--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/kreport2mpa.xml	Mon Mar 06 21:22:31 2023 +0000
@@ -0,0 +1,92 @@
+<tool id="krakentools_kreport2mpa" name="Krakentools: Convert kraken report file" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>to MetaPhlAn-style</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="biotools"/>
+    <expand macro="requirements"/>
+    <expand macro="version"/>
+    <command detect_errors="exit_code"><![CDATA[
+kreport2mpa.py 
+    --report '$report' 
+    --output '$output' 
+    $intermediate_ranks
+    $percentages
+    ]]></command>
+    <inputs>
+        <param argument="--report" type="data" format="tabular" label="Kraken report file" />
+        <param argument="--intermediate-ranks" type="boolean" checked="false" truevalue="--intermediate-ranks" falsevalue="" label="Include intermediate ranks" help="Include non-standard levels. Default only outputs standard levels [D,P,C,O,F,G,S]." />
+        <param argument="--percentages" type="boolean" checked="false" truevalue="--percentages" falsevalue="" label="Use percentage of total reads for output." help="Outputs percentages of reads instead of total reads."/>
+    </inputs>
+    <outputs>
+        <data name="output" format="tabular" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="report" value="sample.tabular"/>
+            <output name="output" file="mpa_output.tabular"/>
+        </test>
+        <test>
+            <param name="report" value="sample.tabular"/>
+            <param name="intermediate_ranks" value="--intermediate-ranks"/>
+            <output name="output" file="mpa_output_intermediate.tabular"/>
+        </test>
+        <test>
+            <param name="report" value="sample.tabular"/>
+            <param name="percentages" value="--percentages"/>
+            <output name="output" file="mpa_output_percentages.tabular"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+KrakenTools is a suite of scripts to be used alongside the Kraken, KrakenUniq, Kraken 2, or Bracken programs. 
+These scripts are designed to help Kraken users with downstream analysis of Kraken results. 
+This program takes a Kraken report file and prints out a MetaPhlAn-style TEXT file.
+
+Input
+------
+A Kraken report file
+
+Output
+------
+A MetaPhlAn-style TEXT file
+
+**Example output:**
+
+``--no-intermediate-ranks``
+
+:: 
+
+    k__Eukaryota	756
+    k__Eukaryota|k__Metazoa	402
+    k__Eukaryota|k__Metazoa|p__Chordata	402
+    k__Eukaryota|k__Metazoa|p__Chordata|c__Mammalia	402
+
+
+``--intermediate-ranks``
+
+::
+
+    x__cellular_organisms	836
+    x__cellular_organisms|k__Eukaryota	756
+    x__cellular_organisms|k__Eukaryota|x__Opisthokonta	747
+    x__cellular_organisms|k__Eukaryota|x__Opisthokonta|k__Metazoa	402
+    x__cellular_organisms|k__Eukaryota|x__Opisthokonta|k__Metazoa|x__Eumetazoa	402
+
+``--percentages``
+
+::
+
+    k__Eukaryota	56.0
+    k__Eukaryota|k__Metazoa	29.78
+    k__Eukaryota|k__Metazoa|p__Chordata	29.78
+    k__Eukaryota|k__Metazoa|p__Chordata|c__Mammalia	29.78
+    k__Eukaryota|k__Metazoa|p__Chordata|c__Mammalia|o__Primates	29.78
+    k__Eukaryota|k__Metazoa|p__Chordata|c__Mammalia|o__Primates|f__Hominidae	29.78
+    k__Eukaryota|k__Metazoa|p__Chordata|c__Mammalia|o__Primates|f__Hominidae|g__Homo	29.78
+
+    ]]></help>
+    <expand macro="citations"/>
+    <creator>
+        <person givenName="Paul" familyName="Zierep" email="zierep@informatik.uni-freiburg.de" />
+    </creator>
+</tool>