--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/taxonomy_krona_chart.xml	Thu Oct 15 15:46:25 2015 -0400
@@ -0,0 +1,129 @@
+<tool id="taxonomy_krona_chart" name="Krona pie chart" version="2.0.0">
+  <description>from taxonomic profile</description>
+  <requirements>
+    <requirement type="package" version="2.5">krona</requirement>
+  </requirements>
+  <version_command>ktImportText | sed -n 's/.*\(KronaTools [[:digit:].]\{1,\}\).*/\1/p'</version_command>
+  <command>
+  <![CDATA[
+
+  #if $type_of_data.input[0].is_of_type('taxonomy'):
+
+        ktImportGalaxy
+        -a
+        -d "${type_of_data.max_rank}"
+        -n "${root_name}"
+        -o "${output}"
+        ${combine_inputs}
+        #for $input_count, $input_dataset in enumerate( $type_of_data.input ):
+            "${input_dataset},${input_count}"
+        #end for
+
+  #else:
+
+        ktImportText
+        -a
+        -n "${root_name}"
+        -o "${output}"
+        ${combine_inputs}
+        #for $input_count, $input_dataset in enumerate( $type_of_data.input ):
+            "${input_dataset},${input_count}"
+        #end for
+
+  #end if
+
+&& [ -d "${output}.files" ] && ( mkdir "${output.extra_files_path}" && mv "${output}.files" "${output.extra_files_path}/" )
+  ]]>
+
+  </command>
+  <inputs>
+    <conditional name="type_of_data">
+      <param name="type_of_data_selector" type="select" label="What is the type of your input data" help="Select between Galaxy Taxonomy and MetaPhlAn Text">
+        <option value="taxonomy" selected="True">Taxonomy</option>
+        <option value="text">MetaPhlAn</option>
+      </param>
+      <when value="taxonomy">
+        <param name="input" type="data" format="taxonomy" multiple="True" label="Input file" help="Select a taxonomy dataset" />
+        <param name="max_rank" type="select" label="show ranks from root to" help="-d; Show all level from root up to this point">
+            <option value="8">Class</option> 
+            <option value="0">Show entire tree</option>
+            <option value="1">Superkingdom</option>
+            <option value="2">Kingdom</option>
+            <option value="3">Subkingdom</option>
+            <option value="4">Superphylum</option>
+            <option value="5">Phylum</option>
+            <option value="6">Subphylum</option>
+            <option value="7">Superclass</option>
+            <option value="9">Subclass</option>
+            <option value="10">Superorder</option>
+            <option value="11">Order</option>
+            <option value="12">Suborder</option>
+            <option value="13">Superfamily</option>
+            <option value="14">Family</option>
+            <option value="15">Subfamily</option>
+            <option value="16">Tribe</option>
+            <option value="17">Subtribe</option>
+            <option value="18">Genus</option>
+            <option value="19">Subgenus</option>
+            <option value="20">Species</option>
+            <option value="21">Subspecies</option>
+        </param>
+      </when>
+      <when value="text">
+        <param name="input" type="data" format="tabular" multiple="True" label="Input file" help="Select a MetaPhlAn dataset" />
+      </when>
+    </conditional>
+    <param name="root_name" type="text" value="Root" label="Provide a name for the basal rank" help="-n; Otherwise it will simply be called &quot;Root&quot;"/>
+    <param name="combine_inputs" type="boolean" truevalue="-c" falsevalue="" selected="False" label="Combine data from multiple datasets?" help="-c; Combine data from each dataset, rather than creating separate datasets within the chart"/>
+  </inputs>
+  <outputs>
+    <data format="html" name="output" label="${tool.name} on ${on_string}: HTML"/>
+  </outputs>
+  <tests>
+    <test>
+      <param name="type_of_data_selector" value="taxonomy"/>
+      <param name="input" value="taxonomy_data.tax" ftype="taxonomy" />
+      <param name="max_rank" value="Genus"/>
+      <param name="root_name" value="Root"/>
+      <param name="combine_inputs" value="False"/>
+      <output name="output" file="krona_test1.html" ftype="html" lines_diff="100"/>
+    </test>
+  </tests>
+  <help>
+**What it does**
+
+This tool renders results of a metagenomic profiling as a zoomable pie chart using Krona_. 
+
+
+.. _Krona: http://sourceforge.net/p/krona/home/krona/
+
+------
+
+**Krona options**
+
+The Galaxy version supports the following options::
+                                                                                                                                                                                      
+  -n   Name of the highest level.
+  -c   Combine data from each file, rather than creating separate datasets within the chart.
+  -d   Maximum depth of wedges to include in the chart.
+
+-----
+
+**License and citation**
+
+This Galaxy tool is Copyright © 2013-2014 `CRS4 Srl.`_ and is released under the `MIT license`_.
+
+.. _CRS4 Srl.: http://www.crs4.it/
+.. _MIT license: http://opensource.org/licenses/MIT
+
+You can use this tool only if you agree to the license terms of: `Krona`_.
+
+.. _Krona: http://sourceforge.net/p/krona/home/krona/
+
+
+  </help>
+  <citations>
+        <citation type="doi">10.1186/1471-2105-12-385</citation>
+        <citation type="doi">10.1093/bioinformatics/btu135</citation>
+    </citations>
+</tool>