<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 
	  $species
      "$tree_definition" 
      $thresholds
      $separation 
      $simthresh
	
  </command>
  <inputs>
    <page>
        <param format="maf" name="alignment" type="data" label="Select MAF alignments that have NOT been masked for nucleotide quality"/>
        
        <param format="txt" name="orthfile" type="data" label="Select raw microsatellite data"/>

     <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="alignment" key="species" />
      </options>
    </param>

   	<param name="tree_definition" 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" 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" 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" 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="regVariation/microsatellite/Galaxy17_unmasked_short.maf.gz"/>
      <param name="orthfile" value="regVariation/microsatellite/Galaxy17_short_raw.txt"/>
      <param name="thresholds" value="9,10,12,12"/>
      <param name="species" value="hg18,panTro2,ponAbe2,rheMac2,calJac1"/>
      <param name="tree_definition" value="((((hg18, panTro2), ponAbe2), rheMac2), calJac1)"/>
      <param name="separation" value="10"/>
      <param name="simthresh" value="85"/>
      <output name="outfile" file="regVariation/microsatellite/Galaxy17_unmasked_results.txt"/>
    </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.

-----

.. class:: warningmark

**Note**

A tab-separated output table (depending on the species being considered) is generated where each row contains all information for a microsatellite locus from multiple species. 
The table typically reads like this:

hg18.chr22	16153057	16153074	A		1	ins=,imot:0:tt;dels=	,9:t>c	-panTro2	hg18:tttttttttttttttttt,ponAbe2:--tttttttttttttttt,panTro2:-----ttttctttttttt

hg18.chr22	16131711	16131722	ATGC	4	NA						,2:C>T	+ponAbe2	hg18:CACGCATGCATG,ponAbe2:CATGCATGCATG,panTro2:CACGCATGCATG,rheMac2:CACGCGTGCATG

Where columns list the following:

1: Chromosome/scaffold/contig  of one of the species. The species chosen is the first species readable in the Newick tree submitted by the user.

2: Start coordinate

3: End coordinate

4: Motif of microsatellite

5: Motif size

6: Insertion and deletion details. Insertions are separated from deletions by a ";", and individual insertions and deletions are separated from others by a comma. For the purpose of illustration, consider the first row listed above:
"imot:0:tt", where imot/imotf again suggest insertion, the number indicates position of insertion within the microsatellite's alignment, and this is followed by identity of nucleotides that are inserted.

7: Substitution details. Individual substitutions are separated by commas. Each entry contains the position of substitution event in the microsatellites' alignment, and the nature of substitution.

8: Inference of birth/death event. Births are indicated by "+", and deaths by "-". Events such as "-hg18:panTro2" suggest death in the common ancestor of hg18 and panTro2, whereas events such as "-hg18.panTro2" indicate parallel, independent death events along the two lineages. Alternative interpretations of the event may also be listed, following a "/", such as:
"+hg18.+panTro2 / +hg18:panTro2"

9: Actual sequences in the alignment, separated by commas.

</help>  


</tool>