--- a/funannotate_annotate.xml	Mon Dec 11 19:18:59 2023 +0000
+++ b/funannotate_annotate.xml	Sun Feb 11 00:08:00 2024 +0000
@@ -1,4 +1,4 @@
-<tool id="funannotate_annotate" name="Funannotate functional" profile="20.01" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
+<tool id="funannotate_annotate" name="Funannotate functional" profile="20.01" version="@TOOL_VERSION@+galaxy5">
     <description>annotation</description>
     <macros>
         <import>macros.xml</import>
@@ -72,27 +72,14 @@
 
 &&
 
-## funannotate sometimes leaves multiple *part.tbl and *part.sqn files
+## Funannotate sometimes leaves multiple *part.tbl and *part.sqn files:
 ## https://github.com/nextgenusfs/funannotate/issues/777
+## The partial tbl files are combined by funannotate and are deleted below.
+## The sqn files are discrete and are collected with discover_datasets.
 find output/annotate_results 
--regex ".*part_[0-9]+\.\(sqn\|tbl\)$"
+-regex ".*part_[0-9]+\.\(tbl\)$"
 -delete
 
-&&
-
-mv output/annotate_results/*.gbk out.gbk &&
-mv output/annotate_results/*.annotations.txt out.annotations.txt &&
-mv output/annotate_results/*.contigs.fsa out.contigs.fsa &&
-mv output/annotate_results/*.agp out.agp &&
-mv output/annotate_results/*.tbl out.tbl &&
-mv output/annotate_results/*.sqn out.sqn &&
-mv output/annotate_results/*.scaffolds.fa out.scaffolds.fa &&
-mv output/annotate_results/*.proteins.fa out.proteins.fa &&
-mv output/annotate_results/*.mrna-transcripts.fa out.mrna-transcripts.fa &&
-mv output/annotate_results/*.cds-transcripts.fa out.cds-transcripts.fa &&
-mv output/annotate_results/*.gff3 out.gff3 &&
-mv output/annotate_results/*.discrepency.report.txt out.discrepency.report.txt &&
-mv output/annotate_results/*.stats.json out.stats.json
     ]]></command>
     <inputs>
 
@@ -164,43 +151,44 @@
         </param>
     </inputs>
     <outputs>
-        <data name='gbk' format='genbank' label="${tool.name} on ${on_string}: annotated genome (genbank)" from_work_dir="out.gbk">
+        <data name='gbk' format='genbank' label="${tool.name} on ${on_string}: annotated genome (genbank)" from_work_dir="output/annotate_results/*.gbk">
             <filter>outputs and 'gbk' in outputs</filter>
         </data>
-        <data name='annot' format='tabular' label="${tool.name} on ${on_string}: all annotations" from_work_dir="out.annotations.txt">
+        <data name='annot' format='tabular' label="${tool.name} on ${on_string}: all annotations" from_work_dir="output/annotate_results/*.annotations.txt">
             <filter>outputs and 'annotations' in outputs</filter>
         </data>
-        <data name='contigs_fsa' format='fasta' label="${tool.name} on ${on_string}: contigs fasta, split at gaps" from_work_dir="out.contigs.fsa">
+        <data name='contigs_fsa' format='fasta' label="${tool.name} on ${on_string}: contigs fasta, split at gaps" from_work_dir="output/annotate_results/*.contigs.fsa">
             <filter>outputs and 'contigs_fsa' in outputs</filter>
         </data>
-        <data name='agp' format='tabular' label="${tool.name} on ${on_string}: AGP file" from_work_dir="out.agp">
+        <data name='agp' format='tabular' label="${tool.name} on ${on_string}: AGP file" from_work_dir="output/annotate_results/*.agp">
             <filter>outputs and 'agp' in outputs</filter>
         </data>
-        <data name='tbl' format='txt' label="${tool.name} on ${on_string}: NCBI tbl annotation file" from_work_dir="out.tbl">
+        <data name='tbl' format='txt' label="${tool.name} on ${on_string}: NCBI tbl annotation file" from_work_dir="output/annotate_results/*.tbl">
             <filter>outputs and 'tbl' in outputs</filter>
         </data>
-        <data name='sqn' format='txt' label="${tool.name} on ${on_string}: NCBI Sequin genome" from_work_dir="out.sqn">
+        <collection name="sqn" type="list" label="${tool.name} on ${on_string}: NCBI Sequin genome files">
+            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.sqn" directory="output/annotate_results" format="txt" recurse="false"/>
             <filter>outputs and 'sqn' in outputs</filter>
-        </data>
-        <data name='fa_scaffolds' format='fasta' label="${tool.name} on ${on_string}: scaffolds sequences" from_work_dir="out.scaffolds.fa">
+        </collection>
+        <data name='fa_scaffolds' format='fasta' label="${tool.name} on ${on_string}: scaffolds sequences" from_work_dir="output/annotate_results/*.scaffolds.fa">
             <filter>outputs and 'scaffolds_fa' in outputs</filter>
         </data>
-        <data name='fa_proteins' format='fasta' label="${tool.name} on ${on_string}: protein sequences" from_work_dir="out.proteins.fa">
+        <data name='fa_proteins' format='fasta' label="${tool.name} on ${on_string}: protein sequences" from_work_dir="output/annotate_results/*.proteins.fa">
             <filter>outputs and 'proteins_fa' in outputs</filter>
         </data>
-        <data name='fa_transcripts_mrna' format='fasta' label="${tool.name} on ${on_string}: transcript mRNA sequences" from_work_dir="out.mrna-transcripts.fa">
+        <data name='fa_transcripts_mrna' format='fasta' label="${tool.name} on ${on_string}: transcript mRNA sequences" from_work_dir="output/annotate_results/*.mrna-transcripts.fa">
             <filter>outputs and 'mrna_transcripts_fa' in outputs</filter>
         </data>
-        <data name='fa_transcripts_cds' format='fasta' label="${tool.name} on ${on_string}: transcript CDS sequences" from_work_dir="out.cds-transcripts.fa">
+        <data name='fa_transcripts_cds' format='fasta' label="${tool.name} on ${on_string}: transcript CDS sequences" from_work_dir="output/annotate_results/*.cds-transcripts.fa">
             <filter>outputs and 'cds_transcripts_fa' in outputs</filter>
         </data>
-        <data name='gff3' format='gff3' label="${tool.name} on ${on_string}: annotation (GFF3)" from_work_dir="out.gff3">
+        <data name='gff3' format='gff3' label="${tool.name} on ${on_string}: annotation (GFF3)" from_work_dir="output/annotate_results/*.gff3">
             <filter>outputs and 'gff3' in outputs</filter>
         </data>
-        <data name='tbl2asn_report' format='txt' label="${tool.name} on ${on_string}: tbl2asn summary report of annotated genome" from_work_dir="out.discrepency.report.txt">
+        <data name='tbl2asn_report' format='txt' label="${tool.name} on ${on_string}: tbl2asn summary report of annotated genome" from_work_dir="output/annotate_results/*.discrepency.report.txt">
             <filter>outputs and 'discrepency' in outputs</filter>
         </data>
-        <data name='stats' format='json' label="${tool.name} on ${on_string}: stats" from_work_dir="out.stats.json">
+        <data name='stats' format='json' label="${tool.name} on ${on_string}: stats" from_work_dir="output/annotate_results/*.stats.json">
             <filter>outputs and 'gbk' in outputs</filter>
         </data>
         <data name='must_fix' format='json' label="${tool.name} on ${on_string}: Gene Name/Product must-fix" from_work_dir="output/annotate_results/Gene2Products.must-fix.txt">
@@ -248,11 +236,13 @@
                     <has_text text="locus_tag" />
                 </assert_contents>
             </output>
-            <output name="sqn">
-                <assert_contents>
-                    <has_text text="Seq-submit" />
-                </assert_contents>
-            </output>
+            <output_collection name="sqn" type="list">
+                <element name="Genus_species">
+                    <assert_contents>
+                        <has_text text="Seq-submit" />
+                    </assert_contents>
+                </element>   
+            </output_collection>
             <output name="fa_scaffolds">
                 <assert_contents>
                     <has_text text=">sample" />
@@ -340,11 +330,13 @@
                     <has_text text="locus_tag" />
                 </assert_contents>
             </output>
-            <output name="sqn">
-                <assert_contents>
-                    <has_text text="Seq-submit" />
-                </assert_contents>
-            </output>
+            <output_collection name="sqn" type="list">
+                <element name="Genus_species">
+                    <assert_contents>
+                        <has_text text="Seq-submit" />
+                    </assert_contents>
+                </element>   
+            </output_collection>
             <output name="fa_scaffolds">
                 <assert_contents>
                     <has_text text=">sample" />