--- a/vapor.xml	Wed Nov 16 13:41:01 2022 +0000
+++ b/vapor.xml	Thu Aug 28 17:53:36 2025 +0000
@@ -1,31 +1,24 @@
-<tool id="vapor" name="VAPOR" version="@TOOL_VERSION@+galaxy3" profile="21.05">
+<tool id="vapor" name="VAPOR" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>
         Classify Influenza samples from short reads sequence data
     </description>
     <macros>
-        <token name="@TOOL_VERSION@">1.0.2</token>
+        <token name="@TOOL_VERSION@">1.0.3</token>
+        <token name="@VERSION_SUFFIX@">0</token>
+        <token name="@PROFILE@">23.0</token>
     </macros>
     <xrefs>
         <xref type="bio.tools">vapor</xref>
     </xrefs>
     <requirements>
         <requirement type="package" version="@TOOL_VERSION@">vapor</requirement>
-        <!-- gawk only required for circumventing current bug in command line
-        tool => remove once fixed (see command section below) -->
-        <requirement type="package" version="5.1.0">gawk</requirement>
     </requirements>
+    <!-- hack needed for version command because vapor does sys.exit(1)
+    after printing version -->
+    <version_command>( vapor.py -v || true )</version_command>
     <command detect_errors="exit_code"><![CDATA[
         #set $total_refs = int($fasta_file.metadata.sequences)
 
-        ## The next two lines for on the fly uppercasing are a workaround for a bug
-        ## in vapor 1.0.2, which caused sequence comparisons to be case-sensitive.
-        ## Got fixed upstream in:
-        ## https://github.com/connor-lab/vapor/commit/b5ec5857cbf53ed45ca7487dac2b4b85ecfe33ea
-        ## but unfortunately no release has been tagged since.
-        ## Remove with next release!!
-        awk '{ if ($0 !~ />/) {print toupper($0)} else {print $0} }' '$fasta_file' > ref_upper.fa &&
-        #set $fasta_file = 'ref_upper.fa'
-
         #if str($fastq_input.fastq_input_selector) == "paired"
             #set r1_ext = $fastq_input.fastq1.extension
             #set r2_ext = $fastq_input.fastq2.extension
@@ -97,7 +90,7 @@
         <data name="output_scores" from_work_dir="out_file" format="tabular" label="${tool.name} on ${on_string}: closest reference scores">
             <filter>output_type == "scores"</filter>
             <actions>
-                <action name="column_names" type="metadata" default="% of query bases in reads,Total score,Query length,Mean score,Reads after culling,Query description" />
+                <action name="column_names" type="metadata" default="Fraction of query bases found in reads,Total score,Query length,Mean score,Reads after culling,Query description" />
             </actions>
         </data>
         <data name="output_fasta" from_work_dir="out_file" format="fasta" label="${tool.name} on ${on_string}: closest reference fasta">
@@ -171,7 +164,7 @@
 VAPOR is a tool for classification of Influenza samples from raw short read sequence data for downstream bioinformatics analysis.
 VAPOR works on a fasta file of full-length reference sequences for a given genome segment and a set of sequenced reads, and attempts to retrieve the reference that is closest to the sequenced strain.
 
-`sub_sample` is not an option here (compared to the tool on GitHub), since you can always build a workflow that preprocesses your reads to a (random) subsample. You can use this output as your reads file for VAPOR.
+The `-s` option of the command-line tool for sub-sampling input reads is not exposed here since you can always build a workflow that preprocesses your reads to a (random) subsample. You can use this output as your reads file for VAPOR.
     ]]>    </help>
     <citations>
         <citation type="doi">10.1093/bioinformatics/btz814</citation>