# HG changeset patch
# User iuc
# Date 1754493839 0
# Node ID b6b87635cf2920a88cc5a88c83b2b48652aa1ea9
# Parent  cf1322aeb137f06d8157dec0e3ba56da9892c1e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth commit a8808d30f9293ff09e3eed63a42db13a7c4eaad2

diff -r cf1322aeb137 -r b6b87635cf29 bwameth.xml
--- a/bwameth.xml	Sun Jun 02 16:38:23 2024 +0000
+++ b/bwameth.xml	Wed Aug 06 15:23:59 2025 +0000
@@ -1,7 +1,9 @@
-<tool id="bwameth" name="bwameth" version="@TOOL_VERSION@+galaxy0" profile="20.05">
-    <description>Fast and accurate aligner of BS-Seq reads.</description>
+<tool id="bwameth" name="bwameth" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>Fast and accurate aligner of BS-Seq reads</description>
     <macros>
-        <token name="@TOOL_VERSION@">0.2.7</token>
+        <token name="@TOOL_VERSION@">0.2.8</token>
+        <token name="@VERSION_SUFFIX@">0</token>
+        <token name="@PROFILE@">20.05</token>
     </macros>
     <requirements>
         <requirement type="package" version="@TOOL_VERSION@">bwameth</requirement>
@@ -88,7 +90,7 @@
                 <option value="indexed">Use a built-in index</option>
             </param>
             <when value="history">
-                <param name="reference" type="data" format="fasta" label="Select a genome" help="in FASTA format" />
+                <param name="reference" type="data" format="fasta" label="Select a genome" help="in FASTA format"/>
             </when>
             <when value="indexed">
                 <param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact your Galaxy admin">
@@ -107,14 +109,14 @@
                 <option value="paired_collection">Paired-end Dataset Collection</option>
             </param>
             <when value="single">
-                <param name="input_singles" type="data" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" label="FASTQ" help="FASTQ file." />
+                <param name="input_singles" type="data" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" label="FASTQ" help="FASTQ file."/>
             </when>
             <when value="paired">
-                <param name="input_mate1" type="data" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" label="First read in pair" help="FASTQ file." />
-                <param name="input_mate2" type="data" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" label="Second read in pair" help="FASTQ file." />
+                <param name="input_mate1" type="data" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" label="First read in pair" help="FASTQ file."/>
+                <param name="input_mate2" type="data" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" label="Second read in pair" help="FASTQ file."/>
             </when>
             <when value="paired_collection">
-                <param name="input_mate1" type="data_collection" collection_type="paired" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" label="FASTQ paired dataset" help="Must have a fastqsanger datatype." />
+                <param name="input_mate1" type="data_collection" collection_type="paired" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" label="FASTQ paired dataset" help="Must have a fastqsanger datatype."/>
             </when>
         </conditional>
         <param name="readGroup" type="text" value="" label="Read group" help="If desired, you can manually add read group information to the resulting BAM file. To do so, you MUST manually specify the entire string, such as '@RG\tID:foo\tSM:bar'">
@@ -122,32 +124,36 @@
         </param>
     </inputs>
     <outputs>
-        <data name="output" format="bam" from_work_dir="output.bam" label="${tool.name} on ${on_string}" />
+        <data name="output" format="bam" from_work_dir="output.bam" label="${tool.name} on ${on_string}"/>
     </outputs>
     <tests>
-        <test>
+        <test expect_num_outputs="1">
             <conditional name="referenceSource">
-                <param name="source" value="history" />
+                <param name="source" value="history"/>
+                <param name="reference" value="ref.fa.gz"/>
             </conditional>
-            <param name="reference" value="ref.fa.gz" />
-            <param name="single_or_paired_opts" value="paired" />
-            <param name="input_mate1" value="t_R1.fastq.gz"/>
-            <param name="input_mate2" value="t_R2.fastq.gz"/>
-            <output file="output.bam" ftype="bam" name="output" lines_diff="4"/><!-- allow for HD and PG lines diff-->
+            <conditional name="single_or_paired">
+                <param name="single_or_paired_opts" value="paired"/>
+                <param name="input_mate1" value="t_R1.fastq.gz"/>
+                <param name="input_mate2" value="t_R2.fastq.gz"/>
+            </conditional>
+            <output file="output.bam" ftype="bam" name="output" lines_diff="7"/>
         </test>
-        <test>
+        <test expect_num_outputs="1">
             <conditional name="referenceSource">
-                <param name="source" value="history" />
+                <param name="source" value="history"/>
+                <param name="reference" value="ref.fa.gz"/>
             </conditional>
-            <param name="reference" value="ref.fa.gz" />
-            <param name="single_or_paired_opts" value="paired_collection" />
-            <param name="input_mate1">
-                <collection type="paired">
-                    <element name="forward" value="t_R1.fastq.gz"/>
-                    <element name="reverse" value="t_R2.fastq.gz"/>
-                </collection>
-            </param>
-            <output file="output.bam" ftype="bam" name="output" lines_diff="4"/><!-- allow for HD and PG lines diff-->
+            <conditional name="single_or_paired">
+                <param name="single_or_paired_opts" value="paired_collection"/>
+                <param name="input_mate1">
+                    <collection type="paired">
+                        <element name="forward" value="t_R1.fastq.gz"/>
+                        <element name="reverse" value="t_R2.fastq.gz"/>
+                    </collection>
+                </param>
+            </conditional>
+            <output file="output.bam" ftype="bam" name="output" lines_diff="7"/>
         </test>
     </tests>
     <help><![CDATA[
@@ -164,4 +170,4 @@
         Eprint = {arXiv:1401.1129},
         }</citation>
     </citations>
-</tool>
+</tool>
\ No newline at end of file
diff -r cf1322aeb137 -r b6b87635cf29 test-data/output.bam
Binary file test-data/output.bam has changed