--- a/maker.xml	Tue Jan 05 08:59:28 2021 +0000
+++ b/maker.xml	Tue Jun 22 10:14:40 2021 +0000
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool id="maker" name="Maker" profile="16.04" version="@VERSION@">
+<tool id="maker" name="Maker" profile="16.04" version="@VERSION@+galaxy@SUFFIX_VERSION@">
     <description>genome annotation pipeline</description>
     <macros>
         <import>macros.xml</import>
@@ -44,7 +44,7 @@
             MPI_CMD="mpiexec -n \${GALAXY_SLOTS:-4}";
         fi &&
 
-        \${MPI_CMD} maker --ignore_nfs_tmp maker_opts.ctl maker_bopts.ctl maker_exe.ctl < /dev/null
+        \${MPI_CMD} maker --ignore_nfs_tmp $advanced.fix_nucleotides maker_opts.ctl maker_bopts.ctl maker_exe.ctl < /dev/null
 
         &&
 
@@ -453,6 +453,7 @@
         </section>
 
         <section name="advanced" title="Advanced settings" expanded="False">
+            <param name="fix_nucleotides" argument="-fix_nucleotides" type="boolean" truevalue="-fix_nucleotides" falsevalue="" checked="false" label="Fix nucleotides" help="This will replace non-IUPAC characters with 'N's."/>
             <param name="other_gff" type="data" format="gff" label="Extra features to pass-through to final Maker generated GFF3 file" optional="True"/>
             <param name="alt_peptide" type="text" value="C" size="1" label="Amino acid used to replace non-standard amino acids in BLAST databases">
                 <validator type="regex" message="This must be a single uppercase letter">^[A-Z]$</validator>
@@ -563,6 +564,15 @@
             <output name="output_gff" file="annot_dfam_up.gff3"/>
             <output name="output_evidences" file="evidences_norm_dfam_up.gff3" compare="sim_size"/>
         </test>
+        <test>
+            <param name="genome" value="genome.fasta"/>
+            <param name="est_evidences|est" value="non_IUPAC.fasta"/>
+            <param name="est_evidences|est2genome" value="1"/>
+            <param name="repeat_masking|repeat_source|source_type" value="no"/>
+            <param name="advanced|fix_nucleotides" value="true"/>
+            <output name="output_gff" file="annot_fix_nucleotides.gff3"/>
+            <output name="output_evidences" file="evidences_fix_nucletides.gff3" compare="sim_size"/>
+        </test>
     </tests>
     <help><![CDATA[
         MAKER is a portable and easily configurable genome annotation pipeline. Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. MAKER identifies repeats, aligns ESTs and proteins to a genome, produces ab-initio gene predictions and automatically synthesizes these data into gene annotations having evidence-based quality values. MAKER is also easily trainable: outputs of preliminary runs can be used to automatically retrain its gene prediction algorithm, producing higher quality gene-models on seusequent runs. MAKER's inputs are minimal and its ouputs can be directly loaded into a GMOD database. They can also be viewed in the Apollo genome browser; this feature of MAKER provides an easy means to annotate, view and edit individual contigs and BACs without the overhead of a database. MAKER should prove especially useful for emerging model organism projects with minimal bioinformatics expertise and computer resources.