Mercurial > repos > devteam > categorize_elements_satisfying_criteria
comparison categorize_elements_satisfying_criteria.xml @ 0:586c1f0e1515 draft default tip
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author | devteam |
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date | Wed, 25 Sep 2013 10:03:03 -0400 |
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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> |