--- a/metaeuk_easy_predict.xml	Wed Sep 01 07:37:08 2021 +0000
+++ b/metaeuk_easy_predict.xml	Thu Oct 21 16:09:42 2021 +0000
@@ -4,7 +4,7 @@
         <xref type="bio.tools">MetaEuk</xref>
     </xrefs>
     <macros>
-        <token name="@TOOL_VERSION@">4.a0f584d</token>
+        <token name="@TOOL_VERSION@">5.34c21f2</token>
     </macros>
     <requirements>
         <requirement type="package" version="@TOOL_VERSION@">metaeuk</requirement>
@@ -25,7 +25,9 @@
             --max-intron '${adv.max_intron}'
             --min-intron '${adv.min_intron}'
         #end if
+        --write-frag-coords $write_frag_coords
         && mv output.fasta.codon.fas '$output'
+        && mv output.fasta.gff '$gff_output'
     ]]></command>
     <inputs>
         <param name="contigs" type="data" format="fasta" label="Contigs to search again" />
@@ -46,9 +48,14 @@
             <when value="no">
             </when>
         </conditional>
+        <param name="write_frag_coords" type="select" value="0" label="Write the contig coords of the stop-to-stop fragment in which putative exon lies" help="The fragment coordinates in square brackets refer to the original fragment in which the exon was found." >
+            <option value="0">Yes</option>
+            <option value="1">No</option>
+        </param>
     </inputs>
     <outputs>
         <data name="output" format="fasta" />
+        <data name="gff_output" format="gff" />
     </outputs>
 
     <tests>
@@ -56,10 +63,12 @@
             <param name="contigs" ftype="fasta" value="contigs.fna" />
             <param name="query" ftype="fasta" value="proteins.faa" />
             <output name="output" ftype="fasta" value="output.fasta" />
+            <output name="gff_output" ftype="gff" value="output.gff" />
         </test>
         <test>
             <param name="contigs" ftype="fasta" value="contigs.fna" />
             <param name="query" ftype="fasta" value="proteins.faa" />
+            <param name="write_frag_coords" value="1" />
             <conditional name="adv">
                 <param name="adv_options" value="yes" />
                 <param name="max_intron" value="1000" />
@@ -67,7 +76,8 @@
             <assert_command>
                 <has_text text="--max-intron '1000'" />
             </assert_command>            
-            <output name="output" ftype="fasta" value="output.fasta" />
+            <output name="output" ftype="fasta" value="output_w_frag_coords.fasta" />
+            <output name="gff_output" ftype="gff" value="output.gff" />
         </test>
     </tests>
     <help><![CDATA[