--- a/busco.xml	Fri Apr 14 08:13:46 2023 +0000
+++ b/busco.xml	Tue Nov 14 13:03:37 2023 +0000
@@ -35,6 +35,7 @@
 --cpu \${GALAXY_SLOTS:-4}
 --evalue ${adv.evalue}
 --limit ${adv.limit}
+--contig_break ${adv.contig_break}
 
 #if $lineage_conditional.selector == 'cached':
     --offline
@@ -48,6 +49,7 @@
 #else if $lineage.lineage_mode == "select_lineage":
     --lineage_dataset '${lineage.lineage_dataset}'
 #end if
+
 #if $busco_mode.mode == 'geno' and $busco_mode.use_augustus.use_augustus_selector == 'yes':
 
     ${busco_mode.use_augustus.long}
@@ -60,6 +62,12 @@
     #end if
 #end if
 
+#if str( $busco_mode.mode ) == "geno":
+    #if $busco_mode.miniprot:
+        --miniprot
+    #end if
+#end if
+    
 #if $outputs and 'image' in $outputs:
     &&
     mkdir BUSCO_summaries
@@ -78,6 +86,7 @@
     cat busco_galaxy/run_*/busco_sequences/*busco_sequences/*.gff >> busco_output.gff 2> /dev/null || true
 #end if
 
+
 ]]>    </command>
     <inputs>
         <param type="data" name="input" format="fasta" label="Sequences to analyse" help="Can be an assembled genome or transcriptome (DNA), or protein sequences from an annotated gene set." />
@@ -102,6 +111,7 @@
                 <option value="prot">annotated gene sets (protein)</option>
             </param>
             <when value="geno">
+                <param name="miniprot" type="boolean" checked="false" label="Generate miniprot output"/>
                 <conditional name="use_augustus">
                     <param name="use_augustus_selector" type="select" label="Use Augustus instead of Metaeuk">
                         <option value="yes">Yes, use Augustus</option>
@@ -162,8 +172,10 @@
         <section name="adv" title="Advanced Options" expanded="False">
             <param argument="--evalue" type="float" value="0.001" min="0" max="1" label="E-value cutoff for BLAST searches." />
             <param argument="--limit" type="integer" value="3" label="How many candidate regions to consider" />
+            <param argument="--contig_break" type="integer" value="10" label="Number of contiguous Ns to signify a break between contigs"/>
         </section>
     </inputs>
+
     <outputs>
         <data name='busco_sum' format='txt' label="${tool.name} on ${on_string}: short summary" from_work_dir="busco_galaxy/run_*/short_summary.txt">
             <filter>outputs and 'short_summary' in outputs</filter>
@@ -178,7 +190,11 @@
         <data name='busco_gff' format='gff3' label="${tool.name} on ${on_string}: GFF" from_work_dir="busco_output.gff">
             <filter>outputs and 'gff' in outputs</filter>
         </data>
+        <data name='busco_miniprot' format='gff3' label="${tool.name} on ${on_string}: Miniprot" from_work_dir="busco_galaxy/run_*/miniprot_output/*.gff">
+            <filter>busco_mode['mode'] == 'geno' and busco_mode['miniprot']</filter>
+        </data>               
     </outputs>
+    
     <tests>
         <test expect_num_outputs="4">
             <param name="input" value="genome.fa" />
@@ -244,7 +260,7 @@
             <output name="summary_image" file="transcriptome_results/summary.png" compare="sim_size" />
             <output name="busco_gff" file="transcriptome_results/out.gff" compare="diff" />
         </test>
-        <test expect_num_outputs="3">
+        <test expect_num_outputs="4">
             <param name="input" value="genome.fa" />
             <conditional name="lineage">
                 <param name="lineage_mode" value="select_lineage" />
@@ -252,6 +268,7 @@
             </conditional>
             <conditional name="busco_mode">
                 <param name="mode" value="geno" />
+                <param name="miniprot" value="true"/>
                 <conditional name="use_augustus">
                     <param name="use_augustus_selector" value="yes" />
                     <conditional name="aug_prediction">
@@ -269,6 +286,8 @@
                     <has_text text="##gff-version 3" />
                 </assert_contents>
             </output>
+            <!-- The miniprot.gff file is too large. A file containing only the first 1000 lines is used for this test. -->
+            <output name="busco_miniprot" file="genome_results/miniprot_1000.gff" compare="contains" lines_diff="304463"/>
         </test>
         <test expect_num_outputs="3">
             <param name="input" value="genome.fa" />