# HG changeset patch
# User petr-novak
# Date 1701181923 0
# Node ID d5508ce50c497e03cb90d2129983b194e32db1a9
# Parent  08b5e23859ed171b5982c24b11125d5c93e45307
planemo upload commit 398baa926d7864efeb2c349c52827fd6988e60e6-dirty

diff -r 08b5e23859ed -r d5508ce50c49 dante_ltr_search.xml
--- a/dante_ltr_search.xml	Mon Oct 23 12:39:09 2023 +0000
+++ b/dante_ltr_search.xml	Tue Nov 28 14:32:03 2023 +0000
@@ -12,6 +12,12 @@
         mv output.gff3 $te_ltr_gff
         &&
         mv output_statistics.csv $statistics
+        &&
+        if [ -f output_summary.html ]; then cp output_summary.html $html_report; fi
+        &&
+        mkdir -p ${html_report.extra_files_path}
+        &&
+        if [ -d output_summary_plots ]; then cp -r output_summary_plots ${html_report.extra_files_path}/; fi
     ]]></command>
     <inputs>
         <param type="data" name="dante" format="gff3" label="GFF3 output from DANTE pipeline - full output"/>
@@ -23,6 +29,8 @@
         based on DANTE annotation $dante.hid and reference $reference.hid" />
         <data name="statistics" format="tabular" label="LTR retrotransposons detection
         summary based on $dante.hid and reference $reference.hid" />
+        <data name="html_report" format="html" label="LTR retrotransposons detection on $dante.hid and $reference.hid report" />
+
     </outputs>
     <help><![CDATA[
         This tool uses output from DANTE annotation pipeline to identify full length LTR
diff -r 08b5e23859ed -r d5508ce50c49 macros.xml
--- a/macros.xml	Mon Oct 23 12:39:09 2023 +0000
+++ b/macros.xml	Tue Nov 28 14:32:03 2023 +0000
@@ -1,6 +1,6 @@
 <macros>
-    <token name="@TOOL_VERSION@">2.3.8</token>
-    <token name="@REQUIREMENT_VERSION@">0.2.3.8</token>
+    <token name="@TOOL_VERSION@">3.5.0</token>
+    <token name="@REQUIREMENT_VERSION@">0.3.5.0</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@REQUIREMENT_VERSION@">dante_ltr</requirement>