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79 lines
3.1 KiB
XML
79 lines
3.1 KiB
XML
<tool id="categorize_elements_satisfying_criteria" name="Categorize Elements" version="1.0.0">
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<description>satisfying criteria</description>
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<command interpreter="perl">
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categorize_elements_satisfying_criteria.pl $inputFile1 $inputFile2 $outputFile1
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</command>
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<inputs>
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<param format="tabular" name="inputFile1" type="data" label="Select file containing categories and their elements"/>
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<param format="tabular" name="inputFile2" type="data" label="Select file containing criteria and elements data"/>
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</inputs>
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<outputs>
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<data format="tabular" name="outputFile1"/>
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</outputs>
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<tests>
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<test>
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<param name="inputFile1" value="categories.tabular" ftype="tabular" />
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<param name="inputFile2" value="criteria_elements_data.tabular" ftype="tabular" />
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<output name="outputFile1" file="categorized_elements.tabular" />
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</test>
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</tests>
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<help>
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.. class:: infomark
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**What it does**
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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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- 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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- 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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- 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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**Example**
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Let the first input file be a group of motif categories as follows::
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Deletion_Hotspots deletionHoptspot1 deletionHoptspot2 deletionHoptspot3
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Dna_Pol_Pause_Frameshift dnaPolPauseFrameshift1 dnaPolPauseFrameshift2 dnaPolPauseFrameshift3 dnaPolPauseFrameshift4
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Indel_Hotspots indelHotspot1
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Insertion_Hotspots insertionHotspot1 insertionHotspot2
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Topoisomerase_Cleavage_Sites topoisomeraseCleavageSite1 topoisomeraseCleavageSite2 topoisomeraseCleavageSite3
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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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10bp 20bp 40bp
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deletionHoptspot1 1 1 2
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deletionHoptspot2 1 1 1
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deletionHoptspot3 0 0 0
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dnaPolPauseFrameshift1 1 1 1
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dnaPolPauseFrameshift2 0 2 1
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dnaPolPauseFrameshift3 0 0 0
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dnaPolPauseFrameshift4 0 1 2
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indelHotspot1 0 0 0
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insertionHotspot1 0 0 1
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insertionHotspot2 1 1 1
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topoisomeraseCleavageSite1 1 1 1
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topoisomeraseCleavageSite2 1 2 1
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topoisomeraseCleavageSite3 0 0 2
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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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10bp 20bp 40bp
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Deletion_Hotspots 2 2 3
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Dna_Pol_Pause_Frameshift 1 4 4
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Indel_Hotspots 0 0 0
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Insertion_Hotspots 1 1 2
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Topoisomerase_Cleavage_Sites 2 3 4
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</help>
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</tool>
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