# HG changeset patch
# User iuc
# Date 1634801540 0
# Node ID 33092577d65dd643f8af01bc6dc273b5fc31bc96
# Parent  1a59958c1f7620141a0b141644babde94a5e657f
"planemo upload commit c70e2e82ba7d3f9ee43c101ab267cdf0847d8864"

diff -r 1a59958c1f76 -r 33092577d65d funannotate_predict.xml
--- a/funannotate_predict.xml	Mon Oct 04 19:37:44 2021 +0000
+++ b/funannotate_predict.xml	Thu Oct 21 07:32:20 2021 +0000
@@ -64,9 +64,9 @@
     --transcript_evidence $est_list
 #end if
 
-#if $evidences.prot_evidence == 'custom':
+#if $evidences.prot_evidence.prot_evidence_source == 'custom':
     --protein_evidence
-    #for $protev in $evidences.protein_evidence:
+    #for $protev in $evidences.prot_evidence.protein_evidence:
         '${protev}'
     #end for
 #end if
@@ -506,9 +506,12 @@
                 <has_text text="Aligning transcript evidence to genome with minimap2"/>
                 <has_text text="Found 16 alignments, wrote GFF3 and Augustus hints to file"/>
                 <has_text text="Extracting hints from RNA-seq BAM file using bam2hints"/>
-                <has_text text="Mapping 13 proteins to genome using diamond and exonerate"/>
-                <has_text text="Found 4 preliminary alignments --> aligning with exonerate"/>
+                <has_text text="Mapping 16 proteins to genome using diamond and exonerate"/>
+                <has_text text="Found 21 preliminary alignments --> aligning with exonerate"/>
             </assert_stderr>
+            <assert_command>
+                <has_text text="--protein_evidence"/>
+            </assert_command>
         </test>
 
         <!-- proteins -->
@@ -577,9 +580,12 @@
                 <not_has_text text="Aligning transcript evidence to genome with minimap2"/>
                 <not_has_text text="Found 16 alignments, wrote GFF3 and Augustus hints to file"/>
                 <not_has_text text="Extracting hints from RNA-seq BAM file using bam2hints"/>
-                <has_text text="Mapping 13 proteins to genome using diamond and exonerate"/>
-                <has_text text="Found 4 preliminary alignments --> aligning with exonerate"/>
+                <has_text text="Mapping 16 proteins to genome using diamond and exonerate"/>
+                <has_text text="Found 21 preliminary alignments --> aligning with exonerate"/>
             </assert_stderr>
+            <assert_command>
+                <has_text text="--protein_evidence"/>
+            </assert_command>
         </test>
     </tests>
     <help><![CDATA[