--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/est-abundance.xml	Wed Oct 16 16:57:55 2019 -0400
@@ -0,0 +1,65 @@
+<tool id="est_abundance" name="Estimate Abundance at Taxonomic Level" version="@VERSION@+galaxy0">
+    <description>Bayesian Reestimation of Abundance with KrakEN</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <edam_topics>
+        <edam_topic>topic_3174</edam_topic>
+        <edam_topic>topic_3697</edam_topic>
+    </edam_topics>
+    <edam_operations>
+        <edam_operation>operation_2238</edam_operation>
+    </edam_operations>
+    <expand macro="requirements" />    
+    <command detect_errors="exit_code"><![CDATA[
+    est_abundance.py 
+    -i '$input' 
+    -k '$kmer_distr.fields.path' 
+    -l $level 
+    -t $threshold 
+    -o '$report'
+    ]]>
+    </command>    
+    <inputs>
+        <param name="input" type="data" format="tabular" label="Kraken report file" />
+        <param label="Select a Kmer distribution" name="kmer_distr" type="select">
+            <options from_data_table="bracken_databases">
+                <validator message="No database is available" type="no_options" />
+            </options>
+        </param>
+        <param name="level" type="select" label="Level" help="Level to push all reads to" >
+            <option value="S" selected="true">Species</option>
+            <option value="G">Genus</option>
+            <option value="F">Family</option>
+            <option value="O">Order</option>
+            <option value="C">Class</option>
+            <option value="P">Phylum</option>
+            <option value="D">Domain</option>
+        </param>
+        <param name="threshold" type="integer" value="10" label="Number of mismatches allowed when matching tag"
+               help="Threshold for the minimum number of reads kraken must assign to a classification for that 
+                     classification to be considered in the final abundance estimation." />
+    </inputs>
+    <outputs>
+        <data name="report" format="tabular" label="${tool.name} on ${on_string}: Report" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="NC_003198.1_simulated_kraken_report.txt" ftype="tabular"/>
+            <param name="level" value="S" />
+            <param name="bracken_database" value="test_entry"/>
+	    <output name="report" file="NC_003198.1_simulated_bracken_report.txt" ftype="tabular"/>
+        </test>
+	<test>
+            <param name="input" value="NC_011750.1_simulated_kraken_report.txt" ftype="tabular"/>
+            <param name="level" value="S" />
+            <param name="bracken_database" value="test_entry"/>
+	    <output name="report" file="NC_011750.1_simulated_bracken_report.txt" ftype="tabular"/>
+        </test>
+    </tests>
+    <help>
+    <![CDATA[
+        Documentation can be found at `site <http://ccb.jhu.edu/software/bracken/index.shtml?t=manual>`_.
+    ]]></help>
+    <expand macro="citations" />
+</tool>