# HG changeset patch
# User kkonganti
# Date 1701273222 18000
# Node ID ddf7a172bf300d33b98ce7fe85b8ac759f48d759
# Parent  5eaaf749472cf2fbcb7c283324d241dafd538128
"planemo upload"

diff -r 5eaaf749472c -r ddf7a172bf30 cfsan_cronology.xml
--- a/cfsan_cronology.xml	Tue Nov 28 15:26:51 2023 -0500
+++ b/cfsan_cronology.xml	Wed Nov 29 10:53:42 2023 -0500
@@ -83,12 +83,12 @@
     </inputs>
     <outputs>
         <data name="multiqc_report" format="html" label="cronology: MultiQC Report on ${on_string}" from_work_dir="multiqc_report.html"/>
-        <data name="mashtree" format="nwk" label="cronology: Genome distance based tree on ${on_string}" from_work_dir="hitsTree.dnd"/>
+        <data name="mashtree" format="newick" label="cronology: Genome distance based tree on ${on_string}" from_work_dir="hitsTree.dnd"/>
         <collection name="itol_metadata" type="list" label="cronology: iTOL Metadata: ${on_string}">
             <discover_datasets pattern="(?P&lt;name&gt;.*)\.txt" ext="txt" directory="./cpipes-output/cat_unique" match_relative_path="true" />
         </collection>
         <collection name="gene_models" type="list" label="cronology: Predicted gene models: ${on_string}">
-            <discover_datasets pattern="(?P&lt;name&gt;.*)\.gff" ext="gff" directory="./cpipes-output/prokka" recurse="true" match_relative_path="true" />
+            <discover_datasets pattern=".*\/(?P&lt;name&gt;.*)\.gff" ext="gff" directory="./cpipes-output/prokka" recurse="true" match_relative_path="true" />
         </collection>
         <collection name="assemblies" type="list" label="cronology: Polished genome assemblies: ${on_string}">
             <discover_datasets pattern="(?P&lt;name&gt;.*)\.fa" ext="fa" directory="./cpipes-output/polypolish" match_relative_path="true" />