<tool id="multispecies_orthologous_microsats" name="Extract orthologous microsatellites" version="1.0.1">
  <description> for multiple (>2) species alignments</description>
  <command interpreter="perl">
    multispecies_MicrosatDataGenerator_interrupted_GALAXY.pl   	
    $input1 
  	$out_file1 
  	$thresholds 
  	$species 
  	"$treedefinition"
  	$separation 
	
  </command>
  <inputs>
    <page>
        <param format="maf" name="input1" type="data" label="Select MAF alignments"/>
       	<param name="separation" size="10" type="integer" value="10" label="Minimum base pair distance between adjacent microsatellite blocks"
    	help="A value of 10 means: Adjacent microsatellites separated by less than 10 base pairs will be excluded from the output."/>
    	<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="species" type="select" label="Select species" display="checkboxes" multiple="true" help="NOTE: Currently users are requested to select one of these three combinations: hg18-panTro2-ponAbe2, hg18-panTro2-ponAbe2-rheMac2 or hg18-panTro2-ponAbe2-rheMac2-calJac1">
      	<options>
        	<filter type="data_meta" ref="input1" key="species" />
      	</options>
    	</param>
    	<param name="treedefinition" 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)"/>
    </page>
  </inputs>
  <outputs>
    <data format="txt" name="out_file1" metadata_source="input1"/>
  </outputs>
  <requirements>
     <requirement type="binary">sputnik</requirement>
  </requirements>
  <tests>
    <test>
      <param name="input1" value="chr22_5sp.maf"/>
      <param name="thresholds" value="9,10,12,12"/>
      <param name="species" value="hg18,panTro2,ponAbe2,rheMac2,calJac1"/>
      <param name="treedefinition" value="((((hg18, panTro2), ponAbe2), rheMac2), calJac1)"/>
      <param name="separation" value="10"/>
      <output name="out_file1" file="chr22_5sp.microraw.tabular"/>
    </test>
  </tests>

 <help> 

.. class:: infomark

**What it does**

This tool finds ortholgous microsatellite blocks between aligned species
  
</help>  


</tool>