--- a/taxonomy_krona_chart.xml	Fri Apr 11 12:48:59 2014 -0400
+++ b/taxonomy_krona_chart.xml	Mon Aug 17 11:36:09 2015 -0400
@@ -1,32 +1,113 @@
-<tool id="taxonomy_krona_chart" name="Krona pie chart" version="1.0.0">
+<tool id="taxonomy_krona_chart" name="Krona pie chart" version="2.0.0">
   <description>from taxonomic profile</description>
   <requirements>
-    <requirement type="package" version="2.4">kronatools</requirement>
+    <requirement type="package" version="2.5">krona</requirement>
   </requirements>
   <version_command>ktImportText | sed -n 's/.*\(KronaTools [[:digit:].]\{1,\}\).*/\1/p'</version_command>
   <command>
-    #if $input.ext == 'taxonomy'
-      ktImportGalaxy "${input}" -o "${output}"
-    #else
-      ktImportText "${input}" -o "${output}"
-    #end if
+  <![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
+
+  ]]>
+
   </command>
   <inputs>
-    <param name="input" type="data" format="tabular" label="Input file" help="Either a 'MetaPhlAn to Krona' result file or a taxonomy file" />
+    <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" size="20" 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 converts the standard result file of a metagenomic profiling in a zoomable pie chart using Krona_.
-It takes as input datasets produced by *MetaPhlAn to Krona*, *Fetch taxonomic representation*, *Find lowest diagnostic rank* and *Filter taxonomy* tools.
+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`_.
@@ -34,15 +115,14 @@
 .. _CRS4 Srl.: http://www.crs4.it/
 .. _MIT license: http://opensource.org/licenses/MIT
 
-If you use this tool in Galaxy, please cite |Cuccuru2014|_.
-
-.. |Cuccuru2014| replace:: Cuccuru, G., Orsini, M., Pinna, A., Sbardellati, A., Soranzo, N., Travaglione, A., Uva, P., Zanetti, G., Fotia, G. (2014) Orione, a web-based framework for NGS analysis in microbiology. *Bioinformatics*, accepted
-.. _Cuccuru2014: http://bioinformatics.oxfordjournals.org/content/early/2014/04/03/bioinformatics.btu135
-
-This tool uses scripts from `Krona`_, which is licensed separately. Please cite |Ondov2011|_.
+You can use this tool only if you agree to the license terms of: `Krona`_.
 
 .. _Krona: http://sourceforge.net/p/krona/home/krona/
-.. |Ondov2011| replace:: Ondov, B. D., Bergman, N. H., Phillippy, A. M. (2011) Interactive metagenomic visualization in a Web browser. *BMC Bioinformatics* 12, 385
-.. _Ondov2011: http://www.biomedcentral.com/1471-2105/12/385
+
+
   </help>
+  <citations>
+        <citation type="doi">10.1186/1471-2105-12-385</citation>
+        <citation type="doi">10.1093/bioinformatics/btu135</citation>
+    </citations>
 </tool>