root/galaxy-central/tools/regVariation/delete_overlapping_indels.xml

<tool id="delete_overlapping_indels" name="Delete Overlapping Indels" version="1.0.0">
  <description>from a chromosome indels file</description>
  
  <command interpreter="perl">
        delete_overlapping_indels.pl $inputFile1 $inputIndelStartColumnNumber2 $inputIndelEndColumnNumber3 $outputFile1
  </command>

  <inputs>
        <param format="tabular" name="inputFile1" type="data" label="Select indels file"/>
        <param type="data_column" name="inputIndelStartColumnNumber2" data_ref="inputFile1" accept_default="true" label="Choose the indel start coordinate column number" />
    <param type="data_column" name="inputIndelEndColumnNumber3" data_ref="inputFile1" accept_default="true" label="Choose the the indel end coordinate column number" />
  </inputs>
  
  <outputs>
    <data format="tabular" name="outputFile1"/>
  </outputs>
  
  <tests>
        <test>
                <param name="inputFile1" value="indels1.tabular" />
        <param name="inputIndelStartColumnNumber2" value="5" />
        <param name="inputIndelEndColumnNumber3" value="6" />
        <output name="outputFile1" file="non_overlapping_indels1.tabular" />     
        </test>
  </tests>
  
  <help> 

.. class:: infomark

**What it does**

This program detects overlapping indels in a chromosome and keeps all non-overlapping indels. As for overlapping indels, the first encountered one is kept and all others are removed. 
It requires three inputs: 

- The first input is a TABULAR format file containing coordinates of indels in blocks extracted from multi-alignment.
- The second input is an integer number representing the number of the column where indel start coordinates are stored in the input file.
- The third input is an integer number representing the number of the column where indel end coordinates are stored in the input file.
- The output is a TABULAR format file containing all non-overlapping indels in the input file, and the first encountered indel of overlapping ones.

Note: The number of the first column is 1.


**Example**

Let us have the following insertions in the human genome. The start and end coordinates of insertions are on columns 5 and 6 respectively::

        3       hg18.chr22_insert       3       hg18.chr22      14508610        14508612        3924    -       panTro2.chr2b   132518950       132518951       3910    +       rheMac2.chr17   14311798        14311799        3896    +
        7       hg18.chr22_insert       13      hg18.chr22      14513678        14513690        348     -       panTro2.chr2b   132517876       132517877       321     +       rheMac2.chr17   14274462        14274463        337     +
        7       hg18.chr22_insert       6       hg18.chr22      14513688        14513699        348     -       panTro2.chr2b   132517879       132517880       321     +       rheMac2.chr17   14274465        14274466        337     +
        25      hg18.chr22_insert       9       hg18.chr22      14529501        14529509        385     -       panTro2.chr22   14528775        14528776        376     -       rheMac2.chr9    42869449        42869450        375     -
        36      hg18.chr22_insert       4       hg18.chr22      14566316        14566319        540     -       panTro2.chr2b   132492077       132492078       533     +       rheMac2.chr10   59230438        59230439        533     -
        40      hg18.chr22_insert       7       hg18.chr22      14508610        14508616        2337    -       panTro2.chr2b   132487750       132487751       2313    +       rheMac2.chr10   59128305        59128306        2332    +
        41      hg18.chr22_insert       4       hg18.chr22      14571556        14571559        2483    -       panTro2.chr2b   132485878       132485879       2481    +       rheMac2.chr10   59126094        59126095        2508    +

By removing the overlapping indels which, we get::

        3       hg18.chr22_insert       3       hg18.chr22      14508610        14508612        3924    -       panTro2.chr2b   132518950       132518951       3910    +       rheMac2.chr17   14311798        14311799        3896    +
        7       hg18.chr22_insert       13      hg18.chr22      14513678        14513690        348     -       panTro2.chr2b   132517876       132517877       321     +       rheMac2.chr17   14274462        14274463        337     +
        25      hg18.chr22_insert       9       hg18.chr22      14529501        14529509        385     -       panTro2.chr22   14528775        14528776        376     -       rheMac2.chr9    42869449        42869450        375     -
        36      hg18.chr22_insert       4       hg18.chr22      14566316        14566319        540     -       panTro2.chr2b   132492077       132492078       533     +       rheMac2.chr10   59230438        59230439        533     -
        41      hg18.chr22_insert       4       hg18.chr22      14571556        14571559        2483    -       panTro2.chr2b   132485878       132485879       2481    +       rheMac2.chr10   59126094        59126095        2508    +

  </help>  
  
</tool>