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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_LB_pruner" name="Phytab_LB_Pruner" version="1.0">
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2 <description>LB_pruner: Identify genes on very long branches.</description>
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3 <requirements>
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4 <requirement type="package">LB_prunerG.pl</requirement>
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5 </requirements>
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6 <command interpreter="python">
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7 phytab_LB_pruner.py -i $data -m $multiplier
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8 </command>
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9 <inputs>
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10 <param format="txt" name="data" type="data" label="Sequence data" help="This should be sequence data in phytab or FASTA"/>
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11 <param name="multiplier" type="float" value="4" label="Multiplier" help="Value of Multiplier, M. Branches longer than M times average are written to
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12 file" >
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13 </param>
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14 </inputs>
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15 <outputs>
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16 <data format="tabular" name="LB pruner results" label="${tool.name} on ${on_string}: results" from_work_dir="data/results.data" />
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17 </outputs>
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18 <tests>
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19 </tests>
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20 <help>
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21 **What it does**
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22
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23 LB pruner will find the average of all branch lengths in each Newick tree. Given the user-input multiplier value (M), if any branch is longer than Mx
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24 the average branch length, that gene will be written to the tab-delimited output file. See outputs section for more information.
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25
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26 ------
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27
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28 **Inputs**
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29
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30 Sequence data file in phytab or FASTA.
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31
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32 Phytab description: http://osiris-phylogenetics.blogspot.com/2012/09/introduction-to-phytab-format.html
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33
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34 Input a table as follows:::
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35 name newick_tree;
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36 name2 newick_tree;
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37 name3 newick_tree;
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38
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39 Enter a value for M, the multiplier.
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40
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41 ------
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42
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43 **Outputs**
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44
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45 Tab delimited file listing any genes longer than Mx the average branch length for each Newick tree. If an internal branch is longer than M times the
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46 average then all members of that clade are written to the out file, with 999 as the length of each branch. The third column is branch length, fourth
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47 column is average branch length for each tree.
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48
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49 -------
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50
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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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56
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57 http://osiris-phylogenetics.blogspot.com/2012/10/citation.html
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58 </help>
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59 </tool>