--- a/funannotate_annotate.xml	Thu Nov 18 21:51:38 2021 +0000
+++ b/funannotate_annotate.xml	Thu Nov 25 09:37:41 2021 +0000
@@ -8,14 +8,6 @@
     </requirements>
     <version_command>funannotate check --show-versions</version_command>
     <command><![CDATA[
-
-#if $uglyTestingHack == "true":
-    ## funannotate_db contains some hard coded path, need to rewrite one for tests (not in real life when using data manager)
-    ## Need to copy too as the test_data is read only on CI
-    cp -r '${database.fields.path}' './hacked_database' &&
-    sed -i.bak 's|/tmp/prout|'`pwd`'/hacked_database|' './hacked_database/trained_species/fly/info.json' &&
-#end if
-
 funannotate annotate
 
 #if $input.input_type == 'gbk'
@@ -28,11 +20,7 @@
 
 --out output
 
-#if $uglyTestingHack == "true":
-    --database `pwd`'/hacked_database'
-#else
-    --database '$database.fields.path'
-#end if
+--database '$database.fields.path'
 
 #if $sbt:
     --sbt '${sbt}'
@@ -122,7 +110,7 @@
             </options>
         </param>
 
-        <param argument="--sbt" type="data" format="sbt" optional="true" label="NCBI submission template file" help="Create it on https://submit.ncbi.nlm.nih.gov/genbank/template/submission/ (or leave empty to use a default one, not suitable for submission at NCBI)" />
+        <param argument="--sbt" type="data" format="txt" optional="true" label="NCBI submission template file" help="Create it on https://submit.ncbi.nlm.nih.gov/genbank/template/submission/ (or leave empty to use a default one, not suitable for submission at NCBI)" />
 
         <param argument="--eggnog" type="data" format="tabular" optional="true" label="Eggnog-mapper annotations file" help="'annotations' output from 'eggNOG Mapper' tool" />
         <param argument="--antismash" type="data" format="genbank" optional="true" label="antiSMASH secondary metabolism results" help="Genbank output from 'Antismash' tool" />
@@ -160,9 +148,6 @@
             <option value="need_curating">TSV file of Gene Name/Product defines that need to be curated</option>
             <option value="new_names_passed">TSV file of Gene Name/Product deflines that passed tbl2asn but are not in Gene2Products database.</option>
         </param>
-
-        <!-- Need this to change path in the test funannotate_db -->
-        <param type="hidden" name="uglyTestingHack" value="" />
     </inputs>
     <outputs>
         <data name='gbk' format='genbank' label="${tool.name} on ${on_string}: annotated genome (genbank)" from_work_dir="out.gbk">