<tool id="phytab_LB_pruner" name="phytab LB pruner">
  <description>LB_pruner: Identify genes on very long branches.</description>
  <requirements>
    <requirement type="package">LB_prunerG.pl</requirement>
  </requirements>
  <command interpreter="python">
    phytab_LB_pruner.py -i $data -m $multiplier
  </command>
  <inputs>
    <param format="txt" name="data" type="data" label="Sequence data" help="This should be sequence data in phytab or fasta"/>
    <param name="multiplier" type="float" value="4" label="Multiplier" help="Value of Multiplier, M. Brances longer than M times average are written to file" >
    </param>
  </inputs>
  <outputs>
    <data format="tabular" name="LB pruner results" label="${tool.name} on ${on_string}: results" from_work_dir="data/results.data" />
  </outputs>
  <tests>
  </tests>
  <help>
Input a table as follows:::
    name	newick_tree;
    name2	newick_tree;
    name3	newick_tree;
Enter a value for M, the multiplier. LB pruner will find the average of all branch 
lengths in each newick tree.  If any branch is longer than Mx the average, that gene will 
be written to the output file. If an internal branch is longer than M times the average, 
then all members of that clade are written to the out file, with 999 as the length of 
each branch.  Third column is branch length, fourth column is average BL for tree.
  </help>
</tool>