<tool id="DNAPropertyCalculator" name="Calculate sequence-specific DNA properties" version="2.0.0">
  <description>for a genome</description>
  <command interpreter="sh">galaxyToolRunner.sh dna.DNAPropertyCalculator -i 
    #if $refGenomeSource.genomeSource == "history":
      $refGenomeSource.ownFile
    #else
      ${refGenomeSource.index.fields.path}
    #end if
	$N -p $property -o $output
  </command>
  <inputs>
    <conditional name="refGenomeSource">
      <param name="genomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options">
        <option value="indexed">Use a built-in index</option>
        <option value="history">Use one from the history</option>
      </param>
      <when value="indexed">
        <param name="index" type="select" label="Select a reference genome" help="if your genome of interest is not listed - contact Galaxy team">
          <options from_data_table="sam_fa_indexes">
            <filter type="sort_by" column="1" />
            <validator type="no_options" message="No indexes are available" />
          </options>
        </param>
      </when>
      <when value="history">
        <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select the reference genome" />
      </when>  <!-- history -->
    </conditional>  <!-- refGenomeSource -->

    <param name="property" type="select" label="Property to calculate">
      <option value="ATG-density">ATG</option>
      <option value="G-content">G</option>
      <option value="C-content">C</option>
      <option value="T-content">T</option>
      <option value="A-content">A</option>
      <option value="GC-content">GC</option>
      <option value="AT-content">AT</option>
      <option value="Pyrimidine-content">Pyrimidine</option>
      <option value="Purine-content">Purine</option>
      <option value="Bendability">Bendability</option>
      <option value="zDNA">zDNA</option>
      <option value="DuplexStabilityFreeEnergy">Duplex Stability Free Energy</option>
      <option value="DuplexStabilityDisruptEnergy">Duplex Stability Disrupt Energy</option>
      <option value="DNADenaturation">DNA Denaturation</option>
      <option value="PropellorTwist">Propellor Twist</option>
      <option value="BaseStacking">Base Stacking</option>
      <option value="ProteinDeformation">Protein Deformation</option>
      <option value="BendingStiffness">Bending Stiffness</option>
      <option value="ProteinDNATwist">Protein DNA Twist</option>
      <option value="bDNATwist">bDNA Twist</option>
      <option value="APhilicity">APhilicity</option>
      <option value="NucleosomePosition">Nucleosome Position (trinucleotide model)</option>
      <option value="Twist">Twist</option>
      <option value="Tilt">Tilt</option>
      <option value="Roll">Roll</option>
      <option value="Slide">Slide</option>
      <option value="Rise">Rise</option>
    </param>
    
    <param name="N" type="boolean" checked="true" truevalue="-n" falsevalue="" label="Output normalized values" />
  </inputs>
  <outputs>
      <data format="wig" name="output" label="Calculate ${property.value_label}">
        <actions>
          <conditional name="refGenomeSource.genomeSource">
            <when value="indexed">
              <action type="metadata" name="dbkey">
                <option type="from_data_table" name="sam_fa_indexes" column="1" offset="0">
                  <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
                  <filter type="param_value" ref="refGenomeSource.index" column="0"/>
                </option>
              </action>
            </when>
            <when value="history">
              <action type="metadata" name="dbkey">
                <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" />
              </action>
            </when>
          </conditional>
        </actions>
      </data>
  </outputs>
  
  <tests>
    <test>
      <param name="genomeSource" value="history"/>
      <param name="ownFile" value="test.fasta"/>
      <param name="property" value="Twist"/>
      <param name="N" value="false"/>
      <output name="output" file="twist.wig"/>
  	</test>
  	<test>
      <param name="genomeSource" value="history"/>
      <param name="ownFile" value="test.fasta"/>
      <param name="property" value="Twist"/>
      <param name="N" value="true"/>
      <output name="output" file="twist.normalized.wig"/>
  	</test>
  </tests>
  
  <help>

This tool will create a new Wig file with genome-wide calculations of sequence-specific DNA properties determined from local n-nucleotide sequences. DNA properties are calculated using AJT_.

.. _AJT: http://www.abeel.be/ajt

-----

**Example**

To calculate GC-content, choose your genome assembly and select "GC" as the property. This will create a new Wig file in which G and C nucleotides are represented by 1, while A and T nucleotides are represented by -1. If you would like to compute GC-content in 10-bp windows, use the WigMath -> Moving average tool to compute a moving average with 10bp windows.

  </help>
</tool>