--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/drep_compare.xml	Tue May 05 06:20:45 2020 -0400
@@ -0,0 +1,62 @@
+<tool id="drep_compare" name="dRep compare" version="@VERSION@.0" python_template_version="3.5">
+    <description>compare a list of genomes</description>
+    <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@
+    ]]></command>
+    <inputs>
+        <expand macro="genomes"/>
+        <expand macro="genome_comparison_options"/>
+        <expand macro="clustering_options"/>
+        <expand macro="taxonomy_options"/>
+        <expand macro="warning_options"/>
+        <expand macro="select_outputs"/>
+    </inputs>
+    <outputs>
+        <expand macro="common_outputs" />
+    </outputs>
+    <tests>
+        <expand macro="test_defaults_log">
+            <has_text text="dRep compare finished" />
+        </expand>
+    </tests>
+    <help><![CDATA[
+**dRep compare**
+
+`dRep <https://drep.readthedocs.io/en/latest/overview.html>`_ performs rapid pair-wise comparison of genome sets.
+
+`dRep compare <https://drep.readthedocs.io/en/latest/overview.html#genome-comparison>`_ can rapidly and accurately compare a list of genomes in a pair-wise manner. This allows identification of groups of organisms that share similar DNA content in terms of Average Nucleotide Identity (ANI).
+
+dRep performs this in two steps:
+
+  - first with a rapid primary algorithm (Mash)
+  - 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.
+
+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.
+
+
+**INPUTS**
+
+  - Genome sets in fasta format.
+
+
+**OUTPUTS**
+
+  - `Figures <https://drep.readthedocs.io/en/latest/example_output.html#figures>`_ that show the relationship of the Genome inputs.
+  - `Warnings <https://drep.readthedocs.io/en/latest/example_output.html#warnings>`_ report two things: de-replicated genome similarity and secondary clusters that were almost different.
+
+
+    ]]></help>
+    <expand macro="citations" />
+</tool>