--- a/hyphy_gard.xml	Wed Aug 21 12:15:51 2019 -0400
+++ b/hyphy_gard.xml	Thu Feb 13 19:54:45 2020 +0000
@@ -19,15 +19,17 @@
             #if str($rate_cond.rate) != 'None':
                 --rate-classes '$rate_classes'
             #end if
+            --output '$translated'
+            --output-lf '$gard_output'
             > '$gard_log'
     ]]></command>
     <inputs>
         <param name="input_file" type="data" format="fasta" label="Input FASTA file"/>
         <conditional name="datatype">
             <param name="value" type="select" label="Type of data">
-                <option value="Nucleotide">Nucleotide</option>
-                <option value="Protein">Amino acid</option>
-                <option value="Codon">Codon</option>
+                <option value="nucleotide">Nucleotide</option>
+                <option value="protein">Amino acid</option>
+                <option value="codon">Codon</option>
             </param>
             <when value="Nucleotide"/>
             <when value="Protein">
@@ -54,8 +56,8 @@
     </inputs>
     <outputs>
         <data name="gard_log" format="txt"/>
-        <data name="gard_output" format="nex" from_work_dir="gard_input.GARD_finalout"/>
-        <data name="translated" format="hyphy_results.json" from_work_dir="gard_input.fa.json"/>
+        <data name="gard_output" format="nex" />
+        <data name="translated" format="hyphy_results.json" />
     </outputs>
     <tests>
         <test>
@@ -65,6 +67,10 @@
     </tests>
     <help><![CDATA[
 GARD (Genetic Algorithm for Recombination Detection) is a method to screen a multiple sequence analysis for the presence of recombination and is extremely useful as a pre-processing step for selection inference. Because recombinant sequences cannot be adequately described with a single phylogenetic history, selection inference on recombinant data often leads to a significant increase in false positives. GARD alleviates this concern by comprehensively screening an alignment for recombination breakpoints and inferring a unique phylogenetic history for each detected recombination block.
+
+See the online documentation_ for more information.
+
+.. _documentation: http://hyphy.org/methods/selection-methods/#gard
     ]]></help>
     <expand macro="citations">
         <citation type="doi">10.1093/molbev/msl051</citation>