--- a/eggnog_mapper.xml	Wed Feb 28 13:20:40 2018 -0500
+++ b/eggnog_mapper.xml	Mon Nov 11 11:50:36 2019 -0500
@@ -1,19 +1,21 @@
-<tool id="eggnog_mapper" name="eggNOG Mapper" version="@VERSION@">
+<tool id="eggnog_mapper" name="eggNOG Mapper" version="@VERSION@.1">
     <description>functional sequence annotation by orthology</description>
     <macros>
-        <token name="@VERSION@">1.0.3</token>
+        <import>eggnog_macros.xml</import>
     </macros>
-    <requirements>
-        <requirement type="package" version="@VERSION@">eggnog-mapper</requirement>
-    </requirements>
-    <version_command>emapper.py --version</version_command>
+    <expand macro="requirements"/>
+    <expand macro="version_command"/>
     <command detect_errors="aggressive"><![CDATA[
         emapper.py
-        --data_dir '$eggnog_data.fields.db'
+        --data_dir '$eggnog_data.fields.path'
         -m $db.mode 
         $translate
         #if ($db.mode == 'hmmer'):
-            --database=$db.database.fields.db
+            #if $db.database.fields.path:
+                --database=$db.database.fields.path
+            #else
+                --database=$db.database
+            #end if
             #if $db.hmm_options.hmm_settings == 'specified':
                 --hmm_maxhits=$db.hmm_options.hmm_maxhits
                 --hmm_evalue=$db.hmm_options.hmm_evalue
@@ -53,9 +55,7 @@
         <inputs>
             <param name="input" type="data" format="fasta" label="Fasta sequences to annotate"/>
             <param name="eggnog_data" type="select" label="Version of eggNOG Database">
-                <options from_data_table="eggnog_mapper">
-                    <filter type="static_value" name="type" value="data" column="2"/>
-                </options>
+                <options from_data_table="eggnog_mapper_db"/>
             </param>
             <param name="translate" type="boolean" truevalue="--translate" falsevalue="" checked="false"
                 label="Are these coding DNA sequences that need to be translated?"/>
@@ -66,9 +66,12 @@
                 </param>
                 <when value="hmmer">
                     <param name="database" type="select" label="HMM target database" help="Choose either the full eggNOG database or a subset of it. Contact your Galaxy admin to have additional HMM databases installed.">
-                        <options from_data_table="eggnog_mapper">
-                            <filter type="static_value" value="hmmer" column="2"/>
+                        <options from_data_table="eggnog_mapper_hmm_dbs">
+                            <!--
+                            <filter type="param_value" ref="eggnog_data" column="1" />
+                            <filter type="unique_value" column="3" />
                             <validator type="no_options" message="No HMM databases are available; request installation from your Galaxy admin." />
+                            -->
                         </options>
                     </param>
                     <conditional name="hmm_options">
@@ -395,15 +398,17 @@
             <param name="input" value="nlim_fragment.fasta" ftype="fasta"/>
             <param name="database" value="ENOG411CB2I"/>
             <param name="mode" value="hmmer"/>
+            <!--
             <param name="test" value="true"/>
-            <param name="eggnog_data" value="eggNOG_4.5"/>
+            -->
+            <param name="eggnog_data" value="4.5"/>
             <param name="no_annot" value="true"/>
             <param name="no_file_comments" value="true"/>
             <output name="hmm_hits" file="HMM_nlim.emapper.hmm_hits" ftype="tabular"/>
         </test>
         <test>
             <param name="input" value="nlim_fragment.fasta" ftype="fasta"/>
-            <param name="eggnog_data" value="eggNOG_4.5"/> <!-- not passed in test, but required for test to work -->
+            <param name="eggnog_data" value="4.5"/> <!-- not passed in test, but required for test to work -->
             <param name="no_annot" value="true"/>
             <param name="mode" value="diamond"/>
             <output name="seed_orthologs" file="DIA_nlim.emapper.seed_orthologs" ftype="tabular"/>
@@ -468,7 +473,5 @@
 - ``eggNOG_HMM_model_annotation``: eggNOG functional description inferred from best matching OG
 
     ]]></help>
-    <citations>
-        <citation type="doi">10.1093/nar/gkv1248</citation>
-    </citations>
+    <expand macro="citations"/>
 </tool>