--- a/flye.xml	Sun Dec 02 12:53:28 2018 -0500
+++ b/flye.xml	Wed Feb 05 19:37:18 2020 -0500
@@ -1,4 +1,4 @@
-<tool id="flye" name="Assembly" version="2.3.7">
+<tool id="flye" name="Flye assembly" version="2.6">
     <description>of long and error-prone reads</description>
     <macros>
         <import>macros.xml</import>
@@ -35,6 +35,12 @@
     #if $m:
         -m '$m'
     #end if
+    #if $asm:
+        --asm-coverage '$asm'
+    #end if
+    ${plasmids}
+    ${meta}
+    ${no_trestle}
     2>&1
     ]]></command>
     <inputs>
@@ -51,12 +57,16 @@
         </param>
         <param argument="-i" type="integer" value="1" label="number of polishing iterations" />
         <param argument="-m" type="integer" optional="true" label="minimum overlap between reads (default: auto)" />
+        <param name="asm" argument="--asm-coverage" type="integer" optional="true" label="reduced coverage for initial disjointing assembly" />
+        <param argument="--plasmids" type="boolean" truevalue="--plasmids" falsevalue="" checked="False" label="rescue short unassembled plasmids" />
+        <param argument="--meta" type="boolean" truevalue="--meta" falsevalue="" checked="False" label="perform metagenomic assembly" />
+        <param name="no_trestle" argument="--no-trestle" type="boolean" truevalue="--no-trestle" falsevalue="" checked="False" label="skip trestle stage" />
     </inputs>
     <outputs>
-        <data name="scaffolds" format="fasta" from_work_dir="out_dir/scaffolds.fasta" label="${tool.name} on ${on_string} (scaffolds)"/>
-        <data name="assembly_info" format="tabular" from_work_dir="out_dir/assembly_info.txt" label="${tool.name} on ${on_string} (assembly_info)"/>
+        <data name="consensus" format="fasta" from_work_dir="out_dir/assembly.fasta" label="${tool.name} on ${on_string} (consensus)"/>
         <data name="assembly_graph" format="graph_dot" from_work_dir="out_dir/assembly_graph.gv" label="${tool.name} on ${on_string} (assembly_graph)"/>
         <data name="assembly_gfa" format="txt" from_work_dir="out_dir/assembly_graph.gfa" label="${tool.name} on ${on_string} (Graphical Fragment Assembly)"/>
+        <data name="assembly_info" format="tabular" from_work_dir="out_dir/assembly_info.txt" label="${tool.name} on ${on_string} (assembly_info)"/>
         <data name="flye_log" format="txt" from_work_dir="out_dir/flye.log" label="${tool.name} on ${on_string} (log)"/>
     </outputs>
     <tests>
@@ -64,27 +74,43 @@
             <param name="inputs" ftype="fasta" value="nanopore.fasta"/>
             <param name="mode" value="--pacbio-raw"/>
             <param name="g" value="10000"/>
-            <output name="scaffolds" file="result1_scaffolds.fasta" ftype="fasta" compare="sim_size"/>
             <output name="assembly_info" file="result1_assembly_info.txt" ftype="tabular" compare="sim_size"/>
             <output name="assembly_graph" file="result1_assembly_graph.dot" ftype="graph_dot" compare="sim_size"/>
             <output name="assembly_gfa" file="result1_assembly_graph.gfa" ftype="txt" compare="sim_size"/>
+            <output name="consensus" file="result1_assembly.fasta" ftype="fasta" compare="sim_size"/>
         </test>
         <test>
             <param name="inputs" ftype="fasta" value="nanopore.fasta"/>
             <param name="mode" value="--nano-raw"/>
             <param name="g" value="10000"/>
-            <output name="scaffolds" file="result2_scaffolds.fasta" ftype="fasta" compare="sim_size"/>
             <output name="assembly_info" file="result2_assembly_info.txt" ftype="tabular" compare="sim_size"/>
             <output name="assembly_graph" file="result2_assembly_graph.dot" ftype="graph_dot" compare="sim_size"/>
             <output name="assembly_gfa" file="result2_assembly_graph.gfa" ftype="txt" compare="sim_size"/>
+            <output name="consensus" file="result2_assembly.fasta" ftype="fasta" compare="sim_size"/>
+        </test>
+        <test>
+            <param name="inputs" ftype="fasta" value="nanopore.fasta"/>
+            <param name="mode" value="--nano-corr"/>
+            <param name="g" value="10000"/>
+            <param name="i" value="2"/>
+            <param name="asm" value="40"/>
+            <output name="assembly_info" file="result3_assembly_info.txt" ftype="tabular" compare="sim_size"/>
+            <output name="assembly_graph" file="result3_assembly_graph.dot" ftype="graph_dot" compare="sim_size"/>
+            <output name="assembly_gfa" file="result3_assembly_graph.gfa" ftype="txt" compare="sim_size"/>
+            <output name="consensus" file="result3_assembly.fasta" ftype="fasta" compare="sim_size"/>
         </test>
         <test>
             <param name="inputs" ftype="fasta" value="nanopore.fasta"/>
             <param name="mode" value="--pacbio-raw"/>
             <param name="g" value="10000"/>
-            <param name="i" value="2"/>
-            <output name="scaffolds" file="result3_scaffolds.fasta" ftype="fasta" compare="sim_size"/>
-            <output name="assembly_gfa" file="result2_assembly_graph.gfa" ftype="txt" compare="sim_size"/>
+            <param name="i" value="1"/>
+            <param name="meta" value="true"/>
+            <param name="plasmids" value="true"/>
+            <param name="no-trestle" value="true"/>
+            <output name="assembly_info" file="result4_assembly_info.txt" ftype="tabular" compare="sim_size"/>
+            <output name="assembly_graph" file="result4_assembly_graph.dot" ftype="graph_dot" compare="sim_size"/>
+            <output name="assembly_gfa" file="result4_assembly_graph.gfa" ftype="txt" compare="sim_size"/>
+            <output name="consensus" file="result4_assembly.fasta" ftype="fasta" compare="sim_size"/>
         </test>
     </tests>
     <help><![CDATA[