--- a/drep_compare.xml	Tue Aug 31 08:03:29 2021 +0000
+++ b/drep_compare.xml	Sat Feb 12 17:38:03 2022 +0000
@@ -1,24 +1,20 @@
-<tool id="drep_compare" name="dRep compare" version="@VERSION@.0" python_template_version="3.5">
+<tool id="drep_compare" name="dRep compare" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" python_template_version="3.5">
     <description>compare a list of genomes</description>
-    <expand macro="bio_tools" />
+    <expand macro="biotools" />
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
-         @PREPARE_GENOMES@         
-         dRep compare outdir
-         @GENOME_COMPARISON_OPTIONS@
-         @CLUSTERING_OPTIONS@
-         @TAXONOMY_OPTIONS@
-         @WARNING_OPTIONS@        
-         @GENOMES@
+@PREPARE_GENOMES@
+dRep compare outdir
+@GENOMES@
+@COMPARISON_CLUSTERING_OPTIONS@
+@WARNING_OPTIONS@
     ]]></command>
     <inputs>
         <expand macro="genomes"/>
-        <expand macro="genome_comparison_options"/>
-        <expand macro="clustering_options"/>
-        <expand macro="taxonomy_options"/>
+        <expand macro="comparison_clustering_options"/>
         <expand macro="warning_options"/>
         <expand macro="select_outputs"/>
     </inputs>
@@ -26,9 +22,24 @@
         <expand macro="common_outputs" />
     </outputs>
     <tests>
-        <expand macro="test_defaults_log">
-            <has_text text="dRep compare finished" />
-        </expand>
+        <test expect_num_outputs="4">
+            <expand macro="test_string_inputs"/>
+            <expand macro="test_default_comparison_clustering_options"/>
+            <expand macro="test_default_warning_options"/>
+            <expand macro="test_default_select_outputs"/>
+            <expand macro="test_log_output">
+                <has_text text="dRep compare finished" />
+            </expand>
+        </test>
+        <test expect_num_outputs="4">
+            <expand macro="test_integer_inputs"/>
+            <expand macro="test_default_comparison_clustering_options"/>
+            <expand macro="test_default_warning_options"/>
+            <expand macro="test_default_select_outputs"/>
+            <expand macro="test_log_output">
+                <has_text text="dRep compare finished" />
+            </expand>
+        </test>
     </tests>
     <help><![CDATA[
 **dRep compare**
@@ -40,9 +51,9 @@
 dRep performs this in two steps:
 
   - first with a rapid primary algorithm (Mash)
-  - second with a more sensitive algorithm (ANIm). 
+  - second with a more sensitive algorithm (ANIm).
 
-We can’t just use Mash because, while incredibly fast, it is not robust to genome incompletenss (see `Choosing parameters <https://drep.readthedocs.io/en/latest/choosing_parameters.html>`_ and `Module Descriptions <https://drep.readthedocs.io/en/latest/module_descriptions.html>`_) and only provides an “estimate” of ANI. ANIm is robust to genome incompleteness and is more accurate, but too slow to perform pair-wise comparisons of longer genome lists.
+We can't just use Mash because, while incredibly fast, it is not robust to genome incompletenss (see `Choosing parameters <https://drep.readthedocs.io/en/latest/choosing_parameters.html>`_ and `Module Descriptions <https://drep.readthedocs.io/en/latest/module_descriptions.html>`_) and only provides an “estimate” of ANI. ANIm is robust to genome incompleteness and is more accurate, but too slow to perform pair-wise comparisons of longer genome lists.
 
 dRep first compares all genomes using Mash, and then only runs the secondary algorithm (ANIm or gANI) on sets of genomes that have at least 90% Mash ANI. This results in a great decrease in the number of (slow) secondary comparisons that need to be run while maintaining the sensitivity of ANIm.