view krona_text.xml @ 1:d6435b34b96b draft

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<tool id="krona-text" name="Visualize  with Krona" version="1">

  <description>Visualise any hierarchical data</description> 

  <requirements>		
    <requirement type="package" version="2.6">krona-tools</requirement>
  </requirements>
        
  <!-- the command to run when user hits execute. Run our Rscript and pass the parameter to it -->
  <command interpreter="bash">
    runKrona.sh $inputfile $isMothur $outputfile


  </command>


  <inputs>
  <!-- parameter examples, see https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax for descriptions -->

    <!-- file from history -->
    <param name="inputfile" type="data" label="Select input file" help="Choose input file from history. Format: count - Hierarchy (tab separated)"/>
    <param name="isMothur" type="boolean" checked="False" truevalue="Y" falsevalue="N" label="is this output from MOTHUR?" help="e.g. taxonomy file generated from Classify.seqs?"/>

    
  </inputs>

  
  <outputs>
    <data format="html" name="outputfile"  from_work_dir="text.krona.html" label="Krona on ${on_string}: HTML"/>
  </outputs>

  <help>
Input file must be a tab-delimited file with first column being a count, rest the hierarchy, for example::

    2	Fats	Saturated fat  
    3	Fats	Unsaturated fat	Monounsaturated fat  
    3	Fats	Unsaturated fat	Polyunsaturated fat  
    13	Carbohydrates	Sugars  
    4	Carbohydrates	Dietary fiber  
    21	Carbohydrates  
    5	Protein  
    4  

Would yield the following graph: http://krona.sourceforge.net/examples/text.krona.html


    
  </help>
</tool>