--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/wfmash.xml	Mon Feb 09 12:40:35 2026 +0000
@@ -0,0 +1,65 @@
+<tool id="wfmash" name="wfmash" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>pangenome-scale aligner</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+#set $reference_fasta_filename = "reference.fa"
+#set $query_fasta_filename = "query.fa"
+
+#if str($reference.ext).endswith('gz')
+    gunzip -c '${reference}' > '${reference_fasta_filename}' &&
+#else
+    ln -s -f '${reference}' '${reference_fasta_filename}' &&
+#end if
+
+    samtools faidx '${reference_fasta_filename}' &&
+
+#if str($query.ext).endswith('gz')
+gunzip -c '${query}' > '${query_fasta_filename}' &&
+#else
+ln -s -f '${query}' '${query_fasta_filename}' &&
+#end if
+samtools faidx '${query_fasta_filename}' &&
+
+wfmash 
+    --threads="\${GALAXY_SLOTS:-1}" 
+    -s $segment_length 
+    -p $pct_identity 
+    $approx_mapping 
+    $no_split 
+    '${reference_fasta_filename}' 
+    '${query_fasta_filename}' 
+    > '${output_paf}' 
+    ]]></command>
+    <inputs>
+        <param name="reference" type="data" format="fasta,fasta.gz" label="Reference sequence" help="FASTA format" />
+        <param name="query" type="data" format="fasta,fasta.gz" label="Query sequence" help="FASTA format"/>
+        <param argument="-s" name="segment_length" type="integer" min="100" value="1000" label="Segment Length" help="Minimum seed length, must be >= 100 bp."/>
+        <param argument="-p" name="pct_identity" type="float" min="0" max="100" value="90" label="Minimum Identity %" help="Percent identity in the mashmap step"/>
+        <param argument="-m" name="approx_mapping" type="boolean" truevalue="-m" falsevalue="" label="Approximate mapping" help="Skip base-level alignment"/>
+        <param argument="-N" name="no_split" type="boolean" optional="true" truevalue="-N" falsevalue="" label="No split" help="Disable splitting of input sequences during mapping (Default: enabled)"/>
+    </inputs>
+    
+    <outputs>
+        <data name="output_paf" format="paf" label="${tool.name} on ${on_string}:  PAF"/>
+    </outputs>
+
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="reference" ftype="fasta" value="ecoli_k12.fa"/> 
+            <param name="query" ftype="fasta" value="ecoli_o157.fa"/>        
+            <param name="pct_identity" value="70"/>
+            <output name="output_paf" file="expected_output_ecoli.paf" sort="true"/>
+        </test>
+    </tests>
+    
+    <help><![CDATA[
+wfmash is designed to make whole genome alignment easy. It can handle high sequence divergence. 
+
+By default, wfmash automatically determines an appropriate identity threshold based on the ANI (Average Nucleotide Identity) distribution of your input sequences. 
+    ]]></help>
+    
+    <expand macro="citations"/>
+</tool>