--- a/funannotate_compare.xml	Wed Jun 26 09:38:43 2024 +0000
+++ b/funannotate_compare.xml	Fri Mar 07 22:36:43 2025 +0000
@@ -9,6 +9,13 @@
     </requirements>
     <version_command>funannotate check --show-versions</version_command>
     <command><![CDATA[
+## Needed by some subprocess invoked internally
+## https://github.com/nextgenusfs/funannotate/issues/905
+export FUNANNOTATE_DB='$database.fields.path' &&
+
+## show detailed info about the reference DB on stdout
+funannotate database &&
+
 #set $inputs = ""
 #for i, f in enumerate($input):
     #set $inputs = $inputs + " input" + str($i) + ".gbk"
@@ -28,7 +35,9 @@
     --run_dnds ${run_dnds}
 #end if
 
-## need to add --outgroup option some day (hard to get an up to date/customizable list)
+#if $outgroup
+    --outgroup '$outgroup'
+#end if
 
 --go_fdr ${go_fdr}
 
@@ -62,7 +71,7 @@
                 <column name="value" index="0" />
                 <column name="name" index="1" />
                 <column name="path" index="3" />
-                <filter type="sort_by" column="0" />
+                <filter type="sort_by" column="0" reverse_sort_order="true"/>
                 <filter type="static_value" column="2" value="1.0" />
             </options>
         </param>
@@ -76,6 +85,14 @@
         <param argument="--go_fdr" type="float" value="0.05" label="P-value for FDR GO-enrichment" />
         <param argument="--heatmap_stdev" type="float" value="1.0" label="Cut-off for heatmap" />
         <param argument="--num_orthos" type="integer" value="500" label="Number of Single-copy orthologs to use for ML" />
+        <param argument="--outgroup" type="select" optional="true" label="Outgroup species" help="Name of species to use for ML outgroup. Default: no outgroup">
+            <options from_data_table="funannotate_options">
+                <column name="value" index="0" />
+                <column name="name" index="1" />
+                <filter type="static_value" column="2" value="outgroup"/>
+                <filter type="param_value" column="3" ref="database"/>
+            </options>
+        </param>
         <param argument="--proteinortho" type="data" format="tabular" optional="true" label="Proteinortho POFF results" help="TSV format, if available"/>
 
         <conditional name="ml">
@@ -122,6 +139,7 @@
             <param name="input" value="compare/Genus_species.gbk,compare/Other_species.gbk,compare/Other_beast.gbk,compare/Yet_another.gbk" />
             <param name="database" value="2021-07-20-120000" />
             <param name="run_dnds" value="full" />
+            <param name="outgroup" value="botrytis_cinerea.dikarya"/>
             <conditional name="ml">
                 <param name="ml_method" value="raxml" />
             </conditional>