<tool id="categorize_elements_satisfying_criteria" name="Categorize Elements" version="1.0.0">
  <description>satisfying criteria</description>
  
  <command interpreter="perl">
  	categorize_elements_satisfying_criteria.pl $inputFile1 $inputFile2 $outputFile1
  </command>

  <inputs>
  	<param format="tabular" name="inputFile1" type="data" label="Select file containing categories and their elements"/>
  	<param format="tabular" name="inputFile2" type="data" label="Select file containing criteria and elements data"/>
  </inputs>
  
  <outputs>
    <data format="tabular" name="outputFile1"/>
  </outputs>

  <tests>
  	<test>
  		<param name="inputFile1" value="categories.tabular" ftype="tabular" />
  		<param name="inputFile2" value="criteria_elements_data.tabular" ftype="tabular" />
    	<output name="outputFile1" file="categorized_elements.tabular" />
  	</test>
  </tests>
  
  	
  <help> 

.. class:: infomark

**What it does**

The program takes as input a set of categories, such that each category contains many elements. It also takes a table relating elements with criteria, such that each element is assigned a number representing the number of times the element satisfies a certain criterion. 

- The first input is a TABULAR format file, such that the left column represents the names of categories and, all other columns represent the names of elements in each category.
- The second input is a TABULAR format file relating elements with criteria, such that the first line represents the names of criteria and the left column represents the names of elements.
- The output is a TABULAR format file relating catergories with criteria, such that each categoy is assigned a number representing the total number of times its elements satisfies a certain criterion.. Each category is assigned as many numbers as criteria.


**Example**

Let the first input file be a group of motif categories as follows::

	Deletion_Hotspots		deletionHoptspot1		deletionHoptspot2		deletionHoptspot3	
	Dna_Pol_Pause_Frameshift	dnaPolPauseFrameshift1		dnaPolPauseFrameshift2		dnaPolPauseFrameshift3		dnaPolPauseFrameshift4
	Indel_Hotspots			indelHotspot1			
	Insertion_Hotspots		insertionHotspot1		insertionHotspot2		
	Topoisomerase_Cleavage_Sites	topoisomeraseCleavageSite1	topoisomeraseCleavageSite2	topoisomeraseCleavageSite3	


And let the second input file represent the number of times each motif occurs in a certain window size of indel flanking regions, as follows::

					10bp	20bp	40bp	
	deletionHoptspot1		1	1	2
	deletionHoptspot2		1	1	1
	deletionHoptspot3		0	0	0
	dnaPolPauseFrameshift1		1	1	1
	dnaPolPauseFrameshift2		0	2	1
	dnaPolPauseFrameshift3		0	0	0
	dnaPolPauseFrameshift4		0	1	2
	indelHotspot1			0	0	0
	insertionHotspot1		0	0	1
	insertionHotspot2		1	1	1
	topoisomeraseCleavageSite1	1	1	1
	topoisomeraseCleavageSite2	1	2	1
	topoisomeraseCleavageSite3	0	0	2

Running the program will give the total number of times the motifs of each category occur in every window size of indel flanking regions::

					10bp	20bp	40bp
	Deletion_Hotspots		2	2	3
	Dna_Pol_Pause_Frameshift	1	4	4
	Indel_Hotspots			0	0	0
	Insertion_Hotspots		1	1	2
	Topoisomerase_Cleavage_Sites	2	3	4

    </help> 
    
</tool>