comparison krona_text.xml @ 0:04021cfd5170 draft default tip

planemo upload for repository https://github.com/kavonrtep/galaxy_packages commit 5269b4297ea690bce0802c3c1cb217f24290f1ec-dirty

0:04021cfd5170

<tool id="krona-text" name="Visualize  with Krona" version="1.1">

  <description>Visualise any hierarchical data</description>

  <requirements>
    <requirement type="package" version="2.6">krona</requirement>
  </requirements>
  <command><![CDATA[
echo "starting" &&
head '${inputfile}' &&

#if "$isMothur" == "Y"
  awk 'BEGIN{FS="\t";OFS="\t"}{print $2,$3}' '${inputfile}' > tempinput &&
  head tempinput &&
  sed -i 's/;/\t/g' tempinput &&

#else
  cp '${inputfile}' tempinput &&

#end if

head tempinput &&
export TERM=dumb &&
ktImportText tempinput
]]></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.otu?"/>


  </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
This tool is a modification of https://toolshed.g2.bx.psu.edu/view/saskia-hiltemann/krona_text/b14f1444e464
  </help>
</tool>