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

リビジョン 2, 3.1 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central

行番号 
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
32The 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
41Let 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
50And 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
67Running 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>
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