--- a/funannotate_annotate.xml	Fri Oct 20 10:07:28 2023 +0000
+++ b/funannotate_annotate.xml	Wed Nov 01 09:52:58 2023 +0000
@@ -3,6 +3,7 @@
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="biotools" />
     <requirements>
         <expand macro="requirements" />
     </requirements>
@@ -66,7 +67,7 @@
 #if $remove:
     --remove '${remove}'
 #end if
-
+--header_length $header_length
 --cpus \${GALAXY_SLOTS:-2}
 
 &&
@@ -112,8 +113,6 @@
             </when>
         </conditional>
 
-
-
         <param name="database" label="Funannotate database" type="select">
             <options from_data_table="funannotate">
                 <column name="value" index="0" />
@@ -144,6 +143,7 @@
         <param argument="--fix" type="data" format="tabular" optional="true" label="Gene/Product names fixed" help="TSV: GeneID	Name	Product" />
         <param argument="--remove" type="data" format="tabular" optional="true" label="Gene/Product names to remove" help="TSV: Gene	Product" />
 
+        <param argument="--header_length" type="integer" value="16" min="1" label="Maximum length of FASTA headers" help="The NCBI max FASTA header length is 16. Increase if you don't submit to NCBI." />
         <param name="outputs" type="select" optional="true" multiple="true" label="Which outputs should be generated">
             <option value="gbk" selected="true">Annotated genome (genbank)</option>
             <option value="annotations">TSV file of all annotations added to genome. (i.e. import into excel)</option>