="text">
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12 <label>Type of data for all partitions</label>
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13 <option value="P">Protein</option>
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14 <option value="D">DNA</option>
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15 </param>
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16 </inputs>
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17 <outputs>
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18 <data format="txt" name="clearcut_stdout" label="${tool.name} on ${on_string}: stdout" />
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19 <data format="tabular" name="clearcut_results" label="${tool.name} on ${on_string}: results" from_work_dir="data/results.data" />
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20 </outputs>
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21 <tests>
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22 </tests>
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23 <help>
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24 **What it does**
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25
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26 This tool uses the the program Clearcut to infer a Neighbor-Joining phylogeny using the fast RNJ algorithm for a data set using uncorrected distances (p-distances).
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28 ------
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29
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30 **Input**
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31 The program will automatically detect possible inputs of two types
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32 1. ALIGNED FASTA file for a single gene family
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33
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34 2. ALIGNED PHYTAB for multiple genes. See
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35 http://osiris-phylogenetics.blogspot.com/2012/09/introduction-to-phytab-format.html for description of phytab format.
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37 ------
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38
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39 **Output**
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40
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41 A phylogenetic tree in newick format. In the Osiris package this can be visualized with a tool like TreeVector.
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44
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45 **Additional Information**
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46
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47 http://bioinformatics.hungry.com/clearcut/
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49 ------
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51 **Citations**
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52
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53 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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54
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55 Current Osiris Citation is here
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57 http://osiris-phylogenetics.blogspot.com/2012/10/citation.html
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58
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59 Additional Citations for this tool
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60
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61 Evans, J., L. Sheneman, and J.A. Foster (2006) Relaxed Neighbor-Joining: A Fast Distance-Based Phylogenetic Tree Construction Method, J. Mol. Evol., 62, 785-792
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62
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63 </help>
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64 </tool>
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