--- a/bealign.xml	Sat Nov 27 10:07:57 2021 +0000
+++ b/bealign.xml	Sun Feb 25 19:30:06 2024 +0000
@@ -1,13 +1,11 @@
-<?xml version="1.0"?>
 <tool id="bioext_bealign" name="Align sequences" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>to a reference using a codon alignment algorithm</description>
     <macros>
         <import>macros.xml</import>
-        <token name="@VERSION_SUFFIX@">0</token>
     </macros>
     <expand macro="requirements">
-        <requirement type="package" version="5.1.0">gawk</requirement>
-        <requirement type="package" version="1.14">samtools</requirement>
+        <requirement type="package" version="5.3.0">gawk</requirement>
+        <requirement type="package" version="1.19.2">samtools</requirement>
     </expand>
     <version_command>bealign --version</version_command>
     <command detect_errors="exit_code">
@@ -143,7 +141,7 @@
                 <option value="dna">DNA</option>
                 <option value="amino">Amino acids</option>
             </param>
-            <param name="score_matrix" argument="--score-matrix" type="select" label="Parametrize using score matrix">
+            <param argument="--score-matrix" type="select" label="Parametrize using score matrix">
                 <option value="BLOSUM62" selected="True">Blocks substitution</option>
                 <option value="DNA65">DNA, 65% expected identity</option>
                 <option value="DNA70">DNA, 70% expected identity</option>
@@ -155,8 +153,8 @@
                 <option value="HIV_BETWEEN_F">HIV between+F</option>
             </param>
             <param argument="--discard" type="boolean" checked="False" truevalue="--discard" falsevalue="" label="Output discarded sequences to a separate dataset" />
-            <param name="reverse_complement" argument="--reverse-complement" type="boolean" checked="False" truevalue="--reverse-complement" falsevalue="" label="Also try to align against reverse complement of reference" />
-            <param name="keep_reference" argument="--keep-reference" type="boolean" checked="False" truevalue="--keep-reference" falsevalue="" label="Include reference as first sequence in aligned BAM" />
+            <param argument="--reverse-complement" type="boolean" checked="False" truevalue="--reverse-complement" falsevalue="" label="Also try to align against reverse complement of reference" />
+            <param argument="--keep-reference" type="boolean" checked="False" truevalue="--keep-reference" falsevalue="" label="Include reference as first sequence in aligned BAM" />
         </section>
     </inputs>
     <outputs>
@@ -165,21 +163,21 @@
             <filter>background_source['sequences']</filter>
         </data>
         <data name="saved_reference" format="fasta" label="${tool.name} on ${on_string} - Reference" >
-            <filter>select_reference['save_reference']</filter>
+            <filter>select_reference['reference_type'] == 'preset' and select_reference['save_reference']</filter>
         </data>
         <data name="discarded_reads" format="fasta">
             <filter>advanced['discard']</filter>
         </data>
     </outputs>
     <tests>
-        <test>
+        <test expect_num_outputs="1">
             <param name="input" ftype="fasta" value="query.fa" />
             <param name="reference_type" value="dataset" />
             <param name="score_matrix" value="HIV_BETWEEN_F" />
             <param name="reference" ftype="fasta" value="reference.fa" />
             <output name="output" file="bealign-out1.bam" ftype="bam" lines_diff="2" />
         </test>
-        <test>
+        <test expect_num_outputs="1">
             <param name="input" ftype="fasta" value="query.fa" />
             <param name="reference_type" value="preset" />
             <param name="reference" value="CoV2-nsp8" />