--- a/bwa.xml	Fri Aug 19 18:51:56 2022 +0000
+++ b/bwa.xml	Fri May 17 21:09:07 2024 +0000
@@ -1,9 +1,6 @@
 <?xml version="1.0"?>
-<tool id="bwa" name="Map with BWA" version="@VERSION@.5">
+<tool id="bwa" name="Map with BWA" version="@TOOL_VERSION@" profile="22.05">
     <description>- map short reads (&lt; 100 bp) against reference genome</description>
-    <xrefs>
-        <xref type="bio.tools">bwa</xref>
-    </xrefs>
     <macros>
         <import>read_group_macros.xml</import>
         <import>bwa_macros.xml</import>
@@ -77,6 +74,7 @@
             </when>
         </xml>
     </macros>
+    <expand macro="bio_tools"/>
     <expand macro="requirements"/>
     <expand macro="stdio"/>
     <command>
@@ -314,41 +312,42 @@
         </data>
     </outputs>
     <tests>
-        <test>
+        <!-- `samtools sort` in the new update adds PG lines to the output so the lines_diff is changed from "2" to "4" -->
+        <test expect_num_outputs="1">
             <param name="reference_source_selector" value="history"/>
             <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
             <param name="input_type_selector" value="single"/>
             <param name="fastq_input1" ftype="fasta" value="bwa-mem-fasta1.fa"/>
             <param name="analysis_type_selector" value="illumina"/>
-            <output name="bam_output" ftype="bam" file="bwa-aln-test1-fasta.bam" lines_diff="2"/>
+            <output name="bam_output" ftype="bam" file="bwa-aln-test1-fasta.bam" lines_diff="4"/>
         </test>
-        <test>
+        <test expect_num_outputs="1">
             <param name="reference_source_selector" value="history"/>
             <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
             <param name="input_type_selector" value="paired"/>
             <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/>
             <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
             <param name="analysis_type_selector" value="illumina"/>
-            <output name="bam_output" ftype="bam" file="bwa-aln-test1.bam" lines_diff="2"/>
+            <output name="bam_output" ftype="bam" file="bwa-aln-test1.bam" lines_diff="4"/>
         </test>
-        <test>
+        <test expect_num_outputs="1">
             <param name="reference_source_selector" value="history"/>
             <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
             <param name="input_type_selector" value="paired"/>
             <param name="fastq_input1" ftype="fastqsanger.gz" value="bwa-mem-fastq1.fq.gz"/>
             <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
             <param name="analysis_type_selector" value="illumina"/>
-            <output name="bam_output" ftype="bam" file="bwa-aln-test1.bam" lines_diff="2"/>
+            <output name="bam_output" ftype="bam" file="bwa-aln-test1.bam" lines_diff="4"/>
         </test>
-        <test>
+        <test expect_num_outputs="1">
             <param name="reference_source_selector" value="history"/>
             <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
             <param name="input_type_selector" value="paired_bam"/>
             <param name="bam_input" ftype="bam" value="bwa-aln-bam-input.bam"/>
             <param name="analysis_type_selector" value="illumina"/>
-            <output name="bam_output" ftype="bam" file="bwa-aln-test2.bam" lines_diff="2"/>
+            <output name="bam_output" ftype="bam" file="bwa-aln-test2.bam" lines_diff="4"/>
         </test>
-        <test>
+        <test expect_num_outputs="1">
             <param name="reference_source_selector" value="history"/>
             <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
             <param name="input_type_selector" value="paired"/>
@@ -358,57 +357,34 @@
             <param name="ID" value="rg1"/>
             <param name="PL" value="CAPILLARY"/>
             <param name="analysis_type_selector" value="illumina"/>
-            <output name="bam_output" ftype="bam" file="bwa-aln-test3.bam" lines_diff="2"/>
+            <output name="bam_output" ftype="bam" file="bwa-aln-test3.bam" lines_diff="5"/>
         </test>
     </tests>
     <help><![CDATA[
-**What is does**
+**What it does**
 
-BWA is a software package for mapping low-divergent sequences against a large reference genome, such as the
-human genome. The bwa-aln algorithm is designed for Illumina sequence reads up to 100bp. For longer reads use
-the separate BWA-MEM Galaxy tool.
+BWA_ is a software package for mapping low-divergent sequences against a large reference genome, such as the human genome.
+The bwa-aln algorithm is designed for Illumina sequence reads up to 100bp. For longer reads use the separate BWA-MEM Galaxy tool.
 
-This Galaxy tool wraps bwa-aln, bwa-samse and -sampe modules of bwa read mapping tool:
+This Galaxy tool wraps the bwa-aln, bwa-samse and -sampe modules of the BWA read mapping tool:
 
 - **bwa aln** - actual mapper placing reads onto the reference sequence
 - **bwa samse** - post-processor converting suffix array coordinates into genome coordinates in SAM format for
   single reads
 - **bam sampe** - post-processor for paired reads
 
+For more details about the different modules of the BWA package see the `BWA manual`_.
 
 The Galaxy implementation takes fastq or BAM (unaligned BAM) datasets as input and produces output in BAM format,
-which can be further processed using various BAM utilities exiting in Galaxy (BAMTools, SAMTools, Picard).
+which can be further processed using various BAM utilities existing in Galaxy (BAMTools, SAMTools, Picard).
 
 -----
 
-**Indices: Selecting reference genomes for BWA**
-
-The Galaxy wrapper for BWA allows you to select between precomputed and user-defined indices for reference genomes
-using the **Will you select a reference genome from your history or use a built-in index?** select box.
-
-This select box has two options:
-
-  1. **Use a built-in genome index** - when selected (this is default), Galaxy provides the user with **Select
-     reference genome index** dropdown. Genomes listed in this dropdown have been pre-indexed with bwa index utility
-     and are ready to be mapped against.
-  2. **Use a genome from the history and build index** - when selected, Galaxy provides the user with **Select
-     reference genome sequence** dropdown. This dropdown is populated by all FASTA formatted files listed in your
-     current history. If your genome of interest is uploaded into history it will be shown there. Selecting a genome
-     from this dropdown will cause Galaxy to first transparently index it using `bwa index` command, and then run
-     mapping with `bwa aln`.
-
-
-If your genome of interest is not listed here you have two choices:
-
-  1. Contact galaxy team using **Help->Support** link at the top of the interface and let us know that an index
-     needs to be added
-  2. Upload your genome of interest as a FASTA file to Galaxy history and selected **Use a genome from the history
-     and build index** option.
-
+@ref_genomes@
 
 @RG@
 
-@info@
+@links@
     ]]></help>
     <citations>
         <citation type="doi">10.1093/bioinformatics/btp324</citation>