--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/humann2_merge_abundance_tables.xml	Thu May 26 10:20:59 2016 -0400
@@ -0,0 +1,86 @@
+<tool id="humann2_merge_abundance_tables" name="Merge" version="0.6.1">
+    <description> HUMAnN2 generated gene and pathway abundance tables</description>
+
+    <macros>
+        <import>humann2_macros.xml</import>
+    </macros>
+
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
+
+    <version_command>
+<![CDATA[
+    humann2_merge_abundance_tables --version
+]]>
+    </version_command>
+
+    <command><![CDATA[
+        humann2_merge_abundance_tables
+
+            --input-genes $input_gene
+            --input-pathways $input_pathway
+
+            #if $gene_mapping_selection.gene_mapping_selection_test == "true":
+                --gene-mapping $gene_mapping
+            #end if 
+
+            #if $pathway_mapping_selection.pathway_mapping_selection_test == "true":
+                --pathway-mapping $pathway-mapping
+            #end if 
+
+            $remove_taxonomy
+                                  
+            -o $output_table
+    ]]></command>
+
+    <inputs>
+        <param name="input_gene" type="data" format="tsv" label="Gene family or EC abundance file" help="(--input-genes)"/>
+
+        <param name="input_pathway" type="data" format="tsv" label="Pathway abundance file" help="(--input-pathways)"/>
+
+        <conditional name="gene_mapping_selection">
+            <param name='gene_mapping_selection_test' type='boolean' checked="false" truevalue='true' falsevalue='false' label="Use a gene mapping file?" help=""/>
+                <when value="true">
+                    <param name="gene_mapping" type="data" format="tsv" label="Gene family to reaction mapping file" help="(--gene-mapping)"/>
+                </when>
+                <when value="false">
+                </when>
+        </conditional>
+        <conditional name="pathway_mapping_selection">
+            <param name='pathway_mapping_selection_test' type='boolean' checked="false" truevalue='true' falsevalue='false' label="Use a pathway mapping file?" help=""/>
+                <when value="true">
+                    <param name="pathway_mapping" type="data" format="tsv" label="Reaction to pathway mapping file" help="(--pathway-mapping)"/>
+                </when>
+                <when value="false">
+                </when>
+        </conditional>
+
+        <param name='remove_taxonomy' type='boolean' checked="false" truevalue='--remove-taxonomy' falsevalue='' label="Remove the taxonomy from the output file?" help="(--remove-taxonomy)"/>
+    </inputs>
+
+    <outputs>
+        <data format="tsv" name="output_table" label="${tool.name} on ${on_string}: Merged table" />
+    </outputs>
+
+    <tests>
+        <test>
+            <param name="input_gene" value="expected_gene_family_abundance.tsv"/>
+            <param name="input_pathway" value="expected_pathway_abundance.tsv"/>
+            <param name="gene_mapping_selection_test" value="false"/>
+            <param name="pathway_mapping_selection" value="false"/>
+            <param name="remove_taxonomy" value="false"/>
+            <output name="output_table" file="merged_gene_families_pathways_abundances.tsv" /> 
+        </test>
+    </tests>
+
+    <help><![CDATA[
+**What it does**
+
+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>`_.
+
+The currest tool merge a table containing gene family abundances with a table containing pathway abundances, given a gene to pathway mapping (default or custom one).
+
+    ]]></help>
+
+    <expand macro="citations"/>
+</tool>
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