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