add WebAtlas pipeline 0.5.3

tools/webatlas/.shed.yml

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+name: webatlas
+owner: iuc
+description: The Galaxy WebAtlas tools to process spatial and single-cell experiment data for visualisation in a web browser using Vitessce.
+homepage_url: https://github.com/haniffalab/webatlas-pipeline
+long_description: The Galaxy WebAtlas tools provide a framework for processing spatial and single-cell experiment data, enabling visualisation with Vitessce.
+remote_repository_url: https://github.com/bgruening/galaxytools/tree/master/tools/webatlas
+categories:
+- Spatial Omics
+- Single Cell
+auto_tool_repositories:
+  name_template: "{{ tool_id }}"
+  description_template: "Wrapper for {{ tool_name }}."
+suite:
+  name: "suite_webatlas"
+  description: "A suite of Galaxy tools to process single-cell and spatial experiment data for visualisation using Vitessce."
+  type: repository_suite_definition

tools/webatlas/consolidate_md.xml

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+<tool id="webatlas_consolidate_md" name="WebAtlas Consolidate Metadata" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" python_template_version="3.5" profile="@PROFILE_VERSION@">
+    <description>Converts an image to Zarr and consolidates metadata</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+        if tiffinfo $input_image | grep "Compression Scheme:" | grep -wq "JPEG";
+        then
+            if od -h -j2 -N2 $input_image | head -n1 | sed 's/[0-9]*  *//' | grep -q -E '002b|2b00';
+            then
+                tiffcp -c none -m 0 -8 $input_image uncompressed.tiff;
+            else
+                tiffcp -c none -m 0 $input_image uncompressed.tiff || tiffcp -c none -m 0 -8 $input_image uncompressed.tiff;
+            fi;
+                bioformats2raw --no-hcs uncompressed.tiff $stem-'$image_type'.zarr;
+        else
+            bioformats2raw --no-hcs $input_image $stem-'$image_type'.zarr;
+        fi;
+        consolidate_md.py --file_in $stem-'$image_type'.zarr &&
+        mkdir -p '$output_zarr.extra_files_path' &&
+        mv $stem-'$image_type'.zarr $output_zarr.extra_files_path
+    ]]></command>
+    <inputs>
+        <param name="input_image" type="data" format="tif,tiff,jpg" label="TIFF or JPEG image" help="Input image to convert to Zarr. JPEG-compressed TIFF images are automatically decompressed before conversion."/>
+        <expand macro="stem"/>
+        <param name="image_type" type="select" label="Input image type" help="Choose the type of input image.">
+            <option value="label">label</option>
+            <option value="raw">raw</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="output_zarr" format="zarr" label="${tool.name} on ${on_string}: Zarr output"/>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="input_image" location="https://zenodo.org/records/20029977/files/visium-breast-cancer-label.tif"/>
+            <param name="stem" value="visium-breast-cancer"/>
+            <param name="image_type" value="label"/>
+            <output name="output_zarr">
+                <extra_files type="file" name="visium-breast-cancer-label.zarr/OME/METADATA.ome.xml">
+                    <assert_contents>
+                        <has_text text="&lt;Description&gt;{&quot;shape&quot;: [21571, 19505]}&lt;/Description&gt;&lt;Pixels BigEndian=&quot;true&quot; DimensionOrder=&quot;XYZCT&quot;"/>
+                    </assert_contents>
+                </extra_files>
+            </output>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="input_image" location="https://zenodo.org/records/20029977/files/tissue_image.tif"/>
+            <param name="stem" value="visium-breast-cancer"/>
+            <param name="image_type" value="raw"/>
+            <output name="output_zarr">
+                <extra_files type="file" name="visium-breast-cancer-raw.zarr/OME/METADATA.ome.xml">
+                    <assert_contents>
+                        <has_text_matching expression="Pixels BigEndian=&quot;true&quot; DimensionOrder=&quot;XYZCT&quot; ID=&quot;Pixels:0&quot; Interleaved=&quot;false&quot; PhysicalSizeX=&quot;0.5475[0-9]+&quot; PhysicalSizeXUnit=&quot;µm&quot; PhysicalSizeY=&quot;0.5476[0-9]+&quot; PhysicalSizeYUnit=&quot;µm&quot; SignificantBits=&quot;8&quot; SizeC=&quot;3&quot; SizeT=&quot;1&quot; SizeX=&quot;19505&quot; SizeY=&quot;21571&quot; SizeZ=&quot;1&quot; Type=&quot;uint8&quot;"/>
+                    </assert_contents>
+                </extra_files>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+This tool converts image data into the Zarr format and consolidates its metadata to improve performance in downstream visualization.
+
+It typically processes label images generated by **WebAtlas Generate Image** and raw images provided as input or generated within the WebAtlas workflow.
+
+----
+
+**Supported Input Types**
+
+- **TIFF image** (including JPEG-compressed TIFF)
+- **JPEG image**
+
+----
+
+**Processing Steps**
+
+- (If applicable) Decompression of JPEG-compressed TIFF images prior to conversion 
+- Conversion of the input image to Zarr format using *bioformats2raw*
+- Consolidation of Zarr metadata
+
+----
+
+**Metadata Consolidation**
+
+Zarr datasets normally store metadata in many small files. This tool consolidates them into a single metadata file.
+
+This can significantly reduce the time necessary to load the metadata in downstream visualization.
+
+----
+
+**Output**
+
+- **Zarr dataset (image with consolidated metadata)**
+
+The output is used as input for the downstream WebAtlas tools **WebAtlas OME Zarr Metadata**, **WebAtlas Build Vitessce Config**, and **WebAtlas Write**.
+    ]]></help>
+    <expand macro="citations"/>
+</tool>