--- a/merge_metaphlan_tables.xml	Fri Mar 19 21:40:18 2021 +0000
+++ b/merge_metaphlan_tables.xml	Mon Apr 19 20:54:50 2021 +0000
@@ -1,55 +1,47 @@
-<tool id="merge_metaphlan_tables" name="Merge" version="@WRAPPER_VERSION@.0">
-
-    <description>MetaPhlAn2 files</description>
-
+<tool id="merge_metaphlan_tables" name="Merge" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>MetaPhlAn abundance tables</description>
     <macros>
-        <import>metaphlan2_macros.xml</import>
+        <import>macros.xml</import>
     </macros>
-
+    <expand macro="edam_ontology"/>
     <expand macro="requirements"/>
-    <expand macro="stdio"/>
-
     <version_command>merge_metaphlan_tables.py -v</version_command>
-
-    <command>
-<![CDATA[
-        merge_metaphlan_tables.py
-            #for $element in $input_files
-                '$element'
-            #end for
-            > '$output'
+    <command detect_errors="aggressive"><![CDATA[
+merge_metaphlan_tables.py
+    #for $element in $inputs
+        '$element'
+    #end for
+    > '$output'
 ]]>
     </command>
-
     <inputs>
-        <param name="input_files" type="data" format="tabular,txt" multiple="True" label="MetaPhlAn2 output file to join" />
+        <param name="inputs" type="data" format="tabular,txt" multiple="true" label="Predicted taxon relative abundance tables generaed by MetaPhlAn" />
     </inputs>
-
     <outputs>
-        <data format="tabular" name="output" label="${tool.name} on ${on_string}: Merged MetaPhlAn2 files" />
+        <data name="output" format="tabular" label="${tool.name} on ${on_string}: Merged taxon relative abundance tables" />
     </outputs>
-
     <tests>
-        <test>
-            <param name="input_files" value="community_profile.tabular,community_profile.tabular"/>
-            <output name="output">
+        <test expect_num_outputs="1">
+            <param name="inputs" value="SRS014464-Anterior_nares-abundances.tabular,SRS014464-Anterior_nares-abundances.tabular"/>
+            <output name="output" ftype="tabular" >
                 <assert_contents>
-                    <has_text text="#SampleID" />
-                    <has_text text="k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides_thetaiotaomicron|t__Bacteroides_thetaiotaomicron_unclassified" />
+                    <has_text text="k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_accolens"/>
+                    <has_text text="dataset_"/>
+                    <has_text text="NCBI_tax_id"/>
+                    <has_text text="clade_name"/>
                 </assert_contents>
             </output>
         </test>
     </tests>
-
     <help><![CDATA[
-
-**What it does**
+What it does
+============
 
-MetaPhlAn is a computational tool to profile the structure and the composition of microbial communities (Bacteria, Archaea, Eukaryotes and Viruses) from metagenomic shotgun sequencing data with species level resolution. For more information, check the `user manual <https://bitbucket.org/biobakery/metaphlan2/>`_.
+MetaPhlAn is a computational tool for profiling the composition of microbial communities (Bacteria, 
+Archaea and Eukaryotes) from metagenomic shotgun sequencing data (i.e. not 16S) with species-level. 
 
-This tool performs a table join on one or more metaphlan output files
-
+This tool performs a table join on one or more tab-separated files with the predicted taxon relative abundances
+that have been generated by MetaPhlAn.
     ]]></help>
-
     <expand macro="citations"/>
 </tool>