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

<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>