diff --git a/tools/metamdbg/macros.xml b/tools/metamdbg/macros.xml
index 16f35cf38b4..22e4b34b53d 100644
--- a/tools/metamdbg/macros.xml
+++ b/tools/metamdbg/macros.xml
@@ -1,5 +1,5 @@
 <macros>
-    <token name="@TOOL_VERSION@">1.3.1</token>
+    <token name="@TOOL_VERSION@">1.4</token>
     <token name="@VERSION_SUFFIX@">0</token>
     <token name="@PROFILE@">25.0</token>
     <xml name="requirements">
diff --git a/tools/metamdbg/metamdbg_asm.xml b/tools/metamdbg/metamdbg_asm.xml
index 32a2b67f221..4676841c8e8 100644
--- a/tools/metamdbg/metamdbg_asm.xml
+++ b/tools/metamdbg/metamdbg_asm.xml
@@ -1,16 +1,16 @@
 <tool id="metamdbg_asm" name="metaMDBG assemble (ASM)" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT">
-  <description>Assemble long-read metagenomes (HiFi / ONT)</description>
-  <macros>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="edam"/>
-  <expand macro="biotools"/>
-  <expand macro="requirements"/>
-  <expand macro="version"/>
-  <command detect_errors="exit_code"><![CDATA[
+    <description>Assemble long-read metagenomes (HiFi / ONT)</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="edam"/>
+    <expand macro="biotools"/>
+    <expand macro="requirements"/>
+    <expand macro="version"/>
+    <command detect_errors="exit_code"><![CDATA[
       mkdir -p assemblyDir &&
 
-      metaMDBG asm 
+      metaMDBG asm
           --out-dir "assemblyDir"
           --threads "\${GALAXY_SLOTS:-4}"
           --in-$inputs.read_type
@@ -18,247 +18,219 @@
             '$r'
           #end for
           --kmer-size $assembly.kmer_size
-          --density-assembly $assembly.density_assembly 
-          --max-k $assembly.max_k 
-          --min-abundance $assembly.min_abundance 
+          --density-assembly $assembly.density_assembly
+          --max-k $assembly.max_k
+          --min-abundance $assembly.min_abundance
           $assembly.all_assembly_graph
-          --min-read-quality $correction.min_read_quality 
+          --min-read-quality $filter_options.min_read_quality
+          --min-contig-length $filter_options.min_contig_length
+          --min-contig-coverage $filter_options.min_contig_coverage
           --density-correction $correction.density_correction 
-          --min-read-identity $correction.min_read_identity 
-          --min-read-overlap $correction.min_read_overlap 
+          --min-read-identity $correction.min_read_identity
+          --min-read-overlap $correction.min_read_overlap
           $correction.skip_correction
           &&
 
       ## Bundle for downstream graphing
       tar -C assemblyDir -czf assemblyDir.tgz . ;
     ]]></command>
-  <inputs>
-    <section name="inputs" title="Input reads" expanded="true">
-      <param name="read_type" type="select" label="Read type" help="maps to --in-*">
-        <option value="hifi">PacBio HiFi (uses --in-hifi)</option>
-        <option value="ont">Nanopore R10.4+ (uses --in-ont)</option>
-      </param>
-      
-      <param name="reads" type="data" format="fastqsanger,fastqsanger.gz"
-            multiple="true" optional="false"
-            label="FASTQ file(s)"
-            help="Select one or more FASTQ files. Multiple files will be assembled together (co-assembly). For individual assemblies of each file in a collection, see https://gxy.io/GTN:F00462"/>
-    </section>
-    <section name="assembly" title="Assembly options (advanced)" expanded="false">
-        <param argument="--kmer-size" type="integer" value="15" min="1" max="51"
-                label="k-mer size"/>
-        <param argument="--density-assembly" type="float" value="0.005" min="0.001" max="1"
-                label="Fraction of k-mers used for assembly"/>
-        <param argument="--max-k" type="integer" value="0" min="0" max="100"
-                label="Stop assembly after k iterations"/>
-        <param argument="--min-abundance" type="integer" value="0" min="0" max="1000"
-                label="Minimum k-min-mer abundance"/>
-        <param name="all_assembly_graph" type="boolean" checked="false" truevalue="--all-assembly-graph" falsevalue=""
-                label="Emit assembly graph at each multi-k iteration"/>
-    </section>
-
-    <section name="correction" title="Correction options (advanced)" expanded="false">
-        <param argument="--min-read-quality" type="integer" value="0" min="0" max="40"
-                label="Minimum read average quality"/>
-        <param argument="--density-correction" type="float" value="0.025" min="0.0001" max="1"
-                label="Fraction of k-mers used for correction"/>
-        <param argument="--min-read-identity" type="float" value="0.96" min="0" max="1"
-                label="Minimum read identity"/>
-        <param  argument="--min-read-overlap" type="integer" value="1000" min="1" max="100000"
-                label="Minimum read overlap length"/>
-        <param name="skip_correction" type="boolean" checked="false" truevalue="--skip-correction" falsevalue=""
-                label="Skip read correction"/>
-    </section>
-  </inputs>
-
-  <outputs>
-    <data name="contigs" format="fasta.gz"
-          from_work_dir="assemblyDir/contigs.fasta.gz"
-          label="${tool.name} on ${on_string}: contigs"/>
-    <data name="assembly_bundle" format="tar.gz"
-          from_work_dir="assemblyDir.tgz"
-          label="${tool.name} on ${on_string}: metaMDBG assembly bundle (tar)"/>
-  </outputs>
-  <tests>
-    <!-- 1) HiFi, single file, defaults -->
-    <test expect_num_outputs="2">
-      <section name="inputs">
-        <param name="read_type" value="hifi"/>
-        <param name="reads" value="hifi_reads_small.fastq.gz"/>
-      </section>
-
-      <assert_command>
-        <has_text text="--in-hifi"/>
-        <has_text text="--kmer-size 15"/>
-        <has_text text="--density-assembly 0.005"/>
-      </assert_command>
-
-      <output name="contigs">
-        <assert_contents>
-          <has_size min="1"/>
-        </assert_contents>
-      </output>
-
-      <output name="assembly_bundle" ftype="tar.gz">
-        <assert_contents>
-          <has_archive_member path="^(\.\/)?contigs\.fasta\.gz$"/>
-          <has_archive_member path="^(\.\/)?tmp\/"/>
-        </assert_contents>
-      </output>
-    </test>
-
-    <!-- 2) ONT, single file, correction parameters -->
-    <test expect_num_outputs="2">
-      <section name="inputs">
-        <param name="read_type" value="ont"/>
-        <param name="reads" value="ont_reads_small.fastq.gz"/>
-      </section>
-      <section name="correction">
-        <param name="min_read_quality" value="0"/>
-        <param name="density_correction" value="0.02"/>
-        <param name="min_read_identity" value="0.95"/>
-        <param name="min_read_overlap" value="800"/>
-        <param name="skip_correction" value="true"/>
-      </section>
-
-      <assert_command>
-        <has_text text="--in-ont"/>
-        <has_text text="--min-read-quality 0"/>
-        <has_text text="--density-correction 0.02"/>
-        <has_text text="--min-read-identity 0.95"/>
-        <has_text text="--min-read-overlap 800"/>
-        <has_text text="--skip-correction"/>
-      </assert_command>
-
-      <output name="contigs">
-        <assert_contents>
-          <has_size min="1"/>
-        </assert_contents>
-      </output>
-      <output name="assembly_bundle" ftype="tar.gz">
-        <assert_contents>
-          <has_archive_member path="^(\.\/)?contigs\.fasta\.gz$"/>
-        </assert_contents>
-      </output>
-    </test>
-
-    <!-- 3) HiFi, single file, custom assembly parameters -->
-    <test expect_num_outputs="2">
-      <section name="inputs">
-        <param name="read_type" value="hifi"/>
-        <param name="reads" value="hifi_reads_small.fastq.gz"/>
-      </section>
-      <section name="assembly">
-        <param name="kmer_size" value="13"/>
-        <param name="density_assembly" value="0.01"/>
-        <param name="max_k" value="8"/>
-        <param name="min_abundance" value="2"/>
-        <param name="all_assembly_graph" value="true"/>
-      </section>
-
-      <assert_command>
-        <has_text text="--kmer-size 13"/>
-        <has_text text="--density-assembly 0.01"/>
-        <has_text text="--max-k 8"/>
-        <has_text text="--min-abundance 2"/>
-        <has_text text="--all-assembly-graph"/>
-      </assert_command>
-
-      <output name="contigs">
-        <assert_contents>
-          <has_size min="1"/>
-        </assert_contents>
-      </output>
-      <output name="assembly_bundle" ftype="tar.gz">
-        <assert_contents>
-          <has_archive_member path="^(\.\/)?contigs\.fasta\.gz$"/>
-          <has_archive_member path="^(\.\/)?tmp\/"/>
-        </assert_contents>
-      </output>
-    </test>
-
-    <!-- 4) HiFi, multi-file co-assembly -->
-    <test expect_num_outputs="2">
-      <section name="inputs">
-        <param name="read_type" value="hifi"/>
-        <param name="reads" value="hifi_reads_small.fastq.gz,hifi_reads_small_2.fastq.gz,hifi_reads_small_3.fastq.gz"/>
-      </section>
-
-      <assert_command>
-        <has_text text="--in-hifi"/>
-        <has_text text=".dat' '"/>
-      </assert_command>
-
-      <output name="contigs">
-        <assert_contents>
-          <has_size min="1"/>
-        </assert_contents>
-      </output>
-
-      <output name="assembly_bundle" ftype="tar.gz">
-        <assert_contents>
-          <has_archive_member path="^(\.\/)?contigs\.fasta\.gz$"/>
-          <has_archive_member path="^(\.\/)?tmp\/"/>
-        </assert_contents>
-      </output>
-    </test>
-
-    <!-- 5) HiFi, single file baseline -->
-    <test expect_num_outputs="2">
-      <section name="inputs">
-        <param name="read_type" value="hifi"/>
-        <param name="reads" value="hifi_reads_small.fastq.gz"/>
-      </section>
-
-      <assert_command>
-        <has_text text="--in-hifi"/>
-      </assert_command>
-
-      <output name="contigs">
-        <assert_contents>
-          <has_size min="1"/>
-        </assert_contents>
-      </output>
-
-      <output name="assembly_bundle" ftype="tar.gz">
-        <assert_contents>
-          <has_archive_member path="^(\.\/)?contigs\.fasta\.gz$"/>
-          <has_archive_member path="^(\.\/)?tmp\/"/>
-        </assert_contents>
-      </output>
-    </test>
-
-    <!-- 6) Both boolean flags enabled -->
-    <test expect_num_outputs="2">
-      <section name="inputs">
-        <param name="read_type" value="hifi"/>
-        <param name="reads" value="hifi_reads_small.fastq.gz"/>
-      </section>
-      <section name="assembly">
-        <param name="all_assembly_graph" value="true"/>
-      </section>
-      <section name="correction">
-        <param name="skip_correction" value="true"/>
-      </section>
-
-      <assert_command>
-        <has_text text="--all-assembly-graph"/>
-        <has_text text="--skip-correction"/>
-      </assert_command>
-
-      <output name="contigs">
-        <assert_contents>
-          <has_size min="1"/>
-        </assert_contents>
-      </output>
-      <output name="assembly_bundle" ftype="tar.gz">
-        <assert_contents>
-          <has_size min="1"/>
-        </assert_contents>
-      </output>
-    </test>
-  </tests>
-  <help><![CDATA[
+    <inputs>
+        <section name="inputs" title="Input reads" expanded="true">
+            <param name="read_type" type="select" label="Read type" help="maps to --in-*">
+                <option value="hifi">PacBio HiFi (uses --in-hifi)</option>
+                <option value="ont">Nanopore R10.4+ (uses --in-ont)</option>
+            </param>
+            <param name="reads" type="data" format="fastqsanger,fastqsanger.gz" multiple="true" optional="false" label="FASTQ file(s)" help="Select one or more FASTQ files. Multiple files will be assembled together (co-assembly). For individual assemblies of each file in a collection, see https://gxy.io/GTN:F00462"/>
+        </section>
+        <section name="filter_options" title="Filter options (advanced)" expanded="false">
+            <param argument="--min-read-quality" type="integer" value="0" min="0" max="40" label="Minimum read average quality"/>
+            <param argument="--min-contig-length" type="integer" value="50" min="1" label="Minimum contig length"/>
+            <param argument="--min-contig-coverage" type="integer" value="1" min="0" label="Minimum contig coverage"/>
+        </section>
+        <section name="assembly" title="Assembly options (advanced)" expanded="false">
+            <param argument="--kmer-size" type="integer" value="15" min="1" max="51" label="k-mer size"/>
+            <param argument="--density-assembly" type="float" value="0.005" min="0.001" max="1" label="Fraction of k-mers used for assembly"/>
+            <param argument="--max-k" type="integer" value="0" min="0" max="100" label="Stop assembly after k iterations"/>
+            <param argument="--min-abundance" type="integer" value="0" min="0" max="1000" label="Minimum k-min-mer abundance"/>
+            <param name="all_assembly_graph" type="boolean" checked="false" truevalue="--all-assembly-graph" falsevalue="" label="Emit assembly graph at each multi-k iteration"/>
+        </section>
+        <section name="correction" title="Correction options (advanced)" expanded="false">
+            <param argument="--density-correction" type="float" value="0.025" min="0.0001" max="1" label="Fraction of k-mers used for correction"/>
+            <param argument="--min-read-identity" type="float" value="0.96" min="0" max="1" label="Minimum read identity"/>
+            <param argument="--min-read-overlap" type="integer" value="1000" min="1" max="100000" label="Minimum read overlap length"/>
+            <param name="skip_correction" type="boolean" checked="false" truevalue="--skip-correction" falsevalue="" label="Skip read correction"/>
+        </section>
+    </inputs>
+    <outputs>
+        <data name="contigs" format="fasta.gz" from_work_dir="assemblyDir/contigs.fasta.gz" label="${tool.name} on ${on_string}: contigs"/>
+        <data name="assembly_bundle" format="tar.gz" from_work_dir="assemblyDir.tgz" label="${tool.name} on ${on_string}: metaMDBG assembly bundle (tar)"/>
+    </outputs>
+    <tests>
+        <!-- 1) HiFi, single file, defaults -->
+        <test expect_num_outputs="2">
+            <section name="inputs">
+                <param name="read_type" value="hifi"/>
+                <param name="reads" value="hifi_reads_small.fastq.gz"/>
+            </section>
+            <assert_command>
+                <has_text text="--in-hifi"/>
+                <has_text text="--kmer-size 15"/>
+                <has_text text="--density-assembly 0.005"/>
+            </assert_command>
+            <output name="contigs">
+                <assert_contents>
+                    <has_size min="1"/>
+                </assert_contents>
+            </output>
+            <output name="assembly_bundle" ftype="tar.gz">
+                <assert_contents>
+                    <has_archive_member path="^(\.\/)?contigs\.fasta\.gz$"/>
+                    <has_archive_member path="^(\.\/)?tmp\/"/>
+                </assert_contents>
+            </output>
+        </test>
+        <!-- 2) ONT, single file, correction parameters -->
+        <test expect_num_outputs="2">
+            <section name="inputs">
+                <param name="read_type" value="ont"/>
+                <param name="reads" value="ont_reads_small.fastq.gz"/>
+            </section>
+            <section name="filter_options">
+                <param name="min_read_quality" value="0"/>
+                <param name="min_contig_length" value="40"/>
+                <param name="min_contig_coverage" value="10"/>
+            </section>
+            <section name="correction">
+                <param name="density_correction" value="0.02"/>
+                <param name="min_read_identity" value="0.95"/>
+                <param name="min_read_overlap" value="800"/>
+                <param name="skip_correction" value="true"/>
+            </section>
+            <assert_command>
+                <has_text text="--in-ont"/>
+                <has_text text="--min-read-quality 0"/>
+                <has_text text="--min-contig-length 40"/>
+                <has_text text="--min-contig-coverage 10"/>
+                <has_text text="--density-correction 0.02"/>
+                <has_text text="--min-read-identity 0.95"/>
+                <has_text text="--min-read-overlap 800"/>
+                <has_text text="--skip-correction"/>
+            </assert_command>
+            <output name="contigs">
+                <assert_contents>
+                    <has_size min="1"/>
+                </assert_contents>
+            </output>
+            <output name="assembly_bundle" ftype="tar.gz">
+                <assert_contents>
+                    <has_archive_member path="^(\.\/)?contigs\.fasta\.gz$"/>
+                </assert_contents>
+            </output>
+        </test>
+        <!-- 3) HiFi, single file, custom assembly parameters -->
+        <test expect_num_outputs="2">
+            <section name="inputs">
+                <param name="read_type" value="hifi"/>
+                <param name="reads" value="hifi_reads_small.fastq.gz"/>
+            </section>
+            <section name="assembly">
+                <param name="kmer_size" value="13"/>
+                <param name="density_assembly" value="0.01"/>
+                <param name="max_k" value="8"/>
+                <param name="min_abundance" value="2"/>
+                <param name="all_assembly_graph" value="true"/>
+            </section>
+            <assert_command>
+                <has_text text="--kmer-size 13"/>
+                <has_text text="--density-assembly 0.01"/>
+                <has_text text="--max-k 8"/>
+                <has_text text="--min-abundance 2"/>
+                <has_text text="--all-assembly-graph"/>
+            </assert_command>
+            <output name="contigs">
+                <assert_contents>
+                    <has_size min="1"/>
+                </assert_contents>
+            </output>
+            <output name="assembly_bundle" ftype="tar.gz">
+                <assert_contents>
+                    <has_archive_member path="^(\.\/)?contigs\.fasta\.gz$"/>
+                    <has_archive_member path="^(\.\/)?tmp\/"/>
+                </assert_contents>
+            </output>
+        </test>
+        <!-- 4) HiFi, multi-file co-assembly -->
+        <test expect_num_outputs="2">
+            <section name="inputs">
+                <param name="read_type" value="hifi"/>
+                <param name="reads" value="hifi_reads_small.fastq.gz,hifi_reads_small_2.fastq.gz,hifi_reads_small_3.fastq.gz"/>
+            </section>
+            <assert_command>
+                <has_text text="--in-hifi"/>
+                <has_text text=".dat' '"/>
+            </assert_command>
+            <output name="contigs">
+                <assert_contents>
+                    <has_size min="1"/>
+                </assert_contents>
+            </output>
+            <output name="assembly_bundle" ftype="tar.gz">
+                <assert_contents>
+                    <has_archive_member path="^(\.\/)?contigs\.fasta\.gz$"/>
+                    <has_archive_member path="^(\.\/)?tmp\/"/>
+                </assert_contents>
+            </output>
+        </test>
+        <!-- 5) HiFi, single file baseline -->
+        <test expect_num_outputs="2">
+            <section name="inputs">
+                <param name="read_type" value="hifi"/>
+                <param name="reads" value="hifi_reads_small.fastq.gz"/>
+            </section>
+            <assert_command>
+                <has_text text="--in-hifi"/>
+            </assert_command>
+            <output name="contigs">
+                <assert_contents>
+                    <has_size min="1"/>
+                </assert_contents>
+            </output>
+            <output name="assembly_bundle" ftype="tar.gz">
+                <assert_contents>
+                    <has_archive_member path="^(\.\/)?contigs\.fasta\.gz$"/>
+                    <has_archive_member path="^(\.\/)?tmp\/"/>
+                </assert_contents>
+            </output>
+        </test>
+        <!-- 6) Both boolean flags enabled -->
+        <test expect_num_outputs="2">
+            <section name="inputs">
+                <param name="read_type" value="hifi"/>
+                <param name="reads" value="hifi_reads_small.fastq.gz"/>
+            </section>
+            <section name="assembly">
+                <param name="all_assembly_graph" value="true"/>
+            </section>
+            <section name="correction">
+                <param name="skip_correction" value="true"/>
+            </section>
+            <assert_command>
+                <has_text text="--all-assembly-graph"/>
+                <has_text text="--skip-correction"/>
+            </assert_command>
+            <output name="contigs">
+                <assert_contents>
+                    <has_size min="1"/>
+                </assert_contents>
+            </output>
+            <output name="assembly_bundle" ftype="tar.gz">
+                <assert_contents>
+                    <has_size min="1"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
 **What this tool does and why**
 
 This tool runs `metaMDBG asm` to assemble long-read metagenomes (PacBio HiFi or ONT R10.4+) using a minimizer-space de Bruijn graph with a multi-k strategy. It produces polished contigs and a tarred snapshot of the assembly directory for downstream graphing and reproducibility.
@@ -299,8 +271,5 @@ Packaging `assemblyDir/` as `assemblyDir.tgz` preserves all artifacts and makes
 For more details about metaMDBG, see the `GitHub repository <https://github.com/GaetanBenoitDev/metaMDBG>`_.
 
   ]]></help>
-
-  <expand macro="citations"/>
+    <expand macro="citations"/>
 </tool>
-
-
diff --git a/tools/metamdbg/metamdbg_gfa.xml b/tools/metamdbg/metamdbg_gfa.xml
index 77273447c5a..6537fd4352b 100644
--- a/tools/metamdbg/metamdbg_gfa.xml
+++ b/tools/metamdbg/metamdbg_gfa.xml
@@ -1,18 +1,19 @@
 <tool id="metamdbg_gfa" name="metaMDBG graph (GFA)" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT">
-  <description>Generate a GFA graph from a metaMDBG assembly or list available k-values</description>
-  <macros><import>macros.xml</import></macros>
-  <expand macro="edam"/>
-  <expand macro="biotools"/>
-  <expand macro="requirements"/>
-  <stdio>
-    <exit_code range="10" level="fatal" description="metaMDBG failed to produce sequence-containing GFA file" />
-    <exit_code range="11" level="fatal" description="metaMDBG failed to produce no-seq GFA file" />
-    <exit_code range="12" level="fatal" description="Failed to extract the input assembly bundle" />
-    <exit_code range="13" level="fatal" description="Could not auto-detect k-values from assembly" />
-  </stdio>
-  <expand macro="version"/>
-
-<command detect_errors="exit_code"><![CDATA[
+    <description>Generate a GFA graph from a metaMDBG assembly or list available k-values</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="edam"/>
+    <expand macro="biotools"/>
+    <expand macro="requirements"/>
+    <stdio>
+        <exit_code range="10" level="fatal" description="metaMDBG failed to produce sequence-containing GFA file"/>
+        <exit_code range="11" level="fatal" description="metaMDBG failed to produce no-seq GFA file"/>
+        <exit_code range="12" level="fatal" description="Failed to extract the input assembly bundle"/>
+        <exit_code range="13" level="fatal" description="Could not auto-detect k-values from assembly"/>
+    </stdio>
+    <expand macro="version"/>
+    <command detect_errors="exit_code"><![CDATA[
     tar -xzf '$assembly_bundle' || exit 12 ;
 
     ## Two modes: list k-values or build the graph
@@ -68,148 +69,148 @@
         cp "\$GFA_NOSEQ" metamdbg.noseq.gfa ;
     #end if
   ]]></command>
-
-  <inputs>
-    <param name="assembly_bundle" type="data" format="tar.gz" label="Assembly bundle (tar.gz from metaMDBG assemble)"/>
-    <conditional name="mode">
-      <param name="action" type="select" label="What do you want to do?">
-        <option value="list" selected="true">List available k-values only (no graph)</option>
-        <option value="graph">Generate GFA graph</option>
-      </param>
-
-      <when value="list"/>
-      <when value="graph">
-        <param name="k" type="integer" optional="true" value="" label="k-mer size"
-                  help="If not specified the largest k is selected automatically. For specifying a value it is suggested to first run in 'List k-values' mode to see available options"/>
-        <param name="reads" type="data" multiple="true" optional="false" 
-              format="fastq,fastq.gz,fastqsanger,fastqsanger.gz" 
-              label="Raw reads used for this assembly"/>
-      </when>
-    </conditional>
-  </inputs>
-
-  <outputs>
-    <!-- Listing mode -->
-    <data name="k_values" format="txt" from_work_dir="k_values.txt"
-          label="${tool.name} on ${on_string}: available k-values">
-      <filter>mode['action'] == 'list'</filter>
-    </data>
-
-    <!-- Graph mode -->
-    <data name="gfa" format="gfa1" from_work_dir="metamdbg.gfa"
-          label="${tool.name} on ${on_string}: GFA">
-      <filter>mode['action'] == 'graph'</filter>
-    </data>
-    
-    <data name="gfa_noseq" format="gfa1" from_work_dir="metamdbg.noseq.gfa"
-          label="${tool.name} on ${on_string}: GFA (no sequences)">
-      <filter>mode['action'] == 'graph'</filter>
-    </data>
-  </outputs>
-
-  <tests>
-    <!-- Test 1: List mode -->
-    <test expect_num_outputs="1">
-      <param name="assembly_bundle" ftype="tar.gz" value="small_assembly_bundle.tar.gz"/>
-      <conditional name="mode">
-        <param name="action" value="list"/>
-      </conditional>
-      <output name="k_values">
-        <assert_contents><has_text text="- 11 (2015 bps)"/></assert_contents>
-      </output>
-    </test>
-
-    <!-- Test 2: Graph mode - Manual k-selection -->
-    <test expect_num_outputs="2">
-      <param name="assembly_bundle" ftype="tar.gz" value="hifi_reads_small_assembly_bundle.tar.gz"/>
-      <conditional name="mode">
-        <param name="action" value="graph"/>
-        <param name="k" value="11"/>
-        <param name="reads" value="hifi_reads_small.fastq.gz"/>
-      </conditional>
-      <output name="gfa">
-        <assert_contents><has_text text="utg0"/></assert_contents>
-      </output>
-      <output name="gfa_noseq">
-        <assert_contents><has_text text="LN:i:"/></assert_contents>
-      </output>
-    </test>
-
-    <!-- Test 3: Graph mode - Auto k-selection -->
-    <test expect_num_outputs="2">
-      <param name="assembly_bundle" ftype="tar.gz" value="hifi_reads_small_assembly_bundle.tar.gz"/>
-      <conditional name="mode">
-        <param name="action" value="graph"/>
-        <param name="reads" value="hifi_reads_small.fastq.gz"/>
-      </conditional>
-      <output name="gfa">
-        <assert_contents><has_text text="utg0"/></assert_contents>
-      </output>
-      <output name="gfa_noseq">
-        <assert_contents><has_text text="LN:i:"/></assert_contents>
-      </output>
-    </test>
-
-    <!-- Test 4: Graph mode - Auto k-selection with multiple reads -->
-    <test expect_num_outputs="2">
-      <param name="assembly_bundle" ftype="tar.gz" value="hifi_reads_small_combined_assembly_bundle.tar.gz"/>
-      <conditional name="mode">
-        <param name="action" value="graph"/>
-        <param name="reads" value="hifi_reads_small.fastq.gz,hifi_reads_small_2.fastq.gz"/>
-      </conditional>
-      <output name="gfa">
-        <assert_contents><has_text text="utg0"/></assert_contents>
-      </output>
-      <output name="gfa_noseq">
-        <assert_contents><has_text text="LN:i:"/></assert_contents>
-      </output>
-    </test>
-
-    <!-- Test 5: Verify auto k-selection chooses correct k (check stderr) -->
-    <test expect_num_outputs="2">
-      <param name="assembly_bundle" ftype="tar.gz" value="hifi_reads_small_assembly_bundle.tar.gz"/>
-      <conditional name="mode">
-        <param name="action" value="graph"/>
-        <param name="reads" value="hifi_reads_small.fastq.gz"/>
-      </conditional>
-      <assert_stderr>
-        <has_text text="Auto-selected k = 11"/>
-      </assert_stderr>
-      <output name="gfa">
-        <assert_contents><has_text text="utg0"/></assert_contents>
-      </output>
-      <output name="gfa_noseq">
-        <assert_contents><has_text text="LN:i:"/></assert_contents>
-      </output>
-    </test>
-
-    <!-- Test 6: Verify manual k-selection with stderr check -->
-    <test expect_num_outputs="2">
-      <param name="assembly_bundle" ftype="tar.gz" value="hifi_reads_small_assembly_bundle.tar.gz"/>
-      <conditional name="mode">
-        <param name="action" value="graph"/>
-        <param name="k" value="11"/>
-        <param name="reads" value="hifi_reads_small.fastq.gz"/>
-      </conditional>
-      <assert_stderr>
-        <has_text text="Using manually specified k = 11"/>
-      </assert_stderr>
-      <output name="gfa">
-        <assert_contents>
-          <has_text text="utg0"/>
-          <has_size min="1000"/>
-        </assert_contents>
-      </output>
-      <output name="gfa_noseq">
-        <assert_contents>
-          <has_text text="LN:i:"/>
-          <has_size min="20"/>
-        </assert_contents>
-      </output>
-    </test>
-  </tests>
-
-  <help><![CDATA[
+    <inputs>
+        <param name="assembly_bundle" type="data" format="tar.gz" label="Assembly bundle (tar.gz from metaMDBG assemble)"/>
+        <conditional name="mode">
+            <param name="action" type="select" label="What do you want to do?">
+                <option value="list" selected="true">List available k-values only (no graph)</option>
+                <option value="graph">Generate GFA graph</option>
+            </param>
+            <when value="list"/>
+            <when value="graph">
+                <param name="k" type="integer" optional="true" value="" label="k-mer size" help="If not specified the largest k is selected automatically. For specifying a value it is suggested to first run in 'List k-values' mode to see available options"/>
+                <param name="reads" type="data" multiple="true" optional="false" format="fastq,fastq.gz,fastqsanger,fastqsanger.gz" label="Raw reads used for this assembly"/>
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <!-- Listing mode -->
+        <data name="k_values" format="txt" from_work_dir="k_values.txt" label="${tool.name} on ${on_string}: available k-values">
+            <filter>mode['action'] == 'list'</filter>
+        </data>
+        <!-- Graph mode -->
+        <data name="gfa" format="gfa1" from_work_dir="metamdbg.gfa" label="${tool.name} on ${on_string}: GFA">
+            <filter>mode['action'] == 'graph'</filter>
+        </data>
+        <data name="gfa_noseq" format="gfa1" from_work_dir="metamdbg.noseq.gfa" label="${tool.name} on ${on_string}: GFA (no sequences)">
+            <filter>mode['action'] == 'graph'</filter>
+        </data>
+    </outputs>
+    <tests>
+        <!-- Test 1: List mode -->
+        <test expect_num_outputs="1">
+            <param name="assembly_bundle" ftype="tar.gz" value="small_assembly_bundle.tar.gz"/>
+            <conditional name="mode">
+                <param name="action" value="list"/>
+            </conditional>
+            <output name="k_values">
+                <assert_contents>
+                    <has_text text="- 11 (2015 bps)"/>
+                </assert_contents>
+            </output>
+        </test>
+        <!-- Test 2: Graph mode - Manual k-selection -->
+        <test expect_num_outputs="2">
+            <param name="assembly_bundle" ftype="tar.gz" value="hifi_reads_small_assembly_bundle.tar.gz"/>
+            <conditional name="mode">
+                <param name="action" value="graph"/>
+                <param name="k" value="11"/>
+                <param name="reads" value="hifi_reads_small.fastq.gz"/>
+            </conditional>
+            <output name="gfa">
+                <assert_contents>
+                    <has_text text="utg0"/>
+                </assert_contents>
+            </output>
+            <output name="gfa_noseq">
+                <assert_contents>
+                    <has_text text="LN:i:"/>
+                </assert_contents>
+            </output>
+        </test>
+        <!-- Test 3: Graph mode - Auto k-selection -->
+        <test expect_num_outputs="2">
+            <param name="assembly_bundle" ftype="tar.gz" value="hifi_reads_small_assembly_bundle.tar.gz"/>
+            <conditional name="mode">
+                <param name="action" value="graph"/>
+                <param name="reads" value="hifi_reads_small.fastq.gz"/>
+            </conditional>
+            <output name="gfa">
+                <assert_contents>
+                    <has_text text="utg0"/>
+                </assert_contents>
+            </output>
+            <output name="gfa_noseq">
+                <assert_contents>
+                    <has_text text="LN:i:"/>
+                </assert_contents>
+            </output>
+        </test>
+        <!-- Test 4: Graph mode - Auto k-selection with multiple reads -->
+        <test expect_num_outputs="2">
+            <param name="assembly_bundle" ftype="tar.gz" value="hifi_reads_small_combined_assembly_bundle.tar.gz"/>
+            <conditional name="mode">
+                <param name="action" value="graph"/>
+                <param name="reads" value="hifi_reads_small.fastq.gz,hifi_reads_small_2.fastq.gz"/>
+            </conditional>
+            <output name="gfa">
+                <assert_contents>
+                    <has_text text="utg0"/>
+                </assert_contents>
+            </output>
+            <output name="gfa_noseq">
+                <assert_contents>
+                    <has_text text="LN:i:"/>
+                </assert_contents>
+            </output>
+        </test>
+        <!-- Test 5: Verify auto k-selection chooses correct k (check stderr) -->
+        <test expect_num_outputs="2">
+            <param name="assembly_bundle" ftype="tar.gz" value="hifi_reads_small_assembly_bundle.tar.gz"/>
+            <conditional name="mode">
+                <param name="action" value="graph"/>
+                <param name="reads" value="hifi_reads_small.fastq.gz"/>
+            </conditional>
+            <assert_stderr>
+                <has_text text="Auto-selected k = 11"/>
+            </assert_stderr>
+            <output name="gfa">
+                <assert_contents>
+                    <has_text text="utg0"/>
+                </assert_contents>
+            </output>
+            <output name="gfa_noseq">
+                <assert_contents>
+                    <has_text text="LN:i:"/>
+                </assert_contents>
+            </output>
+        </test>
+        <!-- Test 6: Verify manual k-selection with stderr check -->
+        <test expect_num_outputs="2">
+            <param name="assembly_bundle" ftype="tar.gz" value="hifi_reads_small_assembly_bundle.tar.gz"/>
+            <conditional name="mode">
+                <param name="action" value="graph"/>
+                <param name="k" value="11"/>
+                <param name="reads" value="hifi_reads_small.fastq.gz"/>
+            </conditional>
+            <assert_stderr>
+                <has_text text="Using manually specified k = 11"/>
+            </assert_stderr>
+            <output name="gfa">
+                <assert_contents>
+                    <has_text text="utg0"/>
+                    <has_size min="1000"/>
+                </assert_contents>
+            </output>
+            <output name="gfa_noseq">
+                <assert_contents>
+                    <has_text text="LN:i:"/>
+                    <has_size min="20"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
 **What this tool does**
 
 Generates an assembly graph in GFA1 format from a metaMDBG assembly bundle.
@@ -275,7 +276,5 @@ The tool extracts your assembly bundle and runs `metaMDBG gfa` to build the grap
 See the `metaMDBG GitHub repository <https://github.com/GaetanBenoitDev/metaMDBG>`_ for additional documentation.
 
   ]]></help>
-
-  <expand macro="citations"/>
+    <expand macro="citations"/>
 </tool>
-
diff --git a/tools/metamdbg/test-data/hifi_reads_small_assembly_bundle.tar.gz b/tools/metamdbg/test-data/hifi_reads_small_assembly_bundle.tar.gz
index 1bd3d44d0d3..80c19bf6027 100644
Binary files a/tools/metamdbg/test-data/hifi_reads_small_assembly_bundle.tar.gz and b/tools/metamdbg/test-data/hifi_reads_small_assembly_bundle.tar.gz differ
diff --git a/tools/metamdbg/test-data/hifi_reads_small_combined_assembly_bundle.tar.gz b/tools/metamdbg/test-data/hifi_reads_small_combined_assembly_bundle.tar.gz
index 5c4a20c1dea..18c043b1100 100644
Binary files a/tools/metamdbg/test-data/hifi_reads_small_combined_assembly_bundle.tar.gz and b/tools/metamdbg/test-data/hifi_reads_small_combined_assembly_bundle.tar.gz differ