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1 <tool id="categorize_elements_satisfying_criteria" name="Categorize Elements" version="1.0.0">
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2 <description>satisfying criteria</description>
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3
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4 <command interpreter="perl">
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5 categorize_elements_satisfying_criteria.pl $inputFile1 $inputFile2 $outputFile1
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6 </command>
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7
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8 <inputs>
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9 <param format="tabular" name="inputFile1" type="data" label="Select file containing categories and their elements"/>
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10 <param format="tabular" name="inputFile2" type="data" label="Select file containing criteria and elements data"/>
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11 </inputs>
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12
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13 <outputs>
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14 <data format="tabular" name="outputFile1"/>
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15 </outputs>
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16
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17 <tests>
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18 <test>
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19 <param name="inputFile1" value="categories.tabular" ftype="tabular" />
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20 <param name="inputFile2" value="criteria_elements_data.tabular" ftype="tabular" />
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21 <output name="outputFile1" file="categorized_elements.tabular" />
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22 </test>
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23 </tests>
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24
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25
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26 <help>
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27
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28 .. class:: infomark
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29
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30 **What it does**
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31
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32 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.
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33
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34 - 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.
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35 - 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.
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36 - 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.
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37
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38
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39 **Example**
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40
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41 Let the first input file be a group of motif categories as follows::
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42
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43 Deletion_Hotspots deletionHoptspot1 deletionHoptspot2 deletionHoptspot3
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44 Dna_Pol_Pause_Frameshift dnaPolPauseFrameshift1 dnaPolPauseFrameshift2 dnaPolPauseFrameshift3 dnaPolPauseFrameshift4
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45 Indel_Hotspots indelHotspot1
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46 Insertion_Hotspots insertionHotspot1 insertionHotspot2
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47 Topoisomerase_Cleavage_Sites topoisomeraseCleavageSite1 topoisomeraseCleavageSite2 topoisomeraseCleavageSite3
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48
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49
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50 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::
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51
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52 10bp 20bp 40bp
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53 deletionHoptspot1 1 1 2
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54 deletionHoptspot2 1 1 1
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55 deletionHoptspot3 0 0 0
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56 dnaPolPauseFrameshift1 1 1 1
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57 dnaPolPauseFrameshift2 0 2 1
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58 dnaPolPauseFrameshift3 0 0 0
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59 dnaPolPauseFrameshift4 0 1 2
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60 indelHotspot1 0 0 0
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61 insertionHotspot1 0 0 1
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62 insertionHotspot2 1 1 1
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63 topoisomeraseCleavageSite1 1 1 1
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64 topoisomeraseCleavageSite2 1 2 1
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65 topoisomeraseCleavageSite3 0 0 2
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66
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67 Running the program will give the total number of times the motifs of each category occur in every window size of indel flanking regions::
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68
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69 10bp 20bp 40bp
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70 Deletion_Hotspots 2 2 3
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71 Dna_Pol_Pause_Frameshift 1 4 4
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72 Indel_Hotspots 0 0 0
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73 Insertion_Hotspots 1 1 2
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74 Topoisomerase_Cleavage_Sites 2 3 4
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75
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76 </help>
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77
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78 </tool>
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