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<tool id="trf" name="Tandem Repeats Finder" version="4.04">
  <description>Detect tandem repeats that have undergone extensive mutational change</description>
  <command interpreter="python">trf_wrapper.py
      $input1 $match $mismatch $delta $mprobability $iprobability $minscore
      $maxperiod $masked $flanking $noredundancy -o $outputdat -k $outputmask -t
      $report -i $indices
  </command>
  <inputs>
    <param format="fasta" name="input1" type="data">
      <label>Sequence</label>
    </param>
    <param name="match" size="4" type="text" value="2">
      <label>Match</label>
    </param>
    <param name="mismatch" size="4" type="text" value="7">
      <label>Mismatch</label>
    </param>
    <param name="delta" size="4" type="text" value="7">
      <label>Indels</label>
    </param>
    <param name="mprobability" size="4" type="integer" value="80" label="Matching probability, %">
        <validator type="in_range" message="(10-100)" min="10" max="100"/>
    </param>
    <param name="iprobability" size="4" type="integer" value="10" label="Indel probability, %">
        <validator type="in_range" message="(10-100)" min="10" max="100"/>
    </param>
    <param name="minscore" size="3" type="integer" value="50">
        <label>Minimum alignment score for repeat reporting</label>
        <validator type="in_range" message="(30-150)" min="30" max="150"/>
    </param>
    <param name="maxperiod" size="4" type="integer" value="500">
        <label>Maximum period size for repeat reporting</label>
        <validator type="in_range" message="(1-2000)" min="1" max="2000"/>
    </param>
    <param name="flanking" type="boolean" checked="no" truevalue="-f" falsevalue="" display="checkboxes">
        <label>Flanking sequence</label>
    </param>
    <param name="masked" type="boolean" checked="no" truevalue="-m" falsevalue="" display="checkboxes">
        <label>Masked Sequence File</label>
    </param>
    <param name="noredundancy" type="boolean" checked="no" truevalue="-r" falsevalue="" display="checkboxes">
        <label>No redundancy elimination</label>
    </param>
  </inputs>
  <outputs>
    <data format="html" name="report" label="${tool.name} on ${on_string}: Report"/>
    <data format="html" name="indices" label="${tool.name} on ${on_string}: Indices"/>
    <data format="tabular" name="outputdat" label="${tool.name} on ${on_string}: Data"/>
    <data format="txt" name="outputmask" label="${tool.name} on ${on_string}: Masked Sequence">
        <filter>masked is True</filter>
    </data>
  </outputs>
  <tests>
      <test>
          <param name="input1" value="trf_input.fasta"/>
          <param name="match" value="2"/>
          <param name="mismatch" value="7"/>
          <param name="delta" value="7"/>
          <param name="mprobability" value="80"/>
          <param name="iprobability" value="10"/>
          <param name="minscore" value="50"/>
          <param name="maxperiod" value="500"/>
          <param name="masked" value="-m"/>
          <param name="flanking" value=""/>
          <param name="noredundancy" value=""/>
          <output name="outputdat" file="trf_out.dat"/>
          <output name="outputmask" file="trf_out.mask"/>
      </test>
  </tests>
  <help>
.. class:: warningmark

The input dataset needs to be in FASTA format.

-----

    Tandem Repeats Finder, Version 4.04

    Copyright (C) Dr. Gary Benson 1999-2004. All rights reserved.


    Please cite:

G. Benson, "Tandem repeats finder: a program to analyze DNA sequences" Nucleic Acids Research (1999) Vol. 27, No. 2, pp. 573-580.


A tandem repeat in DNA is two or more adjacent, approximate copies of a pattern
of nucleotides. Tandem Repeats Finder is a program to locate and display tandem
repeats in DNA sequences. In order to use the program, the user submits a
sequence in FASTA format. There is no need to specify the pattern, the size of
the pattern or any other parameter. The output consists of two files: a repeat
table file and an alignment file. The repeat table contains information about
each repeat, including its location, size, number of copies and nucleotide
content. Clicking on the location indices for one of the table entries opens a
second web browser that shows an alignment of the copies against a consensus
pattern. The program is very fast, analyzing sequences on the order of .5Mb in
just a few seconds. Submitted sequences may be of arbitrary length. Repeats
with pattern size in the range from 1 to 2000 bases are detected.
  </help>
</tool>
<!--
Please use: trf File Match Mismatch Delta PM PI Minscore MaxPeriod [options]
Where: (all weights, penalties, and scores are positive)
  File = sequences input file
  Match  = matching weight
  Mismatch  = mismatching penalty
  Delta = indel penalty
  PM = match probability (whole number)
  PI = indel probability (whole number)
  Minscore = minimum alignment score to report
  MaxPeriod = maximum period size to report
  [options] = one or more of the following :
               -m    masked sequence file
               -f    flanking sequence
               -d    data file
               -h    suppress html output
               -r    no redundancy elimination
Note the sequence file should be in FASTA format:
-->