<tool id="microsatellite_birthdeath" name="Identify microsatellite births and deaths" version="1.0.0">
  <description> and causal mutational mechanisms from previously identified orthologous microsatellite sets</description>
  <command interpreter="perl">
      microsatellite_birthdeath.pl 
      $alignment 
      $orthfile 
      $outfile 
      ${alignment.metadata.species} 
      "$tree_definition" 
      $thresholds
      $separation 
      $simthresh
	
  </command>
  <inputs>
    <page>
        <param format="maf" name="alignment" type="data" label="Select MAF alignments"/>
        
        <param format="txt" name="orthfile" type="data" label="Select raw microsatellite data"/>

    	<param name="tree_definition" size="200" type="text" value= "((((hg18,panTro2),ponAbe2),rheMac2),calJac1)" label="Tree definition of all species above whether or not selected for microsatellite extraction" 
    	help="For example: ((((hg18,panTro2),ponAbe2),rheMac2),calJac1)"/>
      	
      	<param name="separation" size="10" type="integer" value="40" label="Total length of flanking DNA used for sequence-similarity comparisons among species"
    	help="A value of 40 means: 20 bp upstream and 20 bp downstream DNA will be used for similarity comparisons."/>
 
     	<param name="thresholds" size="15" type="text" value="9,10,12,12" label="Minimum Threshold for the number of repeats for microsatellites"
    	help="A value of 9,10,12,12 means: All monos having fewer than 9 repeats, dis having fewer than 5 repeats, tris having fewer than 4 repeats, tetras having fewer than 3 repeats will be excluded from the output."/>

     	<param name="simthresh" size="10" type="integer" value="80" label="Percent sequence similarity of flanking regions (of length same as  the above separation distance"
    	help="Enter a value from 0 to 100"/>


     </page>
  </inputs>
  <outputs>
    <data format="txt" name="outfile" metadata_source="orthfile"/>
  </outputs>
  <tests>
    <test>
      <param name="alignment" value="chr22_5sp.maf"/>
      <param name="orthfile" value="chr22_5sp.microraw.tabular"/>
      <param name="thresholds" value="9,10,12,12"/>
      <param name="tree_definition" value="((((hg18, panTro2), ponAbe2), rheMac2), calJac1)"/>
      <param name="separation" value="40"/>
      <param name="simthresh" value="80"/>
      <output name="outfile" file="chr22_5sp.microtab.tabular"/>
    </test>
  </tests>


 <help> 

.. class:: infomark

**What it does**

This tool uses raw orthologous microsatellite clusters (identified by the tool "Extract orthologous microsatellites") to identify microsatellite births and deaths along individual lineages of a phylogenetic tree.

</help>  


</tool>