<tool id="combineproballelecom" name="Combine read profile probabilities " version="2.0.0">
  <description>from the same allele combination</description>
  <command interpreter="python2.7">combinedprobforallelecombination.py  $input > $output </command>

  <inputs>
    <param name="input" type="data" label="Select microsatellite length profile" />
 
  </inputs>
  <outputs>
    <data name="output" format="tabular" />
  </outputs>
  <tests>
    <!-- Test data with valid values -->
    <test>
      <param name="input" value="probvalueforhetero_out.txt"/>
      <output name="output" file="combineprob_out.txt"/>
    </test>
    
  </tests>
  <help>


.. class:: infomark

**What it does**

- This tool will combine the read profile probabilities for each allele combination in the input and calculates the probability to detect heterozygote for each allele combination and each depth.

**Citation**

When you use this tool, please cite **Fungtammasan A, Ananda G, Hile SE, Su MS, Sun C, Harris R, Medvedev P, Eckert K, Makova KD. 2015. Accurate Typing of Short Tandem Repeats from Genome-wide Sequencing Data and its Applications, Genome Research**
 
**Input**

The input format is the same as output from **Evaluate the probability of the allele combination to generate read profile** tool.

- Column 1 = location of STR locus. 
- Column 2 = length profile (length of STR in each read that mapped to this location in comma separated format). 
- Column 3 = motif of STR in this locus. The input file can contain more than three columns. 
- Column 4 = homozygote/heterozygote label.
- Column 5 = log based 10 of (the probability of homozygote/the probability of heterozygote)
- Column 6 = Allele for most probable homozygote.
- Column 7 = Allele 1 for most probable heterozygote.
- Column 8 = Allele 2 for most probable heterozygote.
- Column 9 = Probability of the allele combination to generate given read profile.
- Column 10 = Number of possible rearrangement of given read profile.
- Column 11 = Probability of the allele combination to generate read profile with any rearrangement (Product of column 9 and column 10)
- Column 12 = Read depth

Only columns 2,3,4,7,8,11 were used in calculation. 

**Output**


The output will contain the following header and columns
 
- Line 1 header: read_depth	allele	heterozygous_prob	motif
- Column 1 = read depth
- Column 2 = allele combination
- Column 3 = probability to detect heterozygote of that allele combination
- Column 4 = motif




</help>
</tool>