--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/taxonomy-to-krona.xml	Tue Mar 20 21:54:35 2018 -0400
@@ -0,0 +1,74 @@
+<tool id="mothur_taxonomy_to_krona" name="Taxonomy-to-Krona" version="1.0">
+    <description>convert a mothur taxonomy file to Krona input format</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <command detect_errors="exit_code"><![CDATA[
+cat $inputfile
+| tail -n +2               ## remove header line
+| cut -f2,3                ## remove first column
+| sed 's/;/\t/g'           ## split taxonomy field on semicolon
+| sed 's/"//g'             ## remove quotation marks
+| sed 's/[ \t]*$//'        ## remove trailing whitespace
+#if $stripconfidences
+| sed -r 's/[(][0-9]+[)]//g'  ## remove confidence scores
+#end if
+> $outputfile
+    ]]></command>
+    <inputs>
+        <param name="inputfile" type="data" format="mothur.cons.taxonomy" label="Taxonomy file"
+            help="Mothur-formatted taxonomy file. Should have 3 columns; OTU-size-taxonomy"/>
+        <param name="stripconfidences" type="boolean" checked="false" label="Strip confidence values?"
+            help="Strip the confidence values enclosed in parentheses behind the taxonomy levels if present. e.g. Bacteria(100);Bacteroidetes(87);.."/>
+    </inputs>
+    <outputs>
+        <data name="outputfile" format="tabular" label="${tool.name} on ${on_string}: krona-formatted taxonomy file"/>
+    </outputs>
+    <tests>
+        <test><!-- test defaults -->
+            <param name="inputfile" value="example.constaxonomy"/>
+            <output name="outputfile">
+                <assert_contents>
+                    <has_line_matching expression="^\d+(\t[\w\d\-()]+)+$"/>
+                    <not_has_text text="Otu01"/>
+                    <not_has_text text=";"/>
+                    <has_text text="Bacteria"/>
+                    <has_text text="(100)"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test><!-- test with stripping of confidence scores -->
+            <param name="inputfile" value="example.constaxonomy"/>
+            <param name="stripconfidences" value="true"/>
+            <output name="outputfile">
+                <assert_contents>
+                    <has_line_matching expression="^\d+(\t[\w\d\-]+)+$"/>
+                    <not_has_text text="Otu01"/>
+                    <not_has_text text=";"/>
+                    <has_text text="Bacteria"/>
+                    <not_has_text text="(100)"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+Krona text input requires a tab-delimited file with first column being a count, and the rest representing 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
+
+This can be input into the Krona tool as generic text format, and would yield this `Krona plot`_.
+
+.. _Krona plot: https://marbl.github.io/Krona/examples/xml.krona.html
+
+    ]]></help>
+    <expand macro="citations">
+        <citation type="doi">10.1186/1471-2105-12-385</citation>
+    </expand>
+</tool>