annotate prop_venn.xml @ 1:cc6707a1e044 draft default tip

added fixes from Brad Langhorst; https://bitbucket.org/account/notifications/read/3443176/patch-for-proportional-venn-tool-in-galaxy; added tool_dependencies for Mako template untested

<tool id="prop_venn" name="proportional venn" version="0.5">
<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="size" label="size" type="integer" help="size of plot ( &lt; 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="${title}"/>
</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>