<tool id="phytab_aliscorecut" name="phytab AliccoreCut" version="1.0">
  <description>Runs Aliscore then Alicut on an aligned sequence in phytab format.</description>
  <requirements>
    <requirement type="package">aliscore and alicut</requirement>
  </requirements>
  <command interpreter="python">
    aliscorecut.py -i $sequence > $aliscorecut_stdout 2>&amp;1
  </command>
  <inputs>
    <param format="txt" name="sequence" type="data" label="Aligned sequence" help="This should be an aligned sqeuence from UCSB Muscle."/>
  </inputs>
  <outputs>
    <data format="txt" name="aliscorecut_stdout" label="${tool.name} on ${on_string}: stdout" />
    <data format="tabular" name="aliscorecut_results" label="${tool.name} on ${on_string}: results" from_work_dir="data/results.data" />
  </outputs>
  <tests>
  </tests>
  <help>
**What it does**

Aliscore identifies ambiguously aligned regions of a multiple sequence alignment. Alicut deletes sites marked by aliscore. This tool combines both into one tool.

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**Inputs**

Aligned sequences in phytab format

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**Outputs**

phytab format

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**Additional information**

For information on phytab format see: http://osiris-phylogenetics.blogspot.com/2012/09/introduction-to-phytab-format.html

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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**Citations**

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.

Current Osiris Citation is here

http://osiris-phylogenetics.blogspot.com/2012/10/citation.html

Additional Citations for this tool

Aliscore: Kuck P, Meusemann K, Dambach J, Thormann B, von Reumont BM, et al. (2010) Parametric and non-parametric masking of randomness in sequence alignments can be improved and leads to better 
resolved trees. Front Zool 7: 10.
  </help>
</tool>