Mercurial > repos > idot > prop_venn
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author | g2cmnty@test-web1.g2.bx.psu.edu |
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date | Wed, 22 Jun 2011 03:28:25 -0400 |
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children | cc6707a1e044 |
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<tool id="prop_venn" name="proportional venn" version="0.4"> <description> from 2-3 sets</description> <command interpreter="python">venner.py #if str( $twoThree['tt']) == 'three': --files $inputFile1,$inputFile2,$twoThree.inputFile3 --columns $column1,$column2,$twoThree.column3 --asNames $asName1,$asName2,$twoThree.asName3 #else: --file $inputFile1,$inputFile2 --columns $column1,$column2 --asNames $asName1,$asName2 #end if --title '$title' --size $size --outname $outPath </command> <inputs> <param name="title" label="title" type="text" help="title of plot" optional="true" value=""/> <param name="name" label="name" type="text" help="name of output file" value="venn of NA"/> <param name="size" label="size" type="integer" help="size of plot ( < 540)" optional="true" value="300"/> <param format="tabular" name="inputFile1" label="input file 1" type="data" help="tabular input file" optional="false"/> <param name="column1" label="column index" type="integer" help="0 based index of element column" optional="false" value="0"/> <param name="asName1" label="as name" type="text" help="nice name for columns on plot" optional="false" value="A"/> <param format="tabular2" name="inputFile2" label="input file 2" type="data" help="tabular input file" optional="false"/> <param name="column2" label="column index file 2" type="integer" help="0 based index of element column" optional="false" value="0"/> <param name="asName2" label="as name file 2" type="text" help="nice name for columns on plot" optional="false" value="B"/> <conditional name="twoThree"> <param name="tt" type="select" label="two or three"> <option value="two" selected="true">two</option> <option value="three">three</option> </param> <when value="two"> </when> <when value="three"> <param format="tabular" name="inputFile3" label="input file 3" type="data" help="tabular input file" optional="false"/> <param name="column3" label="column index file 3" type="integer" help="0 based index of element column" optional="false" value="0"/> <param name="asName3" label="as name file 3" type="text" help="nice name for columns on plot" optional="false" value="C"/> </when> </conditional> </inputs> <outputs> <data name="outPath" format="html" label="${name}"/> </outputs> <help> Proportional Venn Diagram: -------------------------- Creates a proportional Venn diagram from 2 or 3 tab delimited input files. The 0 based column index decides which column is used for extracting the sets to compare between the files. Multiple items with the same value per column are counted as one. Requirements: ------------- - 2-3 tab delimited input files. - 0 based index of the columns to extract for each file Outputs: -------- - Html page with the proportional Venn diagram and a table for the counts in each section. Please turn to *Ido Tamir* in case of problems or suggestions for this tool. </help> </tool>