--- a/hyphy_slac.xml	Thu Jan 17 04:24:25 2019 -0500
+++ b/hyphy_slac.xml	Wed Aug 21 12:27:21 2019 -0400
@@ -4,44 +4,40 @@
     <macros>
         <import>macros.xml</import>
     </macros>
-    <expand macro="requirements" />
-    <expand macro="version_command" />
-    <command detect_errors="exit_code">
-    <![CDATA[
-    ln -s '$input_file' slac_input.fa &&
-    ln -s '$input_nhx' slac_input.nhx &&
-    echo $gencodeid > tool_params &&
-    echo `pwd`/slac_input.fa >> tool_params &&
-    echo `pwd`/slac_input.nhx >> tool_params &&
-    echo '$branches' >> tool_params &&
-    echo '$number_of_samples' >> tool_params &&
-    echo '$p_value' >> tool_params &&
-    @HYPHY_INVOCATION@ \$HYPHY_LIB/TemplateBatchFiles/SelectionAnalyses/SLAC.bf > '$slac_log'
-    ]]>
-    </command>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+        ln -s '$input_file' slac_input.fa &&
+        ln -s '$input_nhx' slac_input.nhx &&
+        @HYPHY_INVOCATION@ slac
+            --alignment ./slac_input.fa
+            --tree ./slac_input.nhx
+            --code '$gencodeid'
+            --branches '$branches'
+            --samples '$number_of_samples'
+            --pvalue '$p_value'
+        > '$slac_log'
+    ]]></command>
     <inputs>
-        <expand macro="inputs" />
-        <expand macro="gencode" />
-        <expand macro="branches" />
-        <param name="p_value" type="float" value=".1" min="0" max="1" label="P-value" />
-        <param name="number_of_samples" type="integer" value="100" min="0" max="100000" label="Number of samples used to assess ancestral reconstruction uncertainty" />
+        <expand macro="inputs"/>
+        <expand macro="gencode"/>
+        <expand macro="branches"/>
+        <param name="p_value" type="float" value=".1" min="0" max="1" label="P-value"/>
+        <param name="number_of_samples" type="integer" value="100" min="0" max="100000" label="Number of samples used to assess ancestral reconstruction uncertainty"/>
     </inputs>
     <outputs>
-        <data name="slac_log" format="txt" />
-        <data name="slac_output" format="json" from_work_dir="slac_input.fa.SLAC.json" />
+        <data name="slac_log" format="txt"/>
+        <data name="slac_output" format="hyphy_results.json" from_work_dir="slac_input.fa.SLAC.json"/>
     </outputs>
     <tests>
         <test>
-            <param name="input_file" ftype="fasta" value="absrel-in1.fa" />
-            <param name="input_nhx" ftype="nhx" value="absrel-in1.nhx" />
-            <output name="slac_output" file="slac-out1.json" compare="sim_size" />
+            <param name="input_file" ftype="fasta" value="absrel-in1.fa"/>
+            <param name="input_nhx" ftype="nhx" value="absrel-in1.nhx"/>
+            <output name="slac_output" file="slac-out1.json" compare="sim_size"/>
         </test>
     </tests>
-    <help>
-        <![CDATA[
+    <help><![CDATA[
 SLAC (Single-Likelihood Ancestor Counting) uses a combination of maximum-likelihood and counting approaches to infer nonsynonymous and synonymous substitution rates on a per-site basis for a given coding alignment and corresponding phylogeny. SLAC assumes that the selection pressure for each site is constant along the entire phylogeny.
-        ]]>
-    </help>
+    ]]></help>
     <expand macro="citations">
         <citation type="doi">10.1093/molbev/msi105</citation>
     </expand>