<tool id="subRate1" name="Estimate substitution rates " version="1.0.0">
  <description> for non-coding regions</description>
  <command interpreter="python">
  	substitution_rates.py 
  	$input 
  	$out_file1
  	#if $region.type == "win":
      ${region.input2} ${region.input2.dbkey} ${region.input2.metadata.chromCol},$region.input2.metadata.startCol,$region.input2.metadata.endCol,$region.input2.metadata.strandCol
    #else:
      "None"
    #end if 
  </command>
  <inputs>
    <param format="maf" name="input" type="data" label="Select pair-wise alignment data"/>
    <conditional name="region">
	      <param name="type" type="select" label="Estimate rates corresponding to" multiple="false">
	         <option value="align">Alignment block</option>
	         <option value="win">Intervals in your history</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>
  </inputs>
  <outputs>
    <data format="tabular" name="out_file1" metadata_source="input"/>
  </outputs>
  
  <tests>
    <test>
      <param name="input" value="Interval2Maf_pairwise_out.maf"/>
      <param name="type" value="align"/>
      <output name="out_file1" file="subRates1.out"/>
    </test>
  </tests>
  
 <help> 

.. class:: infomark

**What it does**

This tool takes a pairwise MAF file as input and estimates substitution rate according to Jukes-Cantor JC69 model. The 3 new columns appended to the output are explained below:

- L: number of nucleotides compared
- N: number of different nucleotides
- p = N/L

-----

.. class:: warningmark

**Note**

Any block/s not containing exactly two sequences, will be omitted. 

  </help>  
</tool>