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+++ b/humann2_renorm_table.xml	Thu Dec 17 08:58:05 2015 -0500
@@ -0,0 +1,67 @@
+<tool id="humann2_renorm_table" name="Renormalize HUMAnN2 table" version="0.1.0">
+    <description></description>
+
+    <requirements>
+        <requirement type="package" version="2.2.4">bowtie2</requirement>
+        <requirement type="package" version="2.0">metaphlan2</requirement>
+        <requirement type="package" version="0.6.13">diamond</requirement>
+        <requirement type="package" version="2.0">humann2</requirement>
+    </requirements>
+
+    <stdio>
+        <exit_code range="1:" />
+    </stdio>
+
+    <version_command>
+<![CDATA[
+    humann2_renorm_table --version
+]]>
+    </version_command>
+
+    <command><![CDATA[
+        humann2_renorm_table
+            -i $input_table
+            -o $output_table
+            --norm $norm
+    ]]></command>
+
+    <inputs>
+        <param name="input_table" type="data" format="tsv" label="Gene/pathway 
+            table" help=""/>
+
+        <param name="norm" type="select" label="Normalization scheme" help="(--norm)">
+            <option value="cpm" selected="true">Copies per million</option>
+            <option value="relab">Relative abundance</option>
+        </param>
+    </inputs>
+
+    <outputs>
+        <data format="tsv" name="output_table" label="Normalized table for 
+            ${on_string} (HUMAnN2)" />
+    </outputs>
+
+    <tests>
+        <test>
+            <param name="input_table" value="humann2_fasta_pathabundance.tsv"/>
+            <param name="norm" value="cpm"/>
+            <output name="output_table" file="humann2_fasta_pathabundance_cpm_renormalized.tsv"/>
+        </test>
+        <test>
+            <param name="input_table" value="humann2_fasta_pathabundance.tsv"/>
+            <param name="norm" value="relab"/>
+            <output name="output_table" file="humann2_fasta_pathabundance_relab_renormalized.tsv"/>
+        </test>
+    </tests>
+
+    <help><![CDATA[
+        **What it does**
+
+        Renorm HUMAnN2 table is a tool for renormalizing table. Each level of a stratified table will be normalized using the desired scheme.
+
+        HUMAnN is a pipeline for efficiently and accuretly profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data. `Read more about the tool <http://huttenhower.sph.harvard.edu/humann2/manual>`_.
+
+    ]]></help>
+
+    <citations>
+    </citations>
+</tool>
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