Add MAGs-visualization Galaxy wrappers

tools/mags_visualization/.shed.yml

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+name: mags_visualization
+owner: iuc
+categories:
+  - Metagenomics
+  - Visualization
+description: Visualization tools for MAG evaluation and analysis
+long_description: |
+  MAGs-visualization is a toolkit for generating publication-ready plots and
+  dashboards for metagenome-assembled genomes (MAGs).
+
+  Suppoerted visualization include:
+
+  - completeness and contamination (CheckM/CheckM2)
+  - taxonomic profiles (GTDB)
+  - clustering (dRep)
+  - abundance patterns (CoverM)
+  - functional annotation (KEGG pathways)
+
+  The Galaxy wrappers provide modular tools corresponding to each visualization type.
+homepage_url: https://github.com/usegalaxy-eu/MAGs-visualization
+remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/main/tools/mags_visualization
+type: unrestricted
+suite:
+  name: "suite_mags_visualization"
+  description: "A suite of MAGs-visualization tools"
+  type: repository_suite_definition
+auto_tool_repositories:
+  name_template: "{{ tool_id }}"
+  description_template: "Wrapper for MAGs-visualization tool: {{ tool_name }}"

tools/mags_visualization/comp_conta.xml

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+<tool id="mags_visualization_comp_conta" name="MAGs-visualization comp-conta" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>Create completeness/contamination plots</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="version_command"/>
+    <command detect_errors="exit_code"><![CDATA[
+        mags-visualization comp-conta
+            --checkm '$checkm'
+            --checkm2 '$checkm2'
+            --mode '$mode_cond.mode'
+            --top_n '$top_n'
+            --format '$format'
+
+        #if $mode_cond.mode == "tax"
+            --gtdb '$mode_cond.gtdb'
+            --tax_level '$mode_cond.tax_level'
+        #end if
+
+        #if $mode_cond.mode == "meta"
+            --metadata '$mode_cond.metadata'
+            --meta_col '$mode_cond.meta_col'
+            --meta_bin_width '$mode_cond.meta_bin_width'
+        #end if
+
+        #if str($fig_size.width) != "" and str($fig_size.height) != ""
+            --fig_size '$fig_size.width' '$fig_size.height'
+        #end if
+
+            -o outputs
+    ]]></command>
+    <inputs>
+        <param argument="--checkm" type="data" format="tabular" label="CheckM results"/>
+        <param argument="--checkm2" type="data" format="tabular" label="CheckM2 results"/>
+
+        <conditional name="mode_cond">
+            <param name="mode" type="select" label="Plot mode">
+                <option value="quality" selected="true">quality</option>
+                <option value="tax">tax</option>
+                <option value="meta">meta</option>
+            </param>
+            <when value="quality"/>
+
+            <when value="tax">
+                <param argument="--gtdb" type="data" format="tabular" label="GTDB annotation table"/>
+                <param argument="--tax_level" type="select" label="Taxonomic level">
+                    <option value="domain">domain</option>
+                    <option value="phylum" selected="true">phylum</option>
+                    <option value="class">class</option>
+                    <option value="order">order</option>
+                    <option value="family">family</option>
+                    <option value="genus">genus</option>
+                    <option value="species">species</option>
+                </param>
+            </when>
+
+            <when value="meta">
+                <param argument="--metadata" type="data" format="tabular" label="Metadata table"/>
+                <param name="meta_col" type="data_column"
+                    data_ref="metadata"
+                    label="Metadata column"
+                    use_header_names="true"
+                    help="Select the column to color by"/>
+                <param name="meta_bin_width" type="float" value="5.0" min="0.1" label="Bin width for numeric metadata"/>
+            </when>
+        </conditional>
+
+        <param argument="--top_n" type="integer" value="30" min="1" label="Top N groups" 
+            help="Number of most abundant groups to display (taxonomic groups or metadata categories)"/>
+
+        <param argument="--format" type="select" label="Output format">
+            <option value="png" selected="true">png</option>
+            <option value="pdf">pdf</option>
+            <option value="svg">svg</option>
+        </param>
+        <section name="fig_size" title="Figure size" expanded="false">
+            <param name="width" type="float" optional="true" min="1" label="Figure width"/>
+            <param name="height" type="float" optional="true" min="1" label="Figure height"/>
+        </section>
+    </inputs>
+    <outputs>
+        <collection name="plots" type="list">
+            <discover_datasets directory="outputs" pattern="(?P&lt;designation&gt;.+)\.(?P&lt;ext&gt;png|pdf|svg)$" visible="true"/>
+        </collection>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="checkm" value="checkm.tsv"/>
+            <param name="checkm2" value="checkm2.tsv"/>
+            <param name="format" value="png"/>
+            <output_collection name="plots" type="list">
+                <element name="comp_conta_marginals_checkm" ftype="png">
+                    <assert_contents>
+                        <has_size min="100000"/>
+                        <has_image_width min="1500"/>
+                        <has_image_height min="1200"/>
+                    </assert_contents>
+                </element>
+                <element name="comp_conta_marginals_checkm2" ftype="png">
+                    <assert_contents>
+                        <has_size min="100000"/>
+                        <has_image_width min="1500"/>
+                        <has_image_height min="1200"/>
+                    </assert_contents>
+                </element>
+            </output_collection>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="checkm" value="checkm.tsv"/>
+            <param name="checkm2" value="checkm2.tsv"/>
+            <param name="mode_cond|mode" value="tax"/>
+            <param name="mode_cond|gtdb" value="gtdb.tsv"/>
+            <param name="mode_cond|tax_level" value="phylum"/>
+            <param name="format" value="pdf"/>
+            <output_collection name="plots" type="list">
+                <element name="comp_conta_by_rank_marginals_CheckM2" ftype="pdf">
+                    <assert_contents>
+                        <has_size min="30000"/>
+                    </assert_contents>
+                </element>
+            </output_collection>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="checkm" value="checkm.tsv"/>
+            <param name="checkm2" value="checkm2.tsv"/>
+            <param name="mode_cond|mode" value="meta"/>
+            <param name="mode_cond|metadata" value="metadata.tsv"/>
+            <param name="mode_cond|meta_col" value="6"/>
+            <param name="mode_cond|meta_bin_width" value="5.0"/>
+            <param name="format" value="svg"/>
+            <output_collection name="plots" type="list">
+                <element name="comp_conta_by_Infection_by_Nosema_ceranae_marginals_CheckM" ftype="svg">
+                    <assert_contents>
+                        <has_size min="100000"/>
+                        <has_text text="Contamination (%)"/>
+                        <has_text text="Completeness (%)"/>
+                        <has_text text="% of MAGs"/>
+                    </assert_contents>
+                </element>
+                <element name="comp_conta_by_Infection_by_Nosema_ceranae_marginals_CheckM2" ftype="svg">
+                    <assert_contents>
+                        <has_size min="100000"/>
+                        <has_text text="Contamination (%)"/>
+                        <has_text text="Completeness (%)"/>
+                        <has_text text="% of MAGs"/>
+                    </assert_contents>
+                </element>
+            </output_collection>
+        </test>
+    </tests>
+    <help><![CDATA[
+**MAGs-visualization: comp-conta**
+
+This tool visualizes MAG quality by plotting genome completeness against contamination using CheckM/ CheckM2 results.
+
+Available modes:
+
+- **quality**:
+  MAGs are colored by quality category based on completeness and contamination thresholds (high, medium, low).
+  This provides an overview of the overall quality distribution of the dataset.
+
+- **tax**:
+  MAGs are colored by taxonomic classification (e.g. phylum) using GTDB annotations.
+  This allows comparison of MAG quality across different taxonomic groups
+
+- **meta**:
+  MAGs are colored based on a user-defined metadata column (e.g. treatment).
+  This shows how MAG quality relates to experimental conditions or sample metadata.
+
+Requirements:
+
+- CheckM / CheckM2 tables
+- GTDB annotations (tax mode)
+- Metadata table (meta mode)
+
+Output:
+
+- Scatter plots of completeness vs contamination with optional grouping
+
+Example output plots are available in the MAGs-visualization use cases with example configurations and parameter choices:
+https://github.com/usegalaxy-eu/MAGs-visualization/tree/main/use-cases
+
+For a direct example (bee microbiome dataset):
+https://github.com/usegalaxy-eu/MAGs-visualization/tree/main/use-cases/bee-use-case/plots
+    ]]></help>
+    <expand macro="citation"/>
+</tool>

tools/mags_visualization/drep_cluster_annot.xml

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+<tool id="mags_visualization_drep_cluster_annot" name="MAGs-visualization drep-cluster-annot" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>Create a dRep cluster plot with optional annotation</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="version_command"/>
+    <command detect_errors="exit_code"><![CDATA[
+        mags-visualization drep-cluster-annot
+            --drep '$drep'
+            --gtdb '$gtdb'
+            --top_n '$top_n'
+            --tax_levels_space '$tax_levels_space'
+            --format '$format'
+
+        #if $checkm2
+            --checkm2 '$checkm2'
+        #end if
+
+        #if $quast
+            --quast '$quast'
+        #end if
+
+        #if $bakta
+            --bakta '$bakta'
+        #end if
+
+        #if $tax_levels
+            --tax_levels
+            #for $tl in $tax_levels
+                '$tl'
+            #end for
+        #end if
+
+        #if str($fig_size.width) != "" and str($fig_size.height) != ""
+            --fig_size '$fig_size.width' '$fig_size.height'
+        #end if
+
+            -o outputs
+    ]]></command>
+    <inputs>
+        <param argument="--drep" type="data" format="csv,tabular" label="dRep cluster table"/>
+        <param argument="--gtdb" type="data" format="tabular" label="GTDB annotation table"/>
+        <param argument="--checkm2" type="data" format="tabular" optional="true" label="CheckM2 table (optional)"/>
+        <param argument="--quast" type="data" format="tabular" optional="true" label="QUAST table (optional)"/>
+        <param argument="--bakta" type="data" format="tabular" optional="true" label="Bakta table (optional)"/>
+        <param argument="--tax_levels" type="select" multiple="true" label="Taxonomy levels">
+            <option value="domain">domain</option>
+            <option value="phylum" selected="true">phylum</option>
+            <option value="class">class</option>
+            <option value="order">order</option>
+            <option value="family">family</option>
+            <option value="genus" selected="true">genus</option>
+            <option value="species">species</option>
+        </param>
+        <param argument="--top_n" type="integer" value="30" min="1" label="Top N clusters"/>
+        <param argument="--tax_levels_space" type="float" value="0.3" min="0.1" max="2.0" label="Spacing between taxonomy columns"/>
+        <param argument="--format" type="select" label="Output format">
+            <option value="png" selected="true">png</option>
+            <option value="pdf">pdf</option>
+            <option value="svg">svg</option>
+        </param>
+        <section name="fig_size" title="Figure size" expanded="false">
+            <param name="width" type="float" optional="true" min="1" label="Figure width"/>
+            <param name="height" type="float" optional="true" min="1" label="Figure height"/>
+        </section>
+    </inputs>
+    <outputs>
+        <collection name="plots" type="list">
+            <discover_datasets directory="outputs" pattern="(?P&lt;designation&gt;.+)\.(?P&lt;ext&gt;png|pdf|svg)$" visible="true"/>
+        </collection>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="drep" value="drep.csv"/>
+            <param name="gtdb" value="gtdb.tsv"/>
+            <param name="format" value="png"/>
+            <param name="top_n" value="30"/>
+            <param name="tax_levels" value="phylum,genus"/>
+            <output_collection name="plots" type="list">
+                <element name="drep_cluster_top30_phylum-genus" ftype="png">
+                    <assert_contents>
+                        <has_size min="500000"/>
+                        <has_image_width min="3300"/>
+                        <has_image_height min="2100"/>
+                    </assert_contents>
+                </element>
+            </output_collection>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="drep" value="drep.csv"/>
+            <param name="gtdb" value="gtdb.tsv"/>
+            <param name="checkm2" value="checkm2.tsv"/>
+            <param name="quast" value="quast.tsv"/>
+            <param name="bakta" value="bakta.tsv"/>
+            <param name="format" value="png"/>
+            <param name="top_n" value="30"/>
+            <param name="tax_levels" value="phylum,genus"/>
+            <output_collection name="plots" type="list">
+                <element name="drep_cluster_top30_phylum-genus" ftype="png">
+                    <assert_contents>
+                        <has_size min="600000"/>
+                        <has_image_width min="3400"/>
+                        <has_image_height min="2100"/>
+                    </assert_contents>
+                </element>
+            </output_collection>
+        </test>
+    </tests>
+    <help><![CDATA[
+**MAGs-visualization: drep-cluster-annot**
+
+This tool visualizes genome clusters generated by dRep and annotates them using GTDB taxonomy.
+
+Clusters are grouped by taxonomic levels (e.g. phylum, genus) based on representative genomes.
+
+Optional annotations can be included:
+
+- CheckM2 (genome quality)
+- QUAST (assembly statistics)
+- Bakta (annotation summaries)
+
+Requirements:
+
+- dRep clustering table
+- GTDB taxonomy table
+
+Output:
+
+- Cluster plots with taxonomic grouping and optional annotations
+
+
+Example output plots are available in the MAGs-visualization use cases with example configurations and parameter choices:
+https://github.com/usegalaxy-eu/MAGs-visualization/tree/main/use-cases
+
+For a direct example (bee microbiome dataset):
+https://github.com/usegalaxy-eu/MAGs-visualization/tree/main/use-cases/bee-use-case/plots   
+    ]]></help>
+    <expand macro="citation"/>
+</tool>