--- a/humann2.xml	Mon Feb 22 07:09:45 2016 -0500
+++ b/humann2.xml	Thu Mar 31 03:35:17 2016 -0400
@@ -1,25 +1,21 @@
-<tool id="humann2" name="HUMAnN2" version="0.1.0">
+<tool id="humann2" name="HUMAnN2" version="0.5.0">
     <description>to profile the presence/absence and abundance of microbial pathways</description>
 
-    <requirements>
-        <requirement type="package" version="2.2.5">bowtie2</requirement>
-        <requirement type="package" version="2.0">metaphlan2</requirement>
-        <requirement type="package" version="0.7.10">diamond</requirement>
-        <requirement type="package" version="2.0">humann2</requirement>
-    </requirements>
+    <macros>
+        <import>humann2_macros.xml</import>
+    </macros>
 
-    <stdio>
-        <exit_code range="1:" />
-    </stdio>
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
 
     <version_command>
 <![CDATA[
-    \${HUMANN2_DIR}/humann2 --version
+    humann2 --version
 ]]>
     </version_command>
 
     <command><![CDATA[
-        \${HUMANN2_DIR}/humann2 
+        humann2 
             -i "$input_file"
         
             #if $taxonomic_profile.taxonomic_profile_test:
@@ -67,7 +63,7 @@
                 falsevalue='false' label="Use a custom taxonomic profile?" 
                 help="The file must have been created by MetaPhlan"/>
             <when value="true">
-                <param name="taxonomic_profile_file" type="data" format="" label="Taxonomic profile 
+                <param name="taxonomic_profile_file" type="data" format="tabular,txt" label="Taxonomic profile 
                     file" help=""/>
             </when>
             <when value="false" />
@@ -227,31 +223,31 @@
     </tests>
 
     <help><![CDATA[
-        **What it does**
+**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>`_.
+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>`_.
 
-        ----- 
+----- 
 
-        **Input**
+**Input**
 
-        Usually, a single file is the input. It must be one of the following types:
+Usually, a single file is the input. It must be one of the following types:
 
-            - filtered shotgun sequencing metagenome file (fastq, fastq.gz, fasta, or fasta.gz format)
-            - alignment file (sam, bam or blastm8 format)
-            - gene table file (tsv or biom format)
+- filtered shotgun sequencing metagenome file (fastq, fastq.gz, fasta, or fasta.gz format)
+- alignment file (sam, bam or blastm8 format)
+- gene table file (tsv or biom format)
 
-        A file with taxonomic profiles can also be given to be use to select pangenomes in ChocoPhlan database.
+A file with taxonomic profiles can also be given to be use to select pangenomes in ChocoPhlan database.
 
-        ----- 
+----- 
 
-        **Outputs**
+**Outputs**
 
-        HUMAnN creates three output files:
+HUMAnN creates three output files:
 
-            - Gene family abundance
-            - Pathway abundance
-            - Pathway coverage
+- Gene family abundance
+- Pathway abundance
+- Pathway coverage
 
     ]]></help>