<tool id="indelRates_3way" name="Estimate Indel Rates" version="1.0.0">
  <description> for 3-way alignments</description>
  <requirements>
    <requirement type="package" version="0.7.1">bx-python</requirement>
    <requirement type="package" version="1.0.0">galaxy-ops</requirement>
  </requirements>
  <command interpreter="python">
    getIndelRates_3way.py $input1 $out_file1 
    #if $region.type == "align"
        "None"
    #else
        $region.input2 $input2.dbkey $input2.metadata.chromCol,$input2.metadata.startCol,$input2.metadata.endCol,$input2.metadata.strandCol
    #end if
  </command>
  <inputs>
    <page>
        <param format="tabular" name="input1" type="data" label="Select dataset containing Indels"/>
        
        <conditional name="region">
          <param name="type" type="select" label="Estimate rates corresponding to" multiple="false">
            <option value="win" selected="True">Intervals in your history</option>
            <option value="align">Alignment block</option>
         </param>
         <when value="win">
            <param format="interval" name="input2" type="data" label="Choose intervals">
                <validator type="unspecified_build" />
            </param>
          </when>
          <when value="align" />
      </conditional>
     
    </page>
  </inputs>
  <outputs>
    <data format="tabular" name="out_file1" metadata_source="input1"/>
  </outputs>

  <tests>
    <test>
      <param name="input1" value="indels_3way.tabular"/>
      <param name="type" value="align"/>
      <output name="out_file1" file="indelrates_3way.tabular"/>
    </test>
  </tests>

 <help> 

.. class:: infomark

**What it does**

This tool estimates the insertion and deletion rates for alignments in a window of specified size. Rates are computed over the total adjusted lengths (adjusted by disregarding masked bases) of all the alignments blocks from the indel file that fall within that window.
  
-----

.. class:: warningmark

**Note**

This tool only works on the output of the 'Estimate Indel Rates for 3-way alignments' tool.   

</help>  


</tool>