<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>