diff --git a/tools/odgi/build.xml b/tools/odgi/build.xml
index 1399fd80439..28eb1bf0f5e 100644
--- a/tools/odgi/build.xml
+++ b/tools/odgi/build.xml
@@ -1,4 +1,4 @@
-<tool id="odgi_build" name="odgi build" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
+<tool id="odgi_build" name="odgi build" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="24.1">
     <description>construct a dynamic succinct variation graph</description>
     <macros>
         <import>macros.xml</import>
@@ -6,13 +6,9 @@
     <expand macro="requirements"/>
     <command detect_errors="exit_code"><![CDATA[
 cp '$gfa' input.gfa &&
-
-odgi build
--g input.gfa
--o '$odgi_output'
-$sort
-#if $to_gfa:
-    --to-gfa > '$gfa_output'
+odgi build -g input.gfa -o '$odgi_output' $sort
+#if $to_gfa
+&& odgi view -i '$odgi_output' $to_gfa > '$gfa_output'
 #end if
     ]]></command>
     <inputs>
@@ -31,7 +27,7 @@ $sort
         </data>
     </outputs>
     <tests>
-        <test>
+        <test expect_num_outputs="2">
             <param name="gfa" value="t.gfa" />
             <param name="sort" value="true" />
             <param name="to_gfa" value="true" />
@@ -39,11 +35,21 @@ $sort
             <output name="gfa_output" file="note5.gfa" />
         </test>
     </tests>
-    <help><![CDATA[
-optimized dynamic genome/graph implementation (odgi)
-----------------------------------------------------
+    <help format="markdown"><![CDATA[
+@HELP_HEADER@
+
+`odgi build` converts a GFA file into an ODGI graph, optionally topologically sorting nodes and emitting a companion GFA view.
+
+### Inputs
+
+- **Construct the graph from this GFA input file**: Source GFA file to ingest.
+- **Topological sort the graph**: Apply generalized topological sorting before writing the `.og`.
+- **Output additional GFA file**: Re-export the resulting graph in GFA format.
+
+### Outputs
 
-Construct a dynamic succinct variation graph (build)
+- **odgi**: The constructed graph in ODGI format.
+- **GFA**: Optional GFA view of the constructed graph.
     ]]></help>
     <expand macro="citations">
     </expand>
diff --git a/tools/odgi/cover.xml b/tools/odgi/cover.xml
new file mode 100644
index 00000000000..a348a817fc7
--- /dev/null
+++ b/tools/odgi/cover.xml
@@ -0,0 +1,76 @@
+<tool id="odgi_cover" name="odgi cover" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="24.1">
+    <description>generate path covers for graph components</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+odgi cover
+--idx '$idx'
+--out '$output'
+#if str($hogwild_depth)
+    --hogwild-depth $hogwild_depth
+#end if
+#if str($num_paths_per_component)
+    --num-paths-per-component $num_paths_per_component
+#end if
+#if str($node_windows_size)
+    --node-windows-size $node_windows_size
+#end if
+#if str($min_node_coverage)
+    --min-node-coverage $min_node_coverage
+#end if
+$ignore_paths
+#if str($save_coverages)
+    --write-node-depth '$node_coverages'
+#end if
+@THREADS@
+    ]]></command>
+    <inputs>
+        <expand macro="graph_input_param"/>
+        <param argument="--hogwild-depth" type="float" optional="true" min="0" label="Cover graph to this average depth" help="Randomly cover the graph until reaching the specified average depth."/>
+        <param argument="--num-paths-per-component" type="integer" optional="true" min="1" label="Number of paths to generate per component"/>
+        <param argument="--node-windows-size" type="integer" optional="true" min="2" label="Node window size when extending paths"/>
+        <param argument="--min-node-coverage" type="integer" optional="true" min="1" label="Minimum node coverage to reach"/>
+        <param argument="--ignore-paths" type="boolean" truevalue="--ignore-paths" falsevalue="" checked="false" label="Ignore embedded paths when initializing coverage"/>
+        <param argument="--save-coverages" type="boolean" truevalue="true" falsevalue="" checked="false" label="Write node coverages table" help="Generate a tabular file with per-node coverage statistics."/>
+    </inputs>
+    <outputs>
+        <data name="output" format="odgi" label="${tool.name} on ${on_string}"/>
+        <data name="node_coverages" format="tabular" label="${tool.name} on ${on_string}: node coverages">
+            <filter>save_coverages</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="idx" value="t.og" />
+            <param name="num_paths_per_component" value="2" />
+            <output name="output" file="cover_out.og" ftype="odgi" />
+        </test>
+        <test expect_num_outputs="2">
+            <param name="idx" value="t.og" />
+            <param name="num_paths_per_component" value="2" />
+            <param name="save_coverages" value="true" />
+            <output name="output" file="cover_out.og" ftype="odgi" />
+            <output name="node_coverages" file="cover_node_coverages.tabular" ftype="tabular" />
+        </test>
+    </tests>
+    <help format="markdown"><![CDATA[
+@HELP_HEADER@
+
+`odgi cover` generates path covers for each connected component of the graph.
+
+### Inputs
+
+- **Input odgi graph**: Graph to cover.
+- **Average depth / Paths per component / Node window size / Minimum node coverage**: Control coverage generation heuristics.
+- **Ignore embedded paths**: Start covering from scratch ignoring existing paths.
+- **Write node coverages table**: Emit per-node coverage values.
+
+### Outputs
+
+- **odgi**: Graph augmented with generated cover paths.
+- **node coverages**: Optional tabular coverage summary.
+    ]]></help>
+    <expand macro="citations"/>
+</tool>
diff --git a/tools/odgi/depth.xml b/tools/odgi/depth.xml
new file mode 100644
index 00000000000..894e1bf8c0b
--- /dev/null
+++ b/tools/odgi/depth.xml
@@ -0,0 +1,104 @@
+<tool id="odgi_depth" name="odgi depth" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="24.1">
+    <description>compute path depth statistics</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+odgi depth
+--input '$input'
+#if $subset_paths
+    --subset-paths '$subset_paths'
+#end if
+#if str($path)
+    --path '$path'
+#end if
+#if $paths
+    --paths '$paths'
+#end if
+#if str($graph_pos)
+    --graph-pos '$graph_pos'
+#end if
+#if $graph_pos_file
+    --graph-pos-file '$graph_pos_file'
+#end if
+#if str($path_pos)
+    --path-pos '$path_pos'
+#end if
+#if $path_pos_file
+    --path-pos-file '$path_pos_file'
+#end if
+#if $bed_input
+    --bed-input '$bed_input'
+#end if
+$graph_depth_table
+$graph_depth_vec
+$path_depth
+$self_depth
+$summarize
+#if str($windows_in)
+    --windows-in '$windows_in'
+#end if
+#if str($windows_out)
+    --windows-out '$windows_out'
+#end if
+@THREADS@
+> '$output'
+    ]]></command>
+    <inputs>
+        <expand macro="graph_input_param_input"/>
+        <param argument="--subset-paths" type="data" format="txt" optional="true" label="Subset of paths for depth calculation" help="Text file with one path name per line."/>
+        <param argument="--path" type="text" optional="true" label="Single path to analyze"/>
+        <param argument="--paths" type="data" format="txt" optional="true" label="Report depth for these paths" help="Text file with one path name per line."/>
+        <param argument="--graph-pos" type="text" optional="true" label="Graph position (node[,offset[,strand]])"/>
+        <param argument="--graph-pos-file" type="data" format="txt" optional="true" label="File of graph positions"/>
+        <param argument="--path-pos" type="text" optional="true" label="Path position (path[,offset[,strand]])"/>
+        <param argument="--path-pos-file" type="data" format="txt" optional="true" label="File of path positions"/>
+        <param argument="--bed-input" type="data" format="bed" optional="true" label="BED intervals to evaluate"/>
+        <param argument="--graph-depth-table" type="boolean" truevalue="--graph-depth-table" falsevalue="" checked="false" label="Write node depth/unique depth table"/>
+        <param argument="--graph-depth-vec" type="boolean" truevalue="--graph-depth-vec" falsevalue="" checked="false" label="Write graph depth vector"/>
+        <param argument="--path-depth" type="boolean" truevalue="--path-depth" falsevalue="" checked="false" label="Write per-base path depth"/>
+        <param argument="--self-depth" type="boolean" truevalue="--self-depth" falsevalue="" checked="false" label="Write self depth per base"/>
+        <param argument="--summarize" type="boolean" truevalue="--summarize" falsevalue="" checked="false" label="Summarize depth distribution"/>
+        <param argument="--windows-in" type="text" optional="true" label="Depth windows inside range (LEN:MIN:MAX)"/>
+        <param argument="--windows-out" type="text" optional="true" label="Depth windows outside range (LEN:MIN:MAX)"/>
+    </inputs>
+    <outputs>
+        <expand macro="standard_tabular_output"/>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="input" value="t.og" />
+            <param name="graph_depth_table" value="true" />
+            <output name="output" file="depth_graph_table.tabular" ftype="tabular" />
+        </test>
+        <test expect_num_outputs="1">
+            <param name="input" value="t.og" />
+            <param name="path_depth" value="true" />
+            <output name="output" file="depth_path.tabular" ftype="tabular" />
+        </test>
+        <test expect_num_outputs="1">
+            <param name="input" value="t.og" />
+            <param name="summarize" value="true" />
+            <output name="output" file="depth_summarize.tabular" ftype="tabular" />
+        </test>
+    </tests>
+    <help format="markdown"><![CDATA[
+@HELP_HEADER@
+
+`odgi depth` reports depth metrics for selected paths, positions, or intervals.
+
+### Inputs
+
+- **Input odgi graph**: Graph to profile.
+- **Subset/path/path lists**: Limit the analysis to specific paths.
+- **Positions / BED intervals**: Query exact positions or ranges.
+- **Depth summary toggles**: Emit tables or vectors describing depth per node or path.
+- **Depth windows**: Report intervals within or outside depth ranges.
+
+### Outputs
+
+- **Tabular**: Depth metrics written in tab-separated form.
+    ]]></help>
+    <expand macro="citations"/>
+</tool>
diff --git a/tools/odgi/draw.xml b/tools/odgi/draw.xml
new file mode 100644
index 00000000000..07ac6ee58b5
--- /dev/null
+++ b/tools/odgi/draw.xml
@@ -0,0 +1,125 @@
+<tool id="odgi_draw" name="odgi draw" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="24.1">
+    <description>draw previously-determined 2D layouts of the graph with diverse annotations</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+odgi draw
+--idx '$idx'
+--coords-in '$coords_in'
+#if $png
+    --png '$png_output'
+#end if
+#if $svg
+    --svg '$svg_output'
+#end if
+#if $tsv
+    --tsv '$tsv_output'
+#end if
+#if $path_index
+    --path-index '$path_index'
+#end if
+#if str($png_height)
+    --png-height $png_height
+#end if
+#if str($png_border)
+    --png-border $png_border
+#end if
+$color_paths
+#if str($scale)
+    --scale $scale
+#end if
+#if str($border)
+    --border $border
+#end if
+#if str($line_width)
+    --line-width $line_width
+#end if
+#if str($path_line_spacing)
+    --path-line-spacing $path_line_spacing
+#end if
+#if $bed_file
+    --bed-file '$bed_file'
+#end if
+@THREADS@
+    ]]></command>
+    <inputs>
+        <expand macro="graph_input_param"/>
+        <param argument="--coords-in" type="data" format="txt" label="Layout coordinates file" help="Read the layout coordinates from this .lay format file produced by odgi layout."/>
+        <param argument="--png" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Output PNG rendering"/>
+        <param argument="--svg" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Output SVG rendering"/>
+        <param argument="--tsv" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Output TSV layout"/>
+        <param argument="--path-index" type="data" format="txt" optional="true" label="Path index file"/>
+        <param argument="--png-height" type="integer" optional="true" min="1" label="PNG height" help="Height of PNG rendering in pixels (default: 1000)."/>
+        <param argument="--png-border" type="integer" optional="true" min="0" label="PNG border size" help="Size of PNG border in bp (default: 10)."/>
+        <param argument="--color-paths" type="boolean" truevalue="--color-paths" falsevalue="" checked="false" label="Color paths in PNG output"/>
+        <param argument="--scale" type="float" optional="true" min="0" label="Image scaling factor" help="Default: 1.0"/>
+        <param argument="--border" type="float" optional="true" min="0" label="Image border in approximate bp" help="Default: 100.0"/>
+        <param argument="--line-width" type="float" optional="true" min="0" label="Line width in approximate bp" help="Default: 0.0"/>
+        <param argument="--path-line-spacing" type="float" optional="true" min="0" label="Path line spacing in approximate bp" help="Default: 0.0"/>
+        <param argument="--bed-file" type="data" format="bed" optional="true" label="BED file for node coloring" help="Color nodes based on annotations. Colors from 4th column if present, else from path name."/>
+    </inputs>
+    <outputs>
+        <data name="png_output" format="png" label="${tool.name} on ${on_string}: PNG">
+            <filter>png</filter>
+        </data>
+        <data name="svg_output" format="svg" label="${tool.name} on ${on_string}: SVG">
+            <filter>svg</filter>
+        </data>
+        <data name="tsv_output" format="tabular" label="${tool.name} on ${on_string}: TSV">
+            <filter>tsv</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="idx" value="t.og" />
+            <param name="coords_in" value="t.lay" />
+            <param name="png" value="true" />
+            <param name="svg" value="false" />
+            <param name="tsv" value="false" />
+            <output name="png_output" file="draw_out.png" ftype="png" compare="sim_size" delta="5000"/>
+        </test>
+        <test expect_num_outputs="2">
+            <param name="idx" value="t.og" />
+            <param name="coords_in" value="t.lay" />
+            <param name="png" value="true" />
+            <param name="svg" value="true" />
+            <param name="tsv" value="false" />
+            <param name="color_paths" value="true" />
+            <output name="png_output" file="draw_color.png" ftype="png" compare="sim_size" delta="5000"/>
+            <output name="svg_output" file="draw_out.svg" ftype="svg" />
+        </test>
+        <test expect_num_outputs="1">
+            <param name="idx" value="t.og" />
+            <param name="coords_in" value="t.lay" />
+            <param name="png" value="false" />
+            <param name="svg" value="false" />
+            <param name="tsv" value="true" />
+            <output name="tsv_output" file="draw_out.tabular" ftype="tabular" />
+        </test>
+    </tests>
+    <help format="markdown"><![CDATA[
+@HELP_HEADER@
+
+`odgi draw` renders previously-computed 2D graph layouts (produced by `odgi layout`) into visual outputs.
+
+### Inputs
+
+- **Input odgi graph**: The graph to draw.
+- **Layout coordinates file**: The `.lay` file produced by `odgi layout`.
+- **Path index**: Optional path index file.
+- **BED file**: Optional annotations to color nodes.
+
+### Outputs
+
+- **PNG**: Rasterized image rendering.
+- **SVG**: Vector image rendering.
+- **TSV**: Layout coordinates plus annotations as a table.
+
+### Visualization Options
+
+Control the appearance with height, border, scale, line width, path spacing, and path coloring options.
+    ]]></help>
+    <expand macro="citations"/>
+</tool>
\ No newline at end of file
diff --git a/tools/odgi/extract.xml b/tools/odgi/extract.xml
new file mode 100644
index 00000000000..55eb82afa18
--- /dev/null
+++ b/tools/odgi/extract.xml
@@ -0,0 +1,113 @@
+<tool id="odgi_extract" name="odgi extract" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="24.1">
+    <description>extract subgraphs or parts of a graph</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+odgi extract
+--idx '$idx'
+--out '$output'
+#if $node_list
+    --node-list '$node_list'
+#end if
+#if str($node)
+    --node '$node'
+#end if
+#if str($context_steps)
+    --context-steps $context_steps
+#end if
+#if str($context_bases)
+    --context-bases $context_bases
+#end if
+#if str($path_range)
+    --path-range '$path_range'
+#end if
+#if $bed_file
+    --bed-file '$bed_file'
+#end if
+#if str($pangenomic_range)
+    --pangenomic-range '$pangenomic_range'
+#end if
+#if $paths_to_extract
+    --paths-to-extract '$paths_to_extract'
+#end if
+#if $lace_paths
+    --lace-paths '$lace_paths'
+#end if
+#if str($max_distance_subpaths)
+    --max-distance-subpaths $max_distance_subpaths
+#end if
+#if str($max_merging_iterations)
+    --max-merging-iterations $max_merging_iterations
+#end if
+$full_range
+$inverse
+@THREADS@
+    ]]></command>
+    <inputs>
+        <expand macro="graph_input_param"/>
+        <param argument="--node-list" type="data" format="txt" optional="true" label="Node list file" help="A file with one node id per line to extract from the input graph."/>
+        <param argument="--node" type="integer" optional="true" min="1" label="Single node ID" help="Specify a single node ID from which to begin traversal."/>
+        <param argument="--context-steps" type="integer" optional="true" min="0" label="Context steps" help="Number of steps (nodes) away from the initial subgraph to collect (default: 0 disabled)."/>
+        <param argument="--context-bases" type="integer" optional="true" min="0" label="Context bases" help="Number of bases away from the initial subgraph to collect (default: 0 disabled)."/>
+        <param argument="--path-range" type="text" optional="true" label="Path range" help="Find nodes in the specified path range. Format: path[:pos1[-pos2]] (0-based coordinates)."/>
+        <param argument="--bed-file" type="data" format="bed" optional="true" label="BED file" help="Find nodes in the path range(s) specified in the given BED file."/>
+        <param argument="--pangenomic-range" type="text" optional="true" label="Pangenomic range" help="Find nodes in the specified pangenomic range. Format: pos1-pos2 (0-based coordinates)."/>
+        <param argument="--full-range" type="boolean" truevalue="--full-range" falsevalue="" checked="false" label="Full range" help="Collect all nodes in sorted order between min and max position touched by the given path ranges."/>
+        <param argument="--paths-to-extract" type="data" format="txt" optional="true" label="Paths to extract" help="File with one path name per line to keep in the extracted graph."/>
+        <param argument="--lace-paths" type="data" format="txt" optional="true" label="Lace paths" help="File with one path name per line to fully retain in the extracted graph."/>
+        <param argument="--max-distance-subpaths" type="integer" optional="true" min="0" label="Maximum distance between subpaths" help="Maximum distance between subpaths allowed for merging. Set 0 to disable."/>
+        <param argument="--max-merging-iterations" type="integer" optional="true" min="1" label="Maximum merging iterations" help="Maximum number of iterations when merging close subpaths (default: 3)."/>
+        <param argument="--inverse" type="boolean" truevalue="--inverse" falsevalue="" checked="false" label="Inverse extraction" help="Extract parts of the graph that do NOT meet the query criteria."/>
+    </inputs>
+    <outputs>
+        <data name="output" format="odgi" label="${tool.name} on ${on_string}"/>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="idx" value="t.og" />
+            <param name="node" value="1" />
+            <param name="context_steps" value="2" />
+            <output name="output" file="extract_node.og" ftype="odgi" compare="sim_size" delta="1000"/>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="idx" value="t.og" />
+            <param name="path_range" value="x:0-100" />
+            <output name="output" file="extract_range.og" ftype="odgi" compare="sim_size" delta="1000"/>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="idx" value="t.og" />
+            <param name="node_list" value="node_list.txt" />
+            <param name="inverse" value="true" />
+            <output name="output" file="extract_inverse.og" ftype="odgi" compare="sim_size" delta="1000"/>
+        </test>
+    </tests>
+    <help format="markdown"><![CDATA[
+@HELP_HEADER@
+
+`odgi extract` extracts subgraphs or parts of a graph defined by query criteria such as node IDs, path ranges, BED intervals, or pangenomic ranges.
+
+### Inputs
+
+- **Input odgi graph**: The graph to extract from.
+- **Node list file**: One node ID per line.
+- **Single node ID**: A single node to start traversal from.
+- **Context steps / bases**: Expand the extracted subgraph by N steps or bases.
+- **Path range**: Extract nodes in a path range (format: `path[:pos1[-pos2]]`).
+- **BED file**: Extract nodes in path ranges from a BED file.
+- **Pangenomic range**: Extract nodes in a pangenomic coordinate range.
+- **Paths to extract / Lace paths**: Control which paths are retained.
+
+### Outputs
+
+- **odgi**: The extracted subgraph in ODGI format.
+
+### Notes
+
+- Use **Inverse extraction** to get the complement of the query result.
+- Use **Full range** to avoid splitting paths at node boundaries.
+- **Context steps/bases** expand the subgraph around the initial selection.
+    ]]></help>
+    <expand macro="citations"/>
+</tool>
\ No newline at end of file
diff --git a/tools/odgi/layout.xml b/tools/odgi/layout.xml
new file mode 100644
index 00000000000..8d460b42a27
--- /dev/null
+++ b/tools/odgi/layout.xml
@@ -0,0 +1,138 @@
+<tool id="odgi_layout" name="odgi layout" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="24.1">
+    <description>compute 2D path-guided layouts</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+odgi layout
+--idx '$idx'
+--out '$layout_output'
+#if $tsv
+    $tsv '$layout_tsv'
+#end if
+#if $path_index
+    --path-index '$path_index'
+#end if
+#if $path_sgd_use_paths
+    --path-sgd-use-paths '$path_sgd_use_paths'
+#end if
+#if str($layout_initialization)
+    --layout-initialization '$layout_initialization'
+#end if
+#if str($path_sgd_min_term_updates_paths)
+    --path-sgd-min-term-updates-paths $path_sgd_min_term_updates_paths
+#end if
+#if str($path_sgd_min_term_updates_nodes)
+    --path-sgd-min-term-updates-nodes $path_sgd_min_term_updates_nodes
+#end if
+#if str($path_sgd_delta)
+    --path-sgd-delta $path_sgd_delta
+#end if
+#if str($path_sgd_eta)
+    --path-sgd-eta $path_sgd_eta
+#end if
+#if str($path_sgd_eta_max)
+    --path-sgd-eta-max $path_sgd_eta_max
+#end if
+#if str($path_sgd_iter_max)
+    --path-sgd-iter-max $path_sgd_iter_max
+#end if
+#if str($path_sgd_iteration_max_learning_rate)
+    --path-sgd-iteration-max-learning-rate $path_sgd_iteration_max_learning_rate
+#end if
+#if str($path_sgd_zipf_theta)
+    --path-sgd-zipf-theta $path_sgd_zipf_theta
+#end if
+#if str($path_sgd_zipf_space)
+    --path-sgd-zipf-space $path_sgd_zipf_space
+#end if
+#if str($path_sgd_zipf_space_max)
+    --path-sgd-zipf-space-max $path_sgd_zipf_space_max
+#end if
+#if str($path_sgd_zipf_space_quantization_step)
+    --path-sgd-zipf-space-quantization-step $path_sgd_zipf_space_quantization_step
+#end if
+#if str($path_sgd_snapshot)
+    --path-sgd-snapshot '$path_sgd_snapshot'
+#end if
+@THREADS@
+    ]]></command>
+    <inputs>
+        <expand macro="graph_input_param"/>
+        <param argument="--tsv" type="boolean" truevalue="--tsv" falsevalue="" checked="false" label="Export TSV layout alongside binary layout"/>
+        <param argument="--path-index" type="data" format="txt" optional="true" label="Precomputed path index (.xp)"/>
+        <param argument="--path-sgd-use-paths" type="data" format="txt" optional="true" label="Paths to sample for PG-SGD"/>
+        <param argument="--layout-initialization" type="select" optional="true" label="Layout initialization mode">
+            <option value="d" selected="true">Node rank in X, Gaussian noise in Y (default)</option>
+            <option value="r">Uniform noise in X and Y</option>
+            <option value="u">Node rank in X, uniform noise in Y</option>
+            <option value="g">Gaussian noise in X and Y</option>
+            <option value="h">Hilbert curve initialization</option>
+        </param>
+        <param argument="--path-sgd-min-term-updates-paths" type="float" optional="true" min="0" label="Minimum term updates (paths multiple)"/>
+        <param argument="--path-sgd-min-term-updates-nodes" type="float" optional="true" min="0" label="Minimum term updates (nodes multiple)"/>
+        <param argument="--path-sgd-delta" type="float" optional="true" min="0" label="Maximum displacement threshold (bp)"/>
+        <param argument="--path-sgd-eta" type="float" optional="true" min="0" label="Final learning rate"/>
+        <param argument="--path-sgd-eta-max" type="float" optional="true" min="0" label="Initial learning rate"/>
+        <param argument="--path-sgd-iter-max" type="integer" optional="true" min="1" label="Maximum PG-SGD iterations"/>
+        <param argument="--path-sgd-iteration-max-learning-rate" type="integer" optional="true" min="0" label="Iteration where learning rate peaks"/>
+        <param argument="--path-sgd-zipf-theta" type="float" optional="true" label="Zipf theta"/>
+        <param argument="--path-sgd-zipf-space" type="integer" optional="true" min="1" label="Zipf space size"/>
+        <param argument="--path-sgd-zipf-space-max" type="integer" optional="true" min="1" label="Zipf space max before quantization"/>
+        <param argument="--path-sgd-zipf-space-quantization-step" type="integer" optional="true" min="1" label="Zipf quantization step size"/>
+        <param argument="--path-sgd-snapshot" type="text" optional="true" label="Snapshot prefix for intermediate layouts"/>
+    </inputs>
+    <outputs>
+        <data name="layout_output" format="binary" label="${tool.name} on ${on_string}"/>
+        <data name="layout_tsv" format="tabular" label="${tool.name} on ${on_string}: coordinates">
+            <filter>tsv</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="idx" value="note5_out.og" ftype="odgi"/>
+            <output name="layout_output" ftype="binary">
+                <assert_contents>
+                    <has_size min="100"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="2">
+            <param name="idx" value="note5_out.og" ftype="odgi"/>
+            <param name="tsv" value="true"/>
+            <output name="layout_output" ftype="binary">
+                <assert_contents>
+                    <has_size min="100"/>
+                </assert_contents>
+            </output>
+            <output name="layout_tsv" ftype="tabular">
+                <assert_contents>
+                    <has_n_columns n="4"/>
+                    <has_size min="100"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help format="markdown"><![CDATA[
+@HELP_HEADER@
+
+`odgi layout` computes 2D coordinates for ODGI graphs using path-guided stochastic gradient descent (PG-SGD).
+The binary `.lay` output can be fed into visualization or downstream statistics; optionally export a TSV table of node coordinates.
+
+### Inputs
+
+- **Input odgi graph**: Sorted, id-compacted graph to lay out.
+- **Export TSV layout alongside binary layout**: Produce a human-readable coordinate table as well as the binary `.lay`.
+- **Precomputed path index**: Reuse a `.xp` index to accelerate layout.
+- **Layout initialization mode**: Choose how the initial coordinates are seeded.
+- **PG-SGD parameters**: Min term updates, learning rates, iteration cap, and Zipf sampling controls fine-tune convergence.
+- **Snapshot prefix**: Write intermediate layouts for debugging or animation.
+
+### Outputs
+
+- **Binary**: Primary `.lay` file containing node coordinates.
+- **coordinates**: Optional TSV with node ID, X, Y triples.
+    ]]></help>
+    <expand macro="citations"/>
+</tool>
diff --git a/tools/odgi/macros.xml b/tools/odgi/macros.xml
index 2295c9813ec..98397786124 100644
--- a/tools/odgi/macros.xml
+++ b/tools/odgi/macros.xml
@@ -1,15 +1,33 @@
-<?xml version="1.0"?>
 <macros>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">odgi</requirement>
         </requirements>
     </xml>
-    <token name="@TOOL_VERSION@">0.3</token>
-    <token name="@VERSION_SUFFIX@">1</token>
+    <token name="@TOOL_VERSION@">0.9.3</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@HELP_HEADER@">optimized dynamic genome/graph implementation (odgi)
+----------------------------------------------------</token>
+    <token name="@THREADS@">--threads=\${GALAXY_SLOTS:-1}</token>
+    <xml name="graph_input_param">
+        <param argument="--idx" type="data" format="odgi" label="Input odgi graph"/>
+    </xml>
+    <xml name="graph_input_param_input">
+        <param argument="--input" type="data" format="odgi" label="Input odgi graph"/>
+    </xml>
+    <xml name="group_delim_params">
+        <param argument="--delim" type="text" optional="true" label="Delimiter to define path groups" help="Split path names at this character to group them before summarizing statistics or haplotypes."/>
+        <param argument="--delim-pos" type="integer" optional="true" min="1" label="Use the N-th occurrence of the delimiter" help="Specify which occurrence of the delimiter to use when extracting the group identifier."/>
+    </xml>
+    <xml name="standard_tabular_output">
+        <data name="output" format="tabular" label="${tool.name} on ${on_string}"/>
+    </xml>
+    <xml name="standard_text_output">
+        <data name="output" format="txt" label="${tool.name} on ${on_string}"/>
+    </xml>
     <xml name="citations">
         <citations>
-            <yield />
+            <citation type="doi">10.1093/bioinformatics/btac308</citation>
         </citations>
     </xml>
 </macros>
diff --git a/tools/odgi/normalize.xml b/tools/odgi/normalize.xml
new file mode 100644
index 00000000000..50cf3f9c819
--- /dev/null
+++ b/tools/odgi/normalize.xml
@@ -0,0 +1,51 @@
+<tool id="odgi_normalize" name="odgi normalize" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="24.1">
+    <description>normalize variation graph structure</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+odgi normalize
+--idx '$idx'
+--out '$output'
+#if str($max_iterations)
+    --max-iterations $max_iterations
+#end if
+$debug
+@THREADS@
+    ]]></command>
+    <inputs>
+        <expand macro="graph_input_param"/>
+        <param argument="--max-iterations" type="integer" optional="true" min="1" label="Maximum normalization iterations" help="Number of passes to perform (default 10)."/>
+        <param argument="--debug" type="boolean" truevalue="--debug" falsevalue="" checked="false" label="Print normalization debug information"/>
+    </inputs>
+    <outputs>
+        <data name="output" format="odgi" label="${tool.name} on ${on_string}"/>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="idx" value="note5_out.og" ftype="odgi"/>
+            <output name="output" ftype="odgi">
+                <assert_contents>
+                    <has_size min="100"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help format="markdown"><![CDATA[
+@HELP_HEADER@
+
+`odgi normalize` compacts unitigs and simplifies redundant furcations to produce a normalized graph.
+
+### Inputs
+
+- **Input odgi graph**: Graph to normalize.
+- **Maximum normalization iterations**: Limit the number of passes.
+- **Print normalization debug information**: Emit detailed logs.
+
+### Outputs
+
+- **odgi**: Normalized graph.
+    ]]></help>
+    <expand macro="citations"/>
+</tool>
diff --git a/tools/odgi/overlap.xml b/tools/odgi/overlap.xml
new file mode 100644
index 00000000000..c7a7f60a635
--- /dev/null
+++ b/tools/odgi/overlap.xml
@@ -0,0 +1,62 @@
+<tool id="odgi_overlap" name="odgi overlap" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="24.1">
+    <description>find paths overlapped by query paths</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+odgi overlap
+--input '$input'
+#if $subset_paths
+    --subset-paths '$subset_paths'
+#end if
+#if str($path)
+    --path '$path'
+#end if
+#if $paths
+    --paths '$paths'
+#end if
+#if $bed_input
+    --bed-input '$bed_input'
+#end if
+@THREADS@
+> '$output'
+    ]]></command>
+    <inputs>
+        <expand macro="graph_input_param_input"/>
+        <param argument="--subset-paths" type="data" format="txt" optional="true" label="Subset of paths considered" help="Text file with one path per line."/>
+        <param argument="--path" type="text" optional="true" label="Query path name"/>
+        <param argument="--paths" type="data" format="txt" optional="true" label="Paths to report overlaps for"/>
+        <param argument="--bed-input" type="data" format="bed" optional="true" label="BED intervals on query paths"/>
+    </inputs>
+    <outputs>
+        <expand macro="standard_tabular_output"/>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="input" value="note5_out.og" ftype="odgi"/>
+            <param name="path" value="x"/>
+            <output name="output" ftype="tabular">
+                <assert_contents>
+                    <has_size min="1"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help format="markdown"><![CDATA[
+@HELP_HEADER@
+
+`odgi overlap` lists paths touched by the queried paths or intervals.
+
+### Inputs
+
+- **Input odgi graph**: Graph to query.
+- **Subset/path/path lists**: Limit overlap detection to selected paths.
+- **BED intervals**: Query path ranges.
+
+### Outputs
+
+- **Tabular**: Overlap results in tab-delimited format.
+    ]]></help>
+    <expand macro="citations"/>
+</tool>
diff --git a/tools/odgi/paths.xml b/tools/odgi/paths.xml
new file mode 100644
index 00000000000..86acc1f1393
--- /dev/null
+++ b/tools/odgi/paths.xml
@@ -0,0 +1,85 @@
+<tool id="odgi_paths" name="odgi paths" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="24.1">
+    <description>inspect and report embedded paths</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+odgi paths
+--idx '$idx'
+#if str($delim)
+    --delim '$delim'
+#end if
+#if str($delim_pos)
+    --delim-pos $delim_pos
+#end if
+$list_paths
+$list_paths_start_end
+$haplotypes
+$scale_by_node_len
+$fasta
+#if $out
+    $out '$graph_output'
+#end if
+@THREADS@
+> '$output'
+    ]]></command>
+    <inputs>
+        <expand macro="graph_input_param"/>
+        <expand macro="group_delim_params"/>
+        <param argument="--list-paths" type="boolean" truevalue="--list-paths" falsevalue="" checked="false" label="List all paths"/>
+        <param argument="--list-paths-start-end" type="boolean" truevalue="--list-paths-start-end" falsevalue="" checked="false" label="Include start and end coordinates when listing paths" help="Only applies when listing paths."/>
+        <param argument="--haplotypes" type="boolean" truevalue="--haplotypes" falsevalue="" checked="false" label="Emit haplotype matrix"/>
+        <param argument="--scale-by-node-len" type="boolean" truevalue="--scale-by-node-len" falsevalue="" checked="false" label="Scale haplotype matrix cells by node length"/>
+        <param argument="--fasta" type="boolean" truevalue="--fasta" falsevalue="" checked="false" label="Output each path sequence in FASTA format"/>
+        <param argument="--out" type="boolean" truevalue="--out" falsevalue="" checked="false" label="Write pruned paths to a new graph"/>
+    </inputs>
+    <outputs>
+        <expand macro="standard_text_output"/>
+        <data name="graph_output" format="odgi" label="${tool.name} on ${on_string}: paths graph">
+            <filter>out</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="idx" value="note5_out.og" ftype="odgi"/>
+            <param name="list_paths" value="true"/>
+            <output name="output" ftype="txt">
+                <assert_contents>
+                    <has_text text="x"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="idx" value="note5_out.og" ftype="odgi"/>
+            <param name="fasta" value="true"/>
+            <output name="output" ftype="txt">
+                <assert_contents>
+                    <has_text text=">"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help format="markdown"><![CDATA[
+@HELP_HEADER@
+
+`odgi paths` inspects the embedded paths of an ODGI graph and reports summaries through standard output.
+Common uses include listing path names, emitting FASTA sequences, or exporting a haplotype matrix.
+
+### Inputs
+
+- **Input odgi graph**: Variation graph in `.og` format.
+- **Delimiter to define path groups**: Split path names to aggregate statistics by a shared prefix.
+- **Use the N-th occurrence of the delimiter**: Pick which delimiter occurrence defines the prefix.
+- **List all paths**: Print path names (optionally with coordinates).
+- **Emit haplotype matrix**: Output a tab-delimited haplotype matrix, optionally scaled by node lengths.
+- **Output each path sequence in FASTA format**: Emit sequences as FASTA records.
+- **Write pruned paths to a new graph**: Save the graph after optional path filtering operations.
+
+### Outputs
+
+- **Text**: Console output from `odgi paths` (path listings, haplotype matrices, FASTA, etc.).
+- **paths graph**: Optional ODGI file when writing path-filtered graphs back to disk.
+    ]]></help>
+    <expand macro="citations"/>
+</tool>
diff --git a/tools/odgi/pav.xml b/tools/odgi/pav.xml
new file mode 100644
index 00000000000..fcf177c41b6
--- /dev/null
+++ b/tools/odgi/pav.xml
@@ -0,0 +1,65 @@
+<tool id="odgi_pav" name="odgi pav" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="24.1">
+    <description>compute presence/absence variant ratios</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+odgi pav
+--idx '$idx'
+--bed-file '$bed_file'
+#if $path_groups
+    --path-groups '$path_groups'
+#end if
+$group_by_sample
+$group_by_haplotype
+#if str($binary_values)
+    --binary-values $binary_values
+#end if
+$matrix_output
+@THREADS@
+> '$output'
+    ]]></command>
+    <inputs>
+        <expand macro="graph_input_param"/>
+        <param argument="--bed-file" type="data" format="bed" label="Path ranges (BED)"/>
+        <param argument="--path-groups" type="data" format="tabular" optional="true" label="Optional path grouping file" help="Two-column table with path name and group name to aggregate PAV ratios."/>
+        <param argument="--group-by-sample" type="boolean" truevalue="--group-by-sample" falsevalue="" checked="false" label="Group paths by sample (PanSN)"/>
+        <param argument="--group-by-haplotype" type="boolean" truevalue="--group-by-haplotype" falsevalue="" checked="false" label="Group paths by haplotype (PanSN)"/>
+        <param argument="--binary-values" type="float" optional="true" min="0" max="1" label="Binary threshold" help="Emit 1 when the PAV ratio is greater than or equal to this threshold, else 0."/>
+        <param argument="--matrix-output" type="boolean" truevalue="--matrix-output" falsevalue="" checked="false" label="Output as matrix (rows = path ranges, columns = paths/groups)"/>
+    </inputs>
+    <outputs>
+        <expand macro="standard_tabular_output"/>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="idx" value="note5_out.og" ftype="odgi"/>
+            <param name="bed_file" value="t.bed" ftype="bed"/>
+            <output name="output" ftype="tabular">
+                <assert_contents>
+                    <has_size min="1"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help format="markdown"><![CDATA[
+@HELP_HEADER@
+
+`odgi pav` calculates presence/absence variant (PAV) ratios for each path range in a BED file, optionally grouped by sample, haplotype, or custom path groupings.
+
+### Inputs
+
+- **Input odgi graph**: Variation graph containing the paths of interest.
+- **Path ranges (BED)**: Regions to assess for presence/absence across paths.
+- **Optional path grouping file**: Map path names to group identifiers (two-column, tab-delimited).
+- **Group by sample / haplotype**: Interpret PanSN-style path names and aggregate accordingly.
+- **Binary threshold**: Emit 0/1 calls instead of ratios.
+- **Output as matrix**: Pivot output so rows are ranges and columns are paths/groups.
+
+### Outputs
+
+- **Tabular**: TSV matrix of PAV ratios (or binary values) suitable for downstream visualization or filtering.
+    ]]></help>
+    <expand macro="citations"/>
+</tool>
diff --git a/tools/odgi/position.xml b/tools/odgi/position.xml
new file mode 100644
index 00000000000..cbbe84d0573
--- /dev/null
+++ b/tools/odgi/position.xml
@@ -0,0 +1,105 @@
+<tool id="odgi_position" name="odgi position" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="24.1">
+    <description>translate coordinates between graph paths</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+odgi position
+--target '$target'
+#if $source
+    --source '$source'
+#end if
+#if str($ref_path)
+    --ref-path '$ref_path'
+#end if
+#if $ref_paths
+    --ref-paths '$ref_paths'
+#end if
+#if str($lift_path)
+    --lift-path '$lift_path'
+#end if
+#if $lift_paths
+    --lift-paths '$lift_paths'
+#end if
+#if str($graph_pos)
+    --graph-pos '$graph_pos'
+#end if
+#if $graph_pos_file
+    --graph-pos-file '$graph_pos_file'
+#end if
+#if str($path_pos)
+    --path-pos '$path_pos'
+#end if
+#if $path_pos_file
+    --path-pos-file '$path_pos_file'
+#end if
+#if $bed_input
+    --bed-input '$bed_input'
+#end if
+#if $gff_input
+    --gff-input '$gff_input'
+#end if
+$give_graph_pos
+$all_immediate
+#if str($search_radius)
+    --search-radius $search_radius
+#end if
+#if str($jaccard_context)
+    --jaccard-context $jaccard_context
+#end if
+@THREADS@
+> '$output'
+    ]]></command>
+    <inputs>
+        <param argument="--target" type="data" format="odgi" label="Target odgi graph"/>
+        <param argument="--source" type="data" format="odgi" optional="true" label="Source graph for liftovers"/>
+        <param argument="--ref-path" type="text" optional="true" label="Reference path name"/>
+        <param argument="--ref-paths" type="data" format="txt" optional="true" label="Reference paths list"/>
+        <param argument="--lift-path" type="text" optional="true" label="Lift path common to source and target"/>
+        <param argument="--lift-paths" type="data" format="txt" optional="true" label="Lift paths list"/>
+        <param argument="--graph-pos" type="text" optional="true" label="Single graph position (node,offset,strand)"/>
+        <param argument="--graph-pos-file" type="data" format="txt" optional="true" label="Graph positions file"/>
+        <param argument="--path-pos" type="text" optional="true" label="Single path position (path,offset,strand)"/>
+        <param argument="--path-pos-file" type="data" format="txt" optional="true" label="Path positions file"/>
+        <param argument="--bed-input" type="data" format="bed" optional="true" label="BED ranges to lift"/>
+        <param argument="--gff-input" type="data" format="gff3" optional="true" label="GFF/GTF annotations to lift"/>
+        <param argument="--give-graph-pos" type="boolean" truevalue="--give-graph-pos" falsevalue="" checked="false" label="Emit graph positions instead of path positions"/>
+        <param argument="--all-immediate" type="boolean" truevalue="--all-immediate" falsevalue="" checked="false" label="Emit all immediate positions"/>
+        <param argument="--search-radius" type="integer" optional="true" min="1" label="Search radius (bp)"/>
+        <param argument="--jaccard-context" type="integer" optional="true" min="1" label="Maximum walking distance for Jaccard context"/>
+    </inputs>
+    <outputs>
+        <expand macro="standard_tabular_output"/>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="target" value="note5_out.og" ftype="odgi"/>
+            <param name="path_pos" value="x,0,+"/>
+            <output name="output" ftype="tabular">
+                <assert_contents>
+                    <has_size min="1"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help format="markdown"><![CDATA[
+@HELP_HEADER@
+
+`odgi position` maps positions between graph coordinates and path coordinates, enabling liftover between graphs that share common paths.
+
+### Inputs
+
+- **Target odgi graph**: Graph whose coordinate system you want as output.
+- **Source graph for liftovers**: Optional second graph supplying the original coordinates.
+- **Reference path / Lift path / Path lists**: Guide how positions are translated between source and target graphs.
+- **Graph/path positions or files**: Provide single coordinates or newline-delimited collections; BED and GFF/GTF inputs are supported.
+- **Emit graph positions / Emit all immediate positions**: Control the style of reported coordinates.
+- **Search radius / Maximum walking distance**: Limit traversal during coordinate projection.
+
+### Outputs
+
+- **Tabular**: Coordinate translations (path or graph positions, depending on options).
+    ]]></help>
+    <expand macro="citations"/>
+</tool>
diff --git a/tools/odgi/similarity.xml b/tools/odgi/similarity.xml
new file mode 100644
index 00000000000..04f6ec660fc
--- /dev/null
+++ b/tools/odgi/similarity.xml
@@ -0,0 +1,57 @@
+<tool id="odgi_similarity" name="odgi similarity" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="24.1">
+    <description>tabulate path similarities</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+odgi similarity
+--idx '$idx'
+#if str($delim)
+    --delim '$delim'
+#end if
+#if str($delim_pos)
+    --delim-pos $delim_pos
+#end if
+$distances
+@THREADS@
+> '$output'
+    ]]></command>
+    <inputs>
+        <expand macro="graph_input_param"/>
+        <expand macro="group_delim_params"/>
+        <param argument="--distances" type="boolean" truevalue="--distances" falsevalue="" checked="false" label="Report distances instead of similarities"/>
+    </inputs>
+    <outputs>
+        <expand macro="standard_tabular_output"/>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="idx" value="note5_out.og" ftype="odgi"/>
+            <output name="output" ftype="tabular">
+                <assert_contents>
+                    <has_size min="1"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help format="markdown"><![CDATA[
+@HELP_HEADER@
+
+`odgi similarity` reports pairwise similarities between paths (or path groups) in the input graph.
+Rows are tab-delimited and list each pair alongside their similarity score.
+With the *Report distances instead of similarities* option enabled, an extra column with Euclidean distance is included.
+
+### Inputs
+
+- **Input odgi graph**: Variation graph in `.og` format.
+- **Delimiter to define path groups**: Split path names at the given character and aggregate similarities by group prefix.
+- **Use the N-th occurrence of the delimiter**: Choose which delimiter occurrence defines the group prefix.
+- **Report distances instead of similarities**: Toggle between similarity scores and distances.
+
+### Outputs
+
+- **Tabular**: Similarity (and optionally distance) matrix suitable for downstream filtering or visualization.
+    ]]></help>
+    <expand macro="citations"/>
+</tool>
diff --git a/tools/odgi/sort.xml b/tools/odgi/sort.xml
new file mode 100644
index 00000000000..7897df1c0db
--- /dev/null
+++ b/tools/odgi/sort.xml
@@ -0,0 +1,90 @@
+<tool id="odgi_sort" name="odgi sort" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="24.1">
+    <description>reorder graph nodes using odgi sort</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+odgi sort
+--idx '$idx'
+--out '$output'
+#if str($pipeline)
+    --pipeline '$pipeline'
+#end if
+$breadth_first
+#if str($breadth_first_chunk)
+    --breadth-first-chunk $breadth_first_chunk
+#end if
+$depth_first
+#if str($depth_first_chunk)
+    --depth-first-chunk $depth_first_chunk
+#end if
+$two_way
+$cycle_breaking
+$random
+$dagify_sort
+$path_sgd
+#if $path_sgd_use_paths
+    --path-sgd-use-paths '$path_sgd_use_paths'
+#end if
+#if str($path_sgd_delta)
+    --path-sgd-delta $path_sgd_delta
+#end if
+#if str($path_sgd_iter_max)
+    --path-sgd-iter-max $path_sgd_iter_max
+#end if
+#if str($path_sgd_seed)
+    --path-sgd-seed '$path_sgd_seed'
+#end if
+@THREADS@
+    ]]></command>
+    <inputs>
+        <expand macro="graph_input_param"/>
+        <param argument="--pipeline" type="text" optional="true" label="Sorting pipeline string" help="Concatenate single-letter sorting steps (e.g. bSnSnS) to apply multiple algorithms sequentially."/>
+        <param argument="--breadth-first" type="boolean" truevalue="--breadth-first" falsevalue="" checked="false" label="Breadth-first topological sort"/>
+        <param argument="--breadth-first-chunk" type="integer" optional="true" min="1" label="Breadth-first chunk size"/>
+        <param argument="--depth-first" type="boolean" truevalue="--depth-first" falsevalue="" checked="false" label="Depth-first topological sort"/>
+        <param argument="--depth-first-chunk" type="integer" optional="true" min="1" label="Depth-first chunk size"/>
+        <param argument="--two-way" type="boolean" truevalue="--two-way" falsevalue="" checked="false" label="Two-way topological sort"/>
+        <param argument="--cycle-breaking" type="boolean" truevalue="--cycle-breaking" falsevalue="" checked="false" label="Cycle breaking sort"/>
+        <param argument="--random" type="boolean" truevalue="--random" falsevalue="" checked="false" label="Randomize node order"/>
+        <param argument="--dagify-sort" type="boolean" truevalue="--dagify-sort" falsevalue="" checked="false" label="Sort via DAGified graph"/>
+        <param argument="--path-sgd" type="boolean" truevalue="--path-sgd" falsevalue="" checked="false" label="Apply path-guided 1D SGD"/>
+        <param argument="--path-sgd-use-paths" type="data" format="txt" optional="true" label="Paths to sample for path-guided SGD"/>
+        <param argument="--path-sgd-delta" type="float" optional="true" min="0" label="Maximum displacement threshold (bp)"/>
+        <param argument="--path-sgd-iter-max" type="integer" optional="true" min="1" label="Maximum SGD iterations"/>
+        <param argument="--path-sgd-seed" type="text" optional="true" label="Seed for deterministic SGD"/>
+    </inputs>
+    <outputs>
+        <data name="output" format="odgi" label="${tool.name} on ${on_string}"/>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="idx" value="note5_out.og" ftype="odgi"/>
+            <param name="breadth_first" value="true"/>
+            <output name="output" ftype="odgi">
+                <assert_contents>
+                    <has_size min="100"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help format="markdown"><![CDATA[
+@HELP_HEADER@
+
+`odgi sort` reorders graph nodes using a mix of topological, random, or path-guided strategies.
+Use the pipeline string to chain multiple passes, or enable specific algorithms through dedicated flags.
+
+### Inputs
+
+- **Input odgi graph**: Variation graph to reorder.
+- **Sorting pipeline string**: Sequence of single-letter sort codes (e.g. `bSnSnS`).
+- **Breadth-first / Depth-first / Two-way / Cycle breaking / Random**: Toggle classic ordering algorithms.
+- **Apply path-guided 1D SGD**: Run PG-SGD with optional path list, delta threshold, iteration cap, and deterministic seed.
+
+### Outputs
+
+- **odgi**: The sorted graph written in ODGI format.
+    ]]></help>
+    <expand macro="citations"/>
+</tool>
diff --git a/tools/odgi/stats.xml b/tools/odgi/stats.xml
new file mode 100644
index 00000000000..6dcdfe53e25
--- /dev/null
+++ b/tools/odgi/stats.xml
@@ -0,0 +1,94 @@
+<tool id="odgi_stats" name="odgi stats" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="24.1">
+    <description>summarize variation graph metrics</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+odgi stats
+--idx '$idx'
+$summarize
+$weak_connected_components
+$self_loops
+$nondeterministic_edges
+$base_content
+#if str($delim)
+    --delim '$delim'
+#end if
+$file_size
+#if str($pangenome_sequence_class_counts)
+    --pangenome-sequence-class-counts '$pangenome_sequence_class_counts'
+#end if
+#if $coords_in
+    --coords-in '$coords_in'
+#end if
+$mean_links_length
+$no_gap_links
+$sum_path_nodes_distances
+$penalize_different_orientation
+$path_statistics
+$weighted_feedback_arc
+$weighted_reversing_join
+$links_length_per_nuc
+$yaml
+$multiqc
+@THREADS@
+> '$output'
+    ]]></command>
+    <inputs>
+        <expand macro="graph_input_param"/>
+        <param argument="--summarize" type="boolean" truevalue="--summarize" falsevalue="" checked="true" label="Summarize nodes, edges, paths, steps"/>
+        <param argument="--weak-connected-components" type="boolean" truevalue="--weak-connected-components" falsevalue="" checked="false" label="Report weakly connected components"/>
+        <param argument="--self-loops" type="boolean" truevalue="--self-loops" falsevalue="" checked="false" label="Count nodes with self-loops"/>
+        <param argument="--nondeterministic-edges" type="boolean" truevalue="--nondeterministic-edges" falsevalue="" checked="false" label="Report nondeterministic edges"/>
+        <param argument="--base-content" type="boolean" truevalue="--base-content" falsevalue="" checked="false" label="Summarize base composition"/>
+        <param argument="--delim" type="text" optional="true" label="Group paths using this delimiter"/>
+        <param argument="--file-size" type="boolean" truevalue="--file-size" falsevalue="" checked="false" label="Report file size"/>
+        <param argument="--pangenome-sequence-class-counts" type="text" optional="true" label="Pangenome sequence class split" help="Specify DELIM,POS to aggregate Private/Core/Shell counts by sample."/>
+        <param argument="--coords-in" type="data" format="txt" optional="true" label="2D layout coordinates (binary .lay)"/>
+        <param argument="--mean-links-length" type="boolean" truevalue="--mean-links-length" falsevalue="" checked="false" label="Compute mean links length"/>
+        <param argument="--no-gap-links" type="boolean" truevalue="--no-gap-links" falsevalue="" checked="false" label="Do not penalize gap links"/>
+        <param argument="--sum-path-nodes-distances" type="boolean" truevalue="--sum-path-nodes-distances" falsevalue="" checked="false" label="Compute sum of path node distances"/>
+        <param argument="--penalize-different-orientation" type="boolean" truevalue="--penalize-different-orientation" falsevalue="" checked="false" label="Penalize orientation changes"/>
+        <param argument="--path-statistics" type="boolean" truevalue="--path-statistics" falsevalue="" checked="false" label="Emit per-path statistics"/>
+        <param argument="--weighted-feedback-arc" type="boolean" truevalue="--weighted-feedback-arc" falsevalue="" checked="false" label="Compute weighted feedback arc metric"/>
+        <param argument="--weighted-reversing-join" type="boolean" truevalue="--weighted-reversing-join" falsevalue="" checked="false" label="Compute weighted reversing joins"/>
+        <param argument="--links_length_per_nuc" type="boolean" truevalue="--links_length_per_nuc" falsevalue="" checked="false" label="Compute links length per nucleotide"/>
+        <param argument="--yaml" type="boolean" truevalue="--yaml" falsevalue="" checked="false" label="Report in YAML format"/>
+        <param argument="--multiqc" type="boolean" truevalue="--multiqc" falsevalue="" checked="false" label="Emit full YAML suitable for MultiQC"/>
+    </inputs>
+    <outputs>
+        <expand macro="standard_text_output"/>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="idx" value="note5_out.og" ftype="odgi"/>
+            <param name="summarize" value="true"/>
+            <output name="output" ftype="txt">
+                <assert_contents>
+                    <has_text text="length"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help format="markdown"><![CDATA[
+@HELP_HEADER@
+
+`odgi stats` reports graph-wide metrics, from simple counts to layout-aware quality measures.
+Select the statistics you need, optionally grouping paths or exporting YAML for MultiQC.
+
+### Inputs
+
+- **Input odgi graph**: Graph to summarize.
+- **Summarize nodes, edges, paths, steps**: Emit the core size metrics (enabled by default).
+- **Additional toggles**: Component counts, self-loops, nondeterministic edges, base composition, file size, and layout-aware metrics.
+- **Group paths using this delimiter / Pangenome sequence class split**: Aggregate statistics by sample or cohort.
+- **2D layout coordinates**: Supply a layout to evaluate link metrics in 2D.
+- **Report in YAML format / Emit full YAML suitable for MultiQC**: Choose structured output when integrating with other tooling.
+
+### Outputs
+
+- **Text**: Selected statistics in TSV-style text (or YAML when requested).
+    ]]></help>
+    <expand macro="citations"/>
+</tool>
diff --git a/tools/odgi/test-data/cover_node_coverages.tabular b/tools/odgi/test-data/cover_node_coverages.tabular
new file mode 100644
index 00000000000..202750ab956
--- /dev/null
+++ b/tools/odgi/test-data/cover_node_coverages.tabular
@@ -0,0 +1,2 @@
+component_id	node_id	depth
+0	1	3
diff --git a/tools/odgi/test-data/cover_out.og b/tools/odgi/test-data/cover_out.og
new file mode 100644
index 00000000000..a904cd961d4
Binary files /dev/null and b/tools/odgi/test-data/cover_out.og differ
diff --git a/tools/odgi/test-data/depth_graph_table.tabular b/tools/odgi/test-data/depth_graph_table.tabular
new file mode 100644
index 00000000000..c0bcb8069da
--- /dev/null
+++ b/tools/odgi/test-data/depth_graph_table.tabular
@@ -0,0 +1,16 @@
+#node.id	depth	depth.uniq
+1	1	1
+2	0	0
+3	1	1
+4	0	0
+5	1	1
+6	1	1
+7	0	0
+8	1	1
+9	1	1
+10	0	0
+11	1	1
+12	1	1
+13	0	0
+14	1	1
+15	1	1
diff --git a/tools/odgi/test-data/depth_path.tabular b/tools/odgi/test-data/depth_path.tabular
new file mode 100644
index 00000000000..00beef04ca8
--- /dev/null
+++ b/tools/odgi/test-data/depth_path.tabular
@@ -0,0 +1 @@
+x 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
diff --git a/tools/odgi/test-data/depth_summarize.tabular b/tools/odgi/test-data/depth_summarize.tabular
new file mode 100644
index 00000000000..75084cf6a4a
--- /dev/null
+++ b/tools/odgi/test-data/depth_summarize.tabular
@@ -0,0 +1,2 @@
+#node.count	graph.length	step.count	path.length	mean.node.depth	mean.graph.depth
+15	55	10	50	0.666667	0.909091
diff --git a/tools/odgi/test-data/draw_color.png b/tools/odgi/test-data/draw_color.png
new file mode 100644
index 00000000000..40d19e95056
Binary files /dev/null and b/tools/odgi/test-data/draw_color.png differ
diff --git a/tools/odgi/test-data/draw_out.png b/tools/odgi/test-data/draw_out.png
new file mode 100644
index 00000000000..f85a3130a80
Binary files /dev/null and b/tools/odgi/test-data/draw_out.png differ
diff --git a/tools/odgi/test-data/draw_out.svg b/tools/odgi/test-data/draw_out.svg
new file mode 100644
index 00000000000..db9044fb1b6
--- /dev/null
+++ b/tools/odgi/test-data/draw_out.svg
@@ -0,0 +1,17 @@
+<svg width="200.4981761432064" height="200.1940477977398" viewBox="0 0 200.4981761432064 200.1940477977398" xmlns="http://www.w3.org/2000/svg">
+<line x1="100" x2="100.0799842536748" y1="100.1141247098496" y2="100.1122930506337" stroke="#000000" stroke-width="10"/>
+<line x1="100.0505334847205" x2="100.0605334847205" y1="100.0345303017574" y2="100.1873434210787" stroke="#000000" stroke-width="10"/>
+<line x1="100.0799842504298" x2="100.0899701328327" y1="100.1122930506769" y2="100.1117564514099" stroke="#000000" stroke-width="10"/>
+<line x1="100.0705334847205" x2="100.0805334847205" y1="100.1940477977398" y2="100.083315841" stroke="#000000" stroke-width="10"/>
+<line x1="100.0899701351646" x2="100.0999630344851" y1="100.1117564512619" y2="100.1113637823462" stroke="#000000" stroke-width="10"/>
+<line x1="100.0999630359002" x2="100.1299046443135" y1="100.111363782233" y2="100.1094588007185" stroke="#000000" stroke-width="10"/>
+<line x1="100.1205334847205" x2="100.1305334847205" y1="100" y2="100.1004653551635" stroke="#000000" stroke-width="10"/>
+<line x1="100.1299046437723" x2="100.1398669983202" y1="100.1094588008154" y2="100.1085847639732" stroke="#000000" stroke-width="10"/>
+<line x1="100.1398669989198" x2="100.3292190275417" y1="100.1085847638336" y2="100.0928393316226" stroke="#000000" stroke-width="10"/>
+<line x1="100.3305334847205" x2="100.3405334847205" y1="100.0370891556036" y2="100.0159399227752" stroke="#000000" stroke-width="10"/>
+<line x1="100.3292190337472" x2="100.3391967652875" y1="100.092839331199" y2="100.0921693590164" stroke="#000000" stroke-width="10"/>
+<line x1="100.3391967662335" x2="100.3790889508985" y1="100.0921693589347" y2="100.0892054813574" stroke="#000000" stroke-width="10"/>
+<line x1="100.3905334847205" x2="100.4005334847205" y1="100.0508433960557" y2="100.1483415214069" stroke="#000000" stroke-width="10"/>
+<line x1="100.3790889506809" x2="100.3890529653593" y1="100.0892054812788" y2="100.0883542518979" stroke="#000000" stroke-width="10"/>
+<line x1="100.3890529636418" x2="100.4981761432064" y1="100.0883542523297" y2="100.0743875840721" stroke="#000000" stroke-width="10"/>
+</svg>
diff --git a/tools/odgi/test-data/draw_out.tabular b/tools/odgi/test-data/draw_out.tabular
new file mode 100644
index 00000000000..f1769cb0b4a
--- /dev/null
+++ b/tools/odgi/test-data/draw_out.tabular
@@ -0,0 +1,31 @@
+idx	X	Y
+0	1000	1011.412470984964
+1	1007.998425367478	1011.22930506337
+2	1005.053348472049	1003.453030175744
+3	1006.053348472049	1018.734342107873
+4	1007.998425042978	1011.229305067688
+5	1008.997013283271	1011.175645140995
+6	1007.053348472049	1019.404779773979
+7	1008.053348472049	1008.331584099997
+8	1008.997013516463	1011.175645126192
+9	1009.996303448506	1011.13637823462
+10	1009.996303590017	1011.136378223301
+11	1012.990464431353	1010.945880071854
+12	1012.053348472049	1000
+13	1013.053348472049	1010.046535516353
+14	1012.990464377229	1010.945880081543
+15	1013.986699832024	1010.858476397321
+16	1013.986699891977	1010.85847638336
+17	1032.921902754171	1009.28393316226
+18	1033.053348472049	1003.708915560355
+19	1034.053348472049	1001.593992277521
+20	1032.921903374723	1009.283933119899
+21	1033.919676528749	1009.21693590164
+22	1033.919676623347	1009.216935893468
+23	1037.908895089846	1008.92054813574
+24	1039.053348472049	1005.084339605568
+25	1040.053348472049	1014.834152140687
+26	1037.908895068088	1008.920548127878
+27	1038.90529653593	1008.835425189788
+28	1038.905296364182	1008.835425232971
+29	1049.817614320641	1007.438758407213
diff --git a/tools/odgi/test-data/extract_inverse.og b/tools/odgi/test-data/extract_inverse.og
new file mode 100644
index 00000000000..a99485d2b95
Binary files /dev/null and b/tools/odgi/test-data/extract_inverse.og differ
diff --git a/tools/odgi/test-data/extract_node.og b/tools/odgi/test-data/extract_node.og
new file mode 100644
index 00000000000..1a481c0c15c
Binary files /dev/null and b/tools/odgi/test-data/extract_node.og differ
diff --git a/tools/odgi/test-data/extract_range.og b/tools/odgi/test-data/extract_range.og
new file mode 100644
index 00000000000..d5a4c843c13
Binary files /dev/null and b/tools/odgi/test-data/extract_range.og differ
diff --git a/tools/odgi/test-data/keep_paths.txt b/tools/odgi/test-data/keep_paths.txt
new file mode 100644
index 00000000000..587be6b4c3f
--- /dev/null
+++ b/tools/odgi/test-data/keep_paths.txt
@@ -0,0 +1 @@
+x
diff --git a/tools/odgi/test-data/node_list.txt b/tools/odgi/test-data/node_list.txt
new file mode 100644
index 00000000000..01e79c32a8c
--- /dev/null
+++ b/tools/odgi/test-data/node_list.txt
@@ -0,0 +1,3 @@
+1
+2
+3
diff --git a/tools/odgi/test-data/note5.gfa b/tools/odgi/test-data/note5.gfa
index a11cb81896e..b46a5509f72 100644
--- a/tools/odgi/test-data/note5.gfa
+++ b/tools/odgi/test-data/note5.gfa
@@ -34,4 +34,4 @@ L	13	+	15	+	0M
 S	14	T
 L	14	+	15	+	0M
 S	15	CCAACTCTCTG
-P	x	1+,3+,5+,6+,8+,9+,11+,12+,14+,15+	*,*,*,*,*,*,*,*,*
+P	x	1+,3+,5+,6+,8+,9+,11+,12+,14+,15+	*
diff --git a/tools/odgi/test-data/note5.png b/tools/odgi/test-data/note5.png
index 32438145613..11c9d47a48c 100644
Binary files a/tools/odgi/test-data/note5.png and b/tools/odgi/test-data/note5.png differ
diff --git a/tools/odgi/test-data/note5_out.og b/tools/odgi/test-data/note5_out.og
index c4b5b4e66db..56a27766627 100644
Binary files a/tools/odgi/test-data/note5_out.og and b/tools/odgi/test-data/note5_out.og differ
diff --git a/tools/odgi/test-data/t.bed b/tools/odgi/test-data/t.bed
new file mode 100644
index 00000000000..b42d37bd8be
--- /dev/null
+++ b/tools/odgi/test-data/t.bed
@@ -0,0 +1 @@
+x	0	50
diff --git a/tools/odgi/test-data/t.lay b/tools/odgi/test-data/t.lay
new file mode 100644
index 00000000000..31d71b1e8bd
Binary files /dev/null and b/tools/odgi/test-data/t.lay differ
diff --git a/tools/odgi/test-data/t.og b/tools/odgi/test-data/t.og
new file mode 100644
index 00000000000..56a27766627
Binary files /dev/null and b/tools/odgi/test-data/t.og differ
diff --git a/tools/odgi/untangle.xml b/tools/odgi/untangle.xml
new file mode 100644
index 00000000000..8a364e2c51c
--- /dev/null
+++ b/tools/odgi/untangle.xml
@@ -0,0 +1,104 @@
+<tool id="odgi_untangle" name="odgi untangle" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="24.1">
+    <description>project paths into reference-relative segments</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+odgi untangle
+--idx '$input'
+#if str($query_path)
+    --query-path '$query_path'
+#end if
+#if str($target_path)
+    --target-path '$target_path'
+#end if
+#if $query_paths
+    --query-paths '$query_paths'
+#end if
+#if $target_paths
+    --target-paths '$target_paths'
+#end if
+#if str($merge_dist)
+    --merge-dist $merge_dist
+#end if
+#if str($n_best)
+    --n-best $n_best
+#end if
+#if str($min_jaccard)
+    --min-jaccard $min_jaccard
+#end if
+#if str($cut_every)
+    --cut-every $cut_every
+#end if
+$paf_output
+#if $cut_points_input
+    --cut-points-input '$cut_points_input'
+#end if
+#if $cut_points_output
+    $cut_points_output '$cut_points'
+#end if
+#if $step_index
+    --step-index '$step_index'
+#end if
+@THREADS@
+> '$output'
+    ]]></command>
+    <inputs>
+        <param argument="--input" type="data" format="odgi" label="Input odgi graph"/>
+        <param argument="--query-path" type="text" optional="true" label="Single query path name"/>
+        <param argument="--target-path" type="text" optional="true" label="Single target (reference) path name"/>
+        <param argument="--query-paths" type="data" format="txt" optional="true" label="List of query paths" help="One path name per line."/>
+        <param argument="--target-paths" type="data" format="txt" optional="true" label="List of target (reference) paths" help="One path name per line."/>
+        <param argument="--merge-dist" type="integer" optional="true" min="0" label="Merge segments shorter than this length (bp)"/>
+        <param argument="--n-best" type="integer" optional="true" min="1" label="Number of best mappings to report per segment"/>
+        <param argument="--min-jaccard" type="float" optional="true" min="0" max="1" label="Minimum Jaccard threshold"/>
+        <param argument="--cut-every" type="integer" optional="true" min="1" label="Cut every N base pairs before untangling"/>
+        <param argument="--paf-output" type="boolean" truevalue="--paf-output" falsevalue="" checked="false" label="Emit PAF instead of BEDPE"/>
+        <param argument="--cut-points-input" type="data" format="txt" optional="true" label="Preset cut-point node IDs"/>
+        <param argument="--cut-points-output" type="boolean" truevalue="--cut-points-output" falsevalue="" checked="false" label="Write detected cut-point node IDs"/>
+        <param argument="--step-index" type="data" format="txt" optional="true" label="Precomputed step index"/>
+    </inputs>
+    <outputs>
+        <expand macro="standard_tabular_output"/>
+        <data name="cut_points" format="tabular" label="${tool.name} on ${on_string}: cut points">
+            <filter>cut_points_output</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="input" value="note5_out.og" ftype="odgi"/>
+            <param name="query_path" value="x"/>
+            <param name="target_path" value="x"/>
+            <output name="output" ftype="tabular">
+                <assert_contents>
+                    <has_size min="1"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help format="markdown"><![CDATA[
+@HELP_HEADER@
+
+`odgi untangle` lifts query paths into target (reference) space and reports a BEDPE (or PAF) table describing the projected segments.
+Use it to decompose paralogous regions or explore complex relationships between haplotypes and references.
+
+### Inputs
+
+- **Input odgi graph**: Variation graph in `.og` format.
+- **Single query/target path name**: Directly select paths in the graph.
+- **List of query/target paths**: Supply text files (one path per line) for batch untangling.
+- **Merge segments shorter than this length**: Smooth tiny fragments by merging into neighboring segments.
+- **Number of best mappings / Minimum Jaccard threshold**: Tune sensitivity of reported hits.
+- **Cut every N base pairs**: Enforce regular segments along the sorted graph.
+- **Emit PAF instead of BEDPE**: Toggle output format.
+- **Preset cut-point node IDs / Write detected cut-point node IDs**: Reuse or capture boundary nodes.
+- **Precomputed step index**: Speed up position lookups with an external index.
+
+### Outputs
+
+- **Tabular**: Untangle results as BEDPE (default) or PAF.
+- **cut points**: Optional list of node IDs where untangle introduced boundaries.
+    ]]></help>
+    <expand macro="citations"/>
+</tool>
diff --git a/tools/odgi/validate.xml b/tools/odgi/validate.xml
new file mode 100644
index 00000000000..a5caba7fce5
--- /dev/null
+++ b/tools/odgi/validate.xml
@@ -0,0 +1,43 @@
+<tool id="odgi_validate" name="odgi validate" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="24.1">
+    <description>validate odgi graph structure</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+odgi validate
+--input '$input'
+@THREADS@
+> '$output'
+    ]]></command>
+    <inputs>
+        <expand macro="graph_input_param_input"/>
+    </inputs>
+    <outputs>
+        <expand macro="standard_text_output"/>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="input" value="note5_out.og" ftype="odgi"/>
+            <output name="output" ftype="txt">
+                <assert_contents>
+                    <has_size min="0"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help format="markdown"><![CDATA[
+@HELP_HEADER@
+
+`odgi validate` checks that embedded paths are consistent with the graph topology.
+
+### Inputs
+
+- **Input odgi graph**: Graph to validate.
+
+### Outputs
+
+- **Text**: Validation messages (empty when the graph is valid).
+    ]]></help>
+    <expand macro="citations"/>
+</tool>
diff --git a/tools/odgi/view.xml b/tools/odgi/view.xml
new file mode 100644
index 00000000000..b970a0aca25
--- /dev/null
+++ b/tools/odgi/view.xml
@@ -0,0 +1,56 @@
+<tool id="odgi_view" name="odgi view" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="24.1">
+    <description>project odgi graph into other formats</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+odgi view
+--idx '$idx'
+#if $to_gfa
+    --to-gfa
+#end if
+#if $node_annotation
+    --node-annotation
+#end if
+@THREADS@
+> '$output'
+    ]]></command>
+    <inputs>
+        <expand macro="graph_input_param"/>
+        <param argument="--to-gfa" type="boolean" truevalue="--to-gfa" falsevalue="" checked="true" label="Write graph in GFAv1 format"/>
+        <param argument="--node-annotation" type="boolean" truevalue="--node-annotation" falsevalue="" checked="false" label="Emit node annotations"/>
+        <!--param argument="- -display" type="boolean" truevalue="- -display" falsevalue="" checked="false" label="Print internal graph structures to stderr"/-->
+    </inputs>
+    <outputs>
+        <data name="output" format="gfa1" label="${tool.name} on ${on_string}"/>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="idx" value="note5_out.og" ftype="odgi"/>
+            <param name="to_gfa" value="true"/>
+            <output name="output" ftype="gfa1">
+                <assert_contents>
+                    <has_text text="H"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help format="markdown"><![CDATA[
+@HELP_HEADER@
+
+`odgi view` projects ODGI graphs into other formats such as GFAv1 for inspection or downstream tools.
+
+### Inputs
+
+- **Input odgi graph**: Graph to convert.
+- **Write graph in GFAv1 format**: Output the graph as GFA.
+- **Emit node annotations**: Include path annotations in the GFA output.
+- **Print internal graph structures**: Show structural details on stderr for debugging.
+
+### Outputs
+
+- **GFA**: Projected graph.
+    ]]></help>
+    <expand macro="citations"/>
+</tool>
diff --git a/tools/odgi/vis.xml b/tools/odgi/vis.xml
index a5a227709c7..4fe24cec98d 100644
--- a/tools/odgi/vis.xml
+++ b/tools/odgi/vis.xml
@@ -1,4 +1,4 @@
-<tool id="odgi_viz" name="odgi viz" version="@TOOL_VERSION@">
+<tool id="odgi_viz" name="odgi viz" version="@TOOL_VERSION@" profile="24.1">
     <description>variation graph visualizations</description>
     <macros>
         <import>macros.xml</import>
@@ -16,11 +16,13 @@ odgi viz
 #if str($path_x_padding)
     --path-x-padding=$path_x_padding
 #end if
-$path_per_row
-#if str($link_path_pieces):
+#if $pack_paths
+    $pack_paths
+#end if
+#if str($link_path_pieces)
     --link-path-pieces=$link_path_pieces
 #end if
---threads=\${GALAXY_SLOTS:-1}
+@THREADS@
     ]]></command>
     <inputs>
         <param name="input" type="data" format="odgi" label="odgi input file" />
@@ -30,8 +32,8 @@ $path_per_row
 
         <param argument="--path-height" type="integer" min="0" optional="true" label="Path display height" />
         <param argument="--path-x-padding" type="integer" min="0" optional="true" label="Path x padding" />
-        <param argument="--path-per-row" type="boolean" truevalue="--path-per-row" falsevalue=""
-            label="Display a single path per row rather than packing them" />
+        <param argument="--pack-paths" type="boolean" truevalue="--pack-paths" falsevalue="" checked="true"
+            label="Pack all paths rather than displaying a single path per row" />
 
         <param argument="--link-path-pieces" type="float" optional="true"
             label="Show thin links of this relative width to connect path pieces" />
@@ -47,11 +49,22 @@ $path_per_row
             <output name="output" file="note5.png" ftype="png" />
         </test>
     </tests>
-    <help><![CDATA[
-optimized dynamic genome/graph implementation (odgi)
-----------------------------------------------------
+    <help format="markdown"><![CDATA[
+@HELP_HEADER@
+
+`odgi viz` renders linear visualizations of ODGI graphs as raster images.
+
+### Inputs
+
+- **odgi input file**: Graph to visualize.
+- **Width / Height**: Target PNG dimensions.
+- **Path display height / Path x padding**: Control per-path track sizing.
+- **Pack all paths**: Toggle packed layout versus one path per row.
+- **Show thin links**: Draw connecting lines between fragmented path pieces.
+
+### Outputs
 
-variation graph visualizations (viz)
+- **PNG**: Rendered visualization.
     ]]></help>
     <expand macro="citations" />
 </tool>