Mercurial > repos > iuc > spatialdata_io
diff spatialdata_io.xml @ 0:1f6c780a2635 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/spatialdata commit 87bff76d897c5a4277d9987cf26432a18e0458cd-dirty
| author | iuc |
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| date | Sat, 14 Mar 2026 15:16:08 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/spatialdata_io.xml Sat Mar 14 15:16:08 2026 +0000 @@ -0,0 +1,927 @@ +<tool id="spatialdata_io" name="SpatialData IO" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> + <description>load common spatial omics formats into SpatialData</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <expand macro="creator" /> + <command detect_errors="exit_code"><![CDATA[ + ## CosMX + #if $method_condi.method == 'cosmx': + ## puting all files in working directory instead of input. cosmx should run inside same directory + mkdir -p 'CellComposite' 'CellLabels' 'output' && + #for $image in $method_condi.CellComposite: + #if $image.element_identifier.endswith('.jpg'): + ln -s '$image' 'CellComposite/${image.element_identifier}' && + #else: + ln -s '$image' 'CellComposite/${image.element_identifier}.jpg' && + #end if + #end for + #for $image in $method_condi.CellLabels: + #if $image.element_identifier.endswith('.tiff') or $image.element_identifier.endswith('.tif'): + ln -s '$image' 'CellLabels/${image.element_identifier}' && + #else: + ln -s '$image' 'CellLabels/${image.element_identifier}.tiff' && + #end if + #end for + #if $method_condi.exprMat_file.element_identifier.endswith('.csv'): + ln -s '$method_condi.exprMat_file' '${method_condi.exprMat_file.element_identifier}' && + #else: + ln -s '$method_condi.exprMat_file' '${method_condi.exprMat_file.element_identifier}.csv' && + #end if + #if $method_condi.fov_positions_file.element_identifier.endswith('.csv'): + ln -s '$method_condi.fov_positions_file' '${method_condi.fov_positions_file.element_identifier}' && + #else: + ln -s '$method_condi.fov_positions_file' '${method_condi.fov_positions_file.element_identifier}.csv' && + #end if + #if $method_condi.metadata_file.element_identifier.endswith('.csv'): + ln -s '$method_condi.metadata_file' '${method_condi.metadata_file.element_identifier}' && + #else: + ln -s '$method_condi.metadata_file' '${method_condi.metadata_file.element_identifier}.csv' && + #end if + #if $method_condi.tx_file.element_identifier.endswith('.csv'): + ln -s '$method_condi.tx_file' '${method_condi.tx_file.element_identifier}' && + #else: + ln -s '$method_condi.tx_file' '${method_condi.tx_file.element_identifier}.csv' && + #end if + + ## CURIO + #else if $method_condi.method == 'curio': + mkdir -p 'input' 'output' && + ln -s '$method_condi.anndata' 'input/${method_condi.dataset_id}_anndata.h5ad' && + ln -s '$method_condi.cluster_assignment' 'input/${method_condi.dataset_id}_cluster_assignment.txt' && + ln -s '$method_condi.metrics' 'input/${method_condi.dataset_id}_Metrics.csv' && + ln -s '$method_condi.variable_features_clusters' 'input/${method_condi.dataset_id}_variable_features_clusters.txt' && + ln -s '$method_condi.variable_features_spatial' 'input/${method_condi.dataset_id}_variable_features_spatial_moransi.txt' && + + ## DBIT + #else if $method_condi.method == 'dbit': + ## puting all files in working directory instead of input. dbit should run inside same directory + mkdir -p 'output' && + ln -s '$method_condi.barcode_positions' '${method_condi.dataset_id}_barcode_positions.tabular' && + ln -s '$method_condi.counts' '${method_condi.dataset_id}_counts.h5ad' && + ln -s '$method_condi.tissue_lowres' '${method_condi.dataset_id}_tissue_lowres.png' && + + ## MACSima + #else if $method_condi.method == 'macsima': + mkdir -p 'input' 'output' && + #for $image in $method_condi.tiff_files: + #if $image.element_identifier.endswith('.tif') or $image.element_identifier.endswith('.tiff'): + ln -s '$image' 'input/${image.element_identifier}' && + #else: + ln -s '$image' 'input/${image.element_identifier}.tif' && + #end if + #end for + + ## MERSCOPE + #else if $method_condi.method == 'merscope': + mkdir -p 'input/region/images' 'input/region/vpt_outputs' 'output' && + #for $image in $method_condi.mosaic_images: + #if $image.element_identifier.endswith('.tif'): + ln -s '$image' 'input/region/images/${image.element_identifier}' && + #else: + ln -s '$image' 'input/region/images/${image.element_identifier}.tif' && + #end if + #end for + ln -s '$method_condi.input_micron_to_mosaic' 'input/region/images/micron_to_mosaic_pixel_transform.csv' && + ln -s '$method_condi.cell_by_gene' 'input/region/vpt_outputs/cell_by_gene.csv' && + ln -s '$method_condi.cell_meta' 'input/region/vpt_outputs/cell_metadata.csv' && + ## the tool checks the file name, so the name is hardcoded here, but it does not necessarily have to be from cellpose + ln -s '$method_condi.cells_boundaries' 'input/region/vpt_outputs/cellpose_micron_space.parquet' && + ln -s '$method_condi.transcripts' 'input/region/detected_transcripts.csv' && + + ## Visium + #else if $method_condi.method == 'visium': + mkdir -p 'input/spatial' 'output' && + #if $method_condi.matrix_bool: + ln -s '$method_condi.feature_bc_matrix' 'input/raw_feature_bc_matrix.h5' && + #else: + ln -s '$method_condi.feature_bc_matrix' 'input/filtered_feature_bc_matrix.h5' && + #end if + ln -s '$method_condi.scalefactors_json' 'input/scalefactors_json.json' && + ln -s '$method_condi.fullres_image_file' 'input/fullres_image.tif' && + ln -s '$method_condi.tissue_hires_image' 'input/spatial/tissue_hires_image.png' && + ln -s '$method_condi.tissue_lowres_image' 'input/spatial/tissue_lowres_image.png' && + ln -s '$method_condi.tissue_positions_list' 'input/tissue_positions_list.csv' && + + ## Visium HD + #else if $method_condi.method == 'visium_hd': + mkdir -p 'input' 'output' && + ## Core required file + ln -s '$method_condi.feature_slice' 'input/feature_slice.h5' && + + ## Binned outputs (if included) + #if str($method_condi.include_binned_condi.include_binned) == 'yes': + ## Bin 002um (required for nucleus segmentation if enabled) + #if $method_condi.include_binned_condi.bin002.feature_bc_matrix_002: + mkdir -p 'input/binned_outputs/square_002um/spatial' && + #if $method_condi.matrix_bool: + ln -s '$method_condi.include_binned_condi.bin002.feature_bc_matrix_002' 'input/binned_outputs/square_002um/raw_feature_bc_matrix.h5' && + #else: + ln -s '$method_condi.include_binned_condi.bin002.feature_bc_matrix_002' 'input/binned_outputs/square_002um/filtered_feature_bc_matrix.h5' && + #end if + ln -s '$method_condi.include_binned_condi.bin002.tissue_positions_002' 'input/binned_outputs/square_002um/spatial/tissue_positions.parquet' && + ln -s '$method_condi.include_binned_condi.bin002.scalefactors_json_002' 'input/binned_outputs/square_002um/spatial/scalefactors_json.json' && + #end if + + ## Bin 008um + #if $method_condi.include_binned_condi.bin008.feature_bc_matrix_008: + mkdir -p 'input/binned_outputs/square_008um/spatial' && + #if $method_condi.matrix_bool: + ln -s '$method_condi.include_binned_condi.bin008.feature_bc_matrix_008' 'input/binned_outputs/square_008um/raw_feature_bc_matrix.h5' && + #else: + ln -s '$method_condi.include_binned_condi.bin008.feature_bc_matrix_008' 'input/binned_outputs/square_008um/filtered_feature_bc_matrix.h5' && + #end if + ln -s '$method_condi.include_binned_condi.bin008.tissue_positions_008' 'input/binned_outputs/square_008um/spatial/tissue_positions.parquet' && + ln -s '$method_condi.include_binned_condi.bin008.scalefactors_json_008' 'input/binned_outputs/square_008um/spatial/scalefactors_json.json' && + #end if + + ## Bin 016um + #if $method_condi.include_binned_condi.bin016.feature_bc_matrix_016: + mkdir -p 'input/binned_outputs/square_016um/spatial' && + #if $method_condi.matrix_bool: + ln -s '$method_condi.include_binned_condi.bin016.feature_bc_matrix_016' 'input/binned_outputs/square_016um/raw_feature_bc_matrix.h5' && + #else: + ln -s '$method_condi.include_binned_condi.bin016.feature_bc_matrix_016' 'input/binned_outputs/square_016um/filtered_feature_bc_matrix.h5' && + #end if + ln -s '$method_condi.include_binned_condi.bin016.tissue_positions_016' 'input/binned_outputs/square_016um/spatial/tissue_positions.parquet' && + ln -s '$method_condi.include_binned_condi.bin016.scalefactors_json_016' 'input/binned_outputs/square_016um/spatial/scalefactors_json.json' && + #end if + + ## Nucleus segmentation (requires barcode_mappings at root) + #if str($method_condi.include_binned_condi.include_nucleus_seg_condi.include_nucleus_seg) == 'yes': + mkdir -p 'input/segmented_outputs/' && + ln -s '$method_condi.include_binned_condi.include_nucleus_seg_condi.barcode_mappings' 'input/barcode_mappings.parquet' && + ln -s '$method_condi.include_binned_condi.include_nucleus_seg_condi.nucleus_segmentation' 'input/segmented_outputs/nucleus_segmentations.geojson' && + #end if + #end if + + ## Segmented outputs (cell segmentation) + #if str($method_condi.segmentation_conditional.enable_segmentation) == 'yes': + mkdir -p 'input/segmented_outputs/spatial' && + #if $method_condi.matrix_bool: + ln -s '$method_condi.segmentation_conditional.feature_bc_matrix_seg' 'input/segmented_outputs/raw_feature_cell_matrix.h5' && + #else: + ln -s '$method_condi.segmentation_conditional.feature_bc_matrix_seg' 'input/segmented_outputs/filtered_feature_cell_matrix.h5' && + #end if + ln -s '$method_condi.segmentation_conditional.cell_segmentation' 'input/segmented_outputs/cell_segmentations.geojson' && + ln -s '$method_condi.segmentation_conditional.scalefactors_json_seg' 'input/segmented_outputs/spatial/scalefactors_json.json' && + #end if + + ## Images (placed in spatial/ and/or segmented_outputs/spatial/) + mkdir -p 'input/spatial' && + #if $method_condi.images.tissue_hires: + ln -s '$method_condi.images.tissue_hires' 'input/spatial/tissue_hires_image.png' && + #end if + #if $method_condi.images.tissue_lowres: + ln -s '$method_condi.images.tissue_lowres' 'input/spatial/tissue_lowres_image.png' && + #end if + #if str($method_condi.images.cytassist_image_condi.include_cytassist) == 'yes': + ln -s '$method_condi.images.cytassist_image_condi.cytassist_image' 'input/spatial/cytassist_image.tiff' && + #end if + + ## Microscope image (if provided, create microscope_image directory) + #if $method_condi.images.microscope_image: + mkdir -p 'input/microscope_image' && + ln -s '$method_condi.images.microscope_image' 'input/microscope_image/fullres_image.tiff' && + #end if + + echo "echoing the structure..." && + tree -L 3 input && + + ## XENIUM + #else if $method_condi.method == 'xenium': + mkdir -p 'input/region/morphology_focus/' 'output' && + ## ln -s does not work here. + #if str($method_condi.cell_boundaries) != '': + cp '$method_condi.cell_boundaries' 'input/region/cell_boundaries.parquet' && + #end if + cp '$method_condi.cell_feature_matrix' 'input/region/cell_feature_matrix.h5' && + cp '$method_condi.cells' 'input/region/cells.parquet' && + cp '$method_condi.cells_zarr' 'input/region/cells.zarr.zip' && + cp '$method_condi.experiment_xenium' 'input/region/experiment.xenium' && + #for $image in $method_condi.morphology_focus: + #if $image.element_identifier.endswith('.ome.tiff') or $image.element_identifier.endswith('.ome.tif'): + cp '$image' 'input/region/morphology_focus/${image.element_identifier}' && + #else: + cp '$image' 'input/region/morphology_focus/${image.element_identifier}.ome.tif' && + #end if + #end for + #if str($method_condi.nucleus_boundaries) != '': + cp '$method_condi.nucleus_boundaries' 'input/region/nucleus_boundaries.parquet' && + #end if + #if str($method_condi.transcripts) != '': + cp '$method_condi.transcripts' 'input/region/transcripts.parquet' && + #end if + #if str($method_condi.add_hne_condi.add_hne) == 'yes' or str($method_condi.add_hne_condi.add_hne) == 'yes_accurate': + cp '$method_condi.add_hne_condi.hne_image' 'input/region/he_image.ome.tif' && + #end if + #if str($method_condi.add_if_condi.add_if) == 'yes' or str($method_condi.add_if_condi.add_if) == 'yes_accurate': + cp '$method_condi.add_if_condi.if_image' 'input/region/if_image.ome.tif' && + #end if + #if str($method_condi.add_hne_condi.add_hne) == 'yes_accurate': + cp '$method_condi.add_hne_condi.image_alignment' 'input/region/he_image_alignment.csv' && + #end if + #if str($method_condi.add_if_condi.add_if) == 'yes_accurate': + cp '$method_condi.add_if_condi.image_alignment' 'input/region/if_image_alignment.csv' && + #end if + #end if + + ## run the pipeline + cat 'spdata_io.py' && + python3 'spdata_io.py' && + ## zip the output spatialdata folder + cd output && zip -r ../spatialdata.spatialdata.zip spatialdata/ && cd .. + ]]></command> + <configfiles> + <configfile name="spdata_config" filename="spdata_io.py"> +#if $method_condi.method == 'cosmx': +from spatialdata_io import cosmx +spdata = cosmx(path="./", + dataset_id="$method_condi.dataset_id", + transcripts=$method_condi.transcripts_bool, + ) + +#else if $method_condi.method == 'curio': +from spatialdata_io import curio +spdata = curio(path="./input" + ) + +#else if $method_condi.method == 'dbit': +from spatialdata_io import dbit +spdata = dbit(path="./", + anndata_path="${method_condi.dataset_id}_counts.h5ad", + barcode_position="${method_condi.dataset_id}_barcode_positions.tabular", + image_path="${method_condi.dataset_id}_tissue_lowres.png", + dataset_id="$method_condi.dataset_id", + border=$method_condi.border, + border_scale=$method_condi.border_scale, + ) + +#else if $method_condi.method == 'macsima': +from spatialdata_io import macsima +spdata = macsima(path="./input", + parsing_style="auto", + #if $method_condi.subset: + subset=$method_condi.subset, + #end if + #if $method_condi.subset_c: + subset_c=$method_condi.subset_c, + #end if + max_chunk_size=$method_condi.max_chunk_size, + c_chunks_size=$method_condi.c_chunks_size, + multiscale=$method_condi.multiscale_bool, + transformations=$method_condi.transformations_bool, + #if str($method_condi.scale_factors) != '': + #set scale_factors_list = [int(x.strip()) for x in str($method_condi.scale_factors).split(',')] + scale_factors=$scale_factors_list, + #end if + nuclei_channel_name="$method_condi.nuclei_channel_name", + #if str($method_condi.split_threshold_nuclei_channel) != '': + split_threshold_nuclei_channel=$method_condi.split_threshold_nuclei_channel, + #else: + split_threshold_nuclei_channel=None, + #end if + include_cycle_in_channel_name=$method_condi.include_cycle_in_channel_name_bool, + ) + +#else if $method_condi.method == 'merscope': +from spatialdata_io import merscope +spdata = merscope(path="./input/region", + vpt_outputs="./input/region/vpt_outputs", + #set z_layers_list = [int(x.strip()) for x in str($method_condi.z_layers).split(',')] + z_layers=$z_layers_list, + region_name="$method_condi.region_name", + slide_name="$method_condi.slide_name", + backend="rioxarray", + transcripts=$method_condi.transcripts_bool, + cells_boundaries=$method_condi.cells_boundaries_bool, + cells_table=$method_condi.cells_table_bool, + mosaic_images=$method_condi.mosaic_images_bool, + ) + +#else if $method_condi.method == 'visium': +from spatialdata_io import visium +spdata = visium(path="./input", + dataset_id="$method_condi.dataset_id", + #if $method_condi.matrix_bool: + counts_file='raw_feature_bc_matrix.h5', + #else: + counts_file='filtered_feature_bc_matrix.h5', + #end if + fullres_image_file='fullres_image.tif', + tissue_positions_file='tissue_positions_list.csv', + scalefactors_file='scalefactors_json.json', + var_names_make_unique=True, + ) + +#else if $method_condi.method == 'visium_hd': +from spatialdata_io import visium_hd +spdata = visium_hd(path="./input", + dataset_id="$method_condi.dataset_id", + #if $method_condi.matrix_bool: + filtered_counts_file=False, + #else: + filtered_counts_file=True, + #end if + #if str($method_condi.include_binned_condi.include_binned) == 'no': + load_segmentations_only=True, + #else: + load_segmentations_only=False, + #end if + #if str($method_condi.include_binned_condi.include_binned) == 'yes' and str($method_condi.include_binned_condi.include_nucleus_seg_condi.include_nucleus_seg) == 'yes': + load_nucleus_segmentations=True, + #else: + load_nucleus_segmentations=False, + #end if + bin_size=None, + bins_as_squares=$method_condi.bins_as_squares_bool, + annotate_table_by_labels=$method_condi.annotate_table_by_labels_bool, + #if $method_condi.images.microscope_image: + fullres_image_file="./input/microscope_image/fullres_image.tiff", + #else: + fullres_image_file=None, + #end if + #if str($method_condi.images.cytassist_image_condi.include_cytassist) == 'yes': + load_all_images=True, + #else: + load_all_images=False, + #end if + var_names_make_unique=$method_condi.var_names_make_unique_bool, + ) + +#else if $method_condi.method == 'xenium': +import os +from spatialdata_io import xenium +spdata = xenium(path="./input/region", + #if str($method_condi.cell_boundaries) != '': + cells_boundaries=True, + #else: + cells_boundaries=False, + #end if + #if str($method_condi.nucleus_boundaries) != '': + nucleus_boundaries=True, + #else: + nucleus_boundaries=False, + #end if + cells_as_circles=$method_condi.cells_as_circles_bool, + cells_labels=$method_condi.cells_labels_bool, + nucleus_labels=$method_condi.nucleus_labels_bool, + #if str($method_condi.transcripts) != '': + transcripts=True, + #else: + transcripts=False, + #end if + morphology_mip=$method_condi.morphology_mip_bool, + morphology_focus=$method_condi.morphology_focus_bool, + #if str($method_condi.add_hne_condi.add_hne) == 'yes' or str($method_condi.add_if_condi.add_if) == 'yes': + aligned_images=True, + #else: + aligned_images=False, + #end if + cells_table=$method_condi.cells_table_bool, + gex_only=$method_condi.gex_only_bool, + n_jobs=int(os.getenv("GALAXY_SLOTS")), + ) + +#if str($method_condi.add_if_condi.add_if) == 'yes_accurate': +from spatialdata_io import xenium_aligned_image +spdata["if_image"] = xenium_aligned_image( + image_path="./input/region/if_image.ome.tif", + alignment_file="./input/region/if_image_alignment.csv" +) +#else if str($method_condi.add_hne_condi.add_hne) == 'yes_accurate': +from spatialdata_io import xenium_aligned_image +spdata["he_image"] = xenium_aligned_image( + image_path="./input/region/he_image.ome.tif", + alignment_file="./input/region/he_image_alignment.csv" +) + +#end if +#end if + +print(spdata) +spdata.write("./output/spatialdata", overwrite=True) + </configfile> + </configfiles> + <inputs> + <conditional name="method_condi"> + <param name="method" type="select" label="Spatial Technology"> + <option value="cosmx">CosMx</option> + <option value="dbit">DBiT-seq</option> + <option value="macsima">MACSima</option> + <option value="merscope">MERSCOPE</option> + <option value="visium">10x Genomics Visium</option> + <option value="visium_hd">10x Genomics Visium HD</option> + <option value="xenium">10x Genomics Xenium</option> + </param> + <when value="cosmx"> + <param name="CellComposite" type="data" format="jpg,png,tiff" multiple="true" label="Cell Composite images"/> + <param name="CellLabels" type="data" format="tiff" multiple="true" label="Cell Labels images"/> + <param name="exprMat_file" type="data" format="csv" label="Expression matrix file"/> + <param name="fov_positions_file" type="data" format="csv" label="FOV positions file"/> + <param name="metadata_file" type="data" format="csv" label="Metadata file"/> + <param name="tx_file" type="data" format="csv" label="Transcripts file"/> + <param name="dataset_id" type="text" value="Galaxy" label="Dataset identifier" help="It should match your input files name"> + <sanitizer invalid_char=""> + <valid initial="string.letters,string.digits"> + <add value="_" /> + </valid> + </sanitizer> + <validator type="regex">[0-9a-zA-Z_]+</validator> + </param> + <param name="transcripts_bool" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Load transcripts information?"/> + </when> + <when value="dbit"> + <param name="barcode_positions" type="data" format="tabular" label="Barcode positions file"/> + <param name="counts" type="data" format="h5ad" label="Counts file"/> + <param name="tissue_lowres" type="data" format="png" label="Tissue low resolution image"/> + <param name="dataset_id" type="text" value="Galaxy" label="Dataset identifier" help="It should match your input files name"> + <sanitizer invalid_char=""> + <valid initial="string.letters,string.digits"> + <add value="_" /> + </valid> + </sanitizer> + <validator type="regex">[0-9a-zA-Z_]+</validator> + </param> + <param name="border" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Create a border" help="If True, the square is shrinked toward its center, leaving an empty border." /> + <param name="border_scale" type="float" value="1" label="Border scale factor" help="The factor by which the border is scaled. The default is 1. It corresponds to a border length of (0.125 * length of the square’s edge)"/> + </when> + <when value="macsima"> + <param name="tiff_files" type="data" format="tiff" multiple="true" label="MACSima TIFF images" help="OME-TIFF files from MACSima cyclic imaging experiment"/> + <param name="subset" type="integer" min="0" optional="true" label="Subset the image to the first ``subset`` pixels in x and y dimensions"/> + <param name="subset_c" type="integer" min="0" optional="true" label="Subset the image to the first ``c_subset`` channels"/> + <param name="max_chunk_size" type="integer" min="0" value="1024" label="Maximum chunk size for x and y dimension"/> + <param name="c_chunks_size" type="integer" min="0" value="1" label="Maximum chunk size for x and y dimension"/> + <param name="multiscale_bool" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Create multiscale image?"/> + <param name="transformations_bool" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Whether to add a transformation from pixels to microns to the image"/> + <param name="scale_factors" type="integer" min="0" optional="true" label="Scale factors to use for downsampling" help="If None, scale factors are calculated based on image size."/> + <param name="nuclei_channel_name" type="text" value="DAPI" label="Nuclei channel name"/> + <param name="split_threshold_nuclei_channel" type="integer" min="0" value="2" optional="true" label="Split threshold for nuclei channels" help="If the number of channels that include nuclei_channel_name is greater than this threshold, the nuclei channels are split into a separate stack.."/> + <param name="include_cycle_in_channel_name_bool" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Include cycle number in channel name?" help="If True, prepend cycle number to channel names (e.g., 'R1 DAPI')"/> + </when> + <when value="merscope"> + <param name="slide_name" type="text" value="Galaxy" label="Dataset identifier" help="Prefix used to name the constructed SpatialData elements."> + <sanitizer invalid_char=""> + <valid initial="string.letters,string.digits"> + <add value="_" /> + </valid> + </sanitizer> + <validator type="regex">[0-9a-zA-Z_]+</validator> + </param> + <param name="region_name" type="text" value="region" label="Region name" help="Region name appended to the dataset identifier in the MERSCOPE output."> + <sanitizer invalid_char=""> + <valid initial="string.letters,string.digits"> + <add value="_" /> + </valid> + </sanitizer> + <validator type="regex">[0-9a-zA-Z_]+</validator> + </param> + <param argument="--z_layers" type="text" value="3" optional="false" label="Comma separated list of Indices of the z-layers to consider" help="By default, only the middle layer is considered (layer 3)."> + <expand macro="sanitize_digits"/> + </param> + <param argument="--mosaic-images" type="data" format="tiff" multiple="true" label="MEROSCOPE tiff images"/> + <param name="input_micron_to_mosaic" type="data" format="csv" label="Micron to mosaic mapping file"/> + <param name="cell_by_gene" type="data" format="csv" label="Cell by gene table" help="Cells as rows and Genes as columns"/> + <param name="cell_meta" type="data" format="csv" label="Cell metadata table"/> + <param name="cells_boundaries" type="data" format="parquet" label="Cell boundaries (micron_space)"/> + <param name="transcripts" type="data" format="csv" label="Detected transcripts"/> + <param name="transcripts_bool" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Load transcripts information?"/> + <param name="cells_boundaries_bool" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Load cells boundaries?"/> + <param name="cells_table_bool" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Load cells table?"/> + <param name="mosaic_images_bool" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Load mosaic images?"/> + </when> + <when value="visium"> + <param name="dataset_id" type="text" value="Galaxy" label="Dataset identifier to name the constructed SpatialData elements"> + <sanitizer invalid_char=""> + <valid initial="string.letters,string.digits"> + <add value="_" /> + </valid> + </sanitizer> + <validator type="regex">[0-9a-zA-Z_]+</validator> + </param> + <param name="feature_bc_matrix" type="data" format="h5" label="feature BC matrix (Counts file)"/> + <param name="matrix_bool" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Is the matrix input, raw?" help="If the matrix input is raw, set this to true." /> + <param name="scalefactors_json" type="data" format="json" label="Scale factors file"/> + <param name="fullres_image_file" type="data" format="tiff" label="Full resolution image"/> + <param name="tissue_hires_image" type="data" format="png" label="Tissue high resolution image"/> + <param name="tissue_lowres_image" type="data" format="png" label="Tissue low resolution image"/> + <param name="tissue_positions_list" type="data" format="csv" label="Tissue positions file"/> + </when> + <when value="visium_hd"> + <param name="dataset_id" type="text" value="Galaxy" label="Dataset identifier" help="Name for the constructed SpatialData elements"> + <sanitizer invalid_char=""> + <valid initial="string.letters,string.digits"> + <add value="_" /> + </valid> + </sanitizer> + <validator type="regex">[0-9a-zA-Z_]+</validator> + </param> + <param name="matrix_bool" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Is the matrix input, raw?" help="If the matrix input is raw, set this to true."/> + <param name="feature_slice" type="data" format="h5" label="Feature slice file"/> + <conditional name="include_binned_condi"> + <param name="include_binned" type="select" label="Include binned data?"> + <option value="yes">Yes</option> + <option value="no">No</option> + </param> + <when value="no"/> + <when value="yes"> + <section name="bin008" title="Binned outputs 008"> + <param name="feature_bc_matrix_008" type="data" format="h5" optional="true" label="Feature BC matrix of bin 008"/> + <param name="tissue_positions_008" type="data" format="parquet" optional="true" label="Tissue positions of bin 008"/> + <param name="scalefactors_json_008" type="data" format="json" optional="true" label="Scale factors of bin 008"/> + </section> + <section name="bin016" title="Binned outputs 016"> + <param name="feature_bc_matrix_016" type="data" format="h5" optional="true" label="Feature BC matrix of bin 016"/> + <param name="tissue_positions_016" type="data" format="parquet" optional="true" label="Tissue positions of bin 016"/> + <param name="scalefactors_json_016" type="data" format="json" optional="true" label="Scale factors of bin 016"/> + </section> + <conditional name="include_nucleus_seg_condi"> + <param name="include_nucleus_seg" type="select" label="Include nucleus segmentation?"> + <option value="yes">Yes</option> + <option value="no">No</option> + </param> + <when value="no"> + <section name="bin002" title="Binned outputs 002"> + <param name="feature_bc_matrix_002" type="data" format="h5" optional="true" label="Feature BC matrix of bin 002"/> + <param name="tissue_positions_002" type="data" format="parquet" optional="true" label="Tissue positions of bin 002"/> + <param name="scalefactors_json_002" type="data" format="json" optional="true" label="Scale factors of bin 002"/> + </section> + </when> + <when value="yes"> + <section name="bin002" title="Binned outputs 002"> + <param name="feature_bc_matrix_002" type="data" format="h5" optional="false" label="Feature BC matrix of bin 002"/> + <param name="tissue_positions_002" type="data" format="parquet" optional="false" label="Tissue positions of bin 002"/> + <param name="scalefactors_json_002" type="data" format="json" optional="false" label="Scale factors of bin 002"/> + </section> + <param name="nucleus_segmentation" type="data" format="geojson" optional="false" label="Nucleus segmentation GeoJSON"/> + <param name="barcode_mappings" type="data" format="parquet" optional="false" label="Barcode mappings"/> + </when> + </conditional> + </when> + </conditional> + <conditional name="segmentation_conditional"> + <param name="enable_segmentation" type="select" label="Include segmentation data?"> + <option value="yes">Yes</option> + <option value="no">No</option> + </param> + <when value="no"/> + <when value="yes"> + <param name="feature_bc_matrix_seg" type="data" format="h5" optional="false" label="Feature BC matrix of cell segmentation"/> + <param name="cell_segmentation" type="data" format="geojson" optional="false" label="Cell segmentation GeoJSON"/> + <param name="scalefactors_json_seg" type="data" format="json" optional="false" label="Scale factors of cell segmentation"/> + </when> + </conditional> + <section name="images" title="Images"> + <param name="microscope_image" type="data" format="png,tiff,jpg" optional="true" label="Microscope image" help="Full-resolution microscope image (png/tiff/jpg)"/> + <param name="tissue_hires" type="data" format="png" optional="true" label="Tissue high-res image" help="tissue_hires_image.png"/> + <param name="tissue_lowres" type="data" format="png" optional="true" label="Tissue low-res image" help="tissue_lowres_image.png"/> + <conditional name="cytassist_image_condi"> + <param name="include_cytassist" type="select" label="Include CytAssist image?"> + <option value="yes">Yes</option> + <option value="no">No</option> + </param> + <when value="no"/> + <when value="yes"> + <param name="cytassist_image" type="data" format="tiff" optional="false" label="CytAssist image"/> + </when> + </conditional> + </section> + <param name="bins_as_squares_bool" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Load bins as squares?" help="If True, bins are represented as squares; if False, as circles"/> + <param name="annotate_table_by_labels_bool" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Annotate table by labels?" help="Annotate the AnnData table with cell/nucleus labels"/> + <param name="var_names_make_unique_bool" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Make variable names unique?" help="If True, call .var_names_make_unique() on each AnnData table"/> + </when> + <when value="xenium"> + <param name="cell_feature_matrix" type="data" format="h5" label="Cell feature matrix"/> + <param name="cells" type="data" format="parquet" label="Cells metadata"/> + <param name="cells_zarr" type="data" format="zarr.zip" label="Cells zarr archive"/> + <param name="experiment_xenium" type="data" format="json" label="Experiment xenium file containing specifications"/> + <param name="morphology_focus" type="data" format="ome.tiff" multiple="true" label="Morphology focus images" help="Both MIP and Focus"/> + <param name="cell_boundaries" type="data" optional="true" format="parquet" label="Polygons of cell boundaries"/> + <param name="nucleus_boundaries" type="data" optional="true" format="parquet" label="Polygons of nucleus boundaries"/> + <param name="transcripts" type="data" optional="true" format="parquet" label="Transcripts"/> + <param name="cells_as_circles_bool" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Represent cells as circles?" help="The center and the radius of each circle is computed from the corresponding labels cell"/> + <param name="cells_labels_bool" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Load cells labels?"/> + <param name="nucleus_labels_bool" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Load nucleus labels?"/> + <param name="morphology_mip_bool" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Load morphology MIP?"/> + <param name="morphology_focus_bool" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Load morphology focus?"/> + <param name="cells_table_bool" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Load cells annotation from AnnData?"/> + <param name="gex_only_bool" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Load gene expression only?"/> + <conditional name="add_hne_condi"> + <param name="add_hne" type="select" label="Add H&E image?"> + <option value="yes_accurate">Yes, with accurate alignment</option> + <option value="yes">Yes</option> + <option value="no" selected="true">No</option> + </param> + <when value="no"/> + <when value="yes_accurate"> + <param name="hne_image" type="data" format="ome.tiff" label="H&E image"/> + <param name="image_alignment" type="data" format="csv" label="Image alignment file"/> + </when> + <when value="yes"> + <param name="hne_image" type="data" format="ome.tiff" label="H&E image"/> + </when> + </conditional> + <conditional name="add_if_condi"> + <param name="add_if" type="select" label="Add IF image?"> + <option value="yes_accurate">Yes, with accurate alignment</option> + <option value="yes">Yes</option> + <option value="no" selected="true">No</option> + </param> + <when value="no"/> + <when value="yes_accurate"> + <param name="if_image" type="data" format="ome.tiff" label="IF image"/> + <param name="image_alignment" type="data" format="csv" label="Image alignment file"/> + </when> + <when value="yes"> + <param name="if_image" type="data" format="ome.tiff" label="IF image"/> + </when> + </conditional> + </when> + </conditional> + </inputs> + <outputs> + <data name="spatialdata_output" format="spatialdata.zip" from_work_dir="spatialdata.spatialdata.zip" label="${tool.name} on ${on_string}: spatialdata"/> + </outputs> + <tests> + <!-- test 1: io MERSCOPE full --> + <test> + <conditional name="method_condi"> + <param name="method" value="merscope"/> + <param name="slide_name" value="Test_MERSCOPE"/> + <param name="region_name" value="sample_region"/> + <param name="mosaic_images" location="https://zenodo.org/records/18746346/files/mosaic_Cellbound1_z2.tif,https://zenodo.org/records/18746346/files/mosaic_Cellbound1_z3.tif,https://zenodo.org/records/18746346/files/mosaic_Cellbound2_z2.tif,https://zenodo.org/records/18746346/files/mosaic_Cellbound2_z3.tif,https://zenodo.org/records/18746346/files/mosaic_Cellbound3_z2.tif,https://zenodo.org/records/18746346/files/mosaic_Cellbound3_z3.tif,https://zenodo.org/records/18746346/files/mosaic_DAPI_z2.tif,https://zenodo.org/records/18746346/files/mosaic_DAPI_z3.tif,https://zenodo.org/records/18746346/files/mosaic_PolyT_z2.tif,https://zenodo.org/records/18746346/files/mosaic_PolyT_z3.tif"/> + <param name="z_layers" value="3"/> + <param name="input_micron_to_mosaic" location="https://zenodo.org/records/18746346/files/merscope_micron_to_mosaic_pixel_transform.csv"/> + <param name="cell_by_gene" location="https://zenodo.org/records/18746346/files/merscope_cell_by_gene.csv"/> + <param name="cell_meta" location="https://zenodo.org/records/18746346/files/merscope_cell_metadata.csv"/> + <param name="cells_boundaries" location="https://zenodo.org/records/18746346/files/merscope_cellpose2_micron_space.parquet"/> + <param name="transcripts" location="https://zenodo.org/records/18746346/files/merscope_detected_transcripts.csv"/> + </conditional> + <assert_stdout> + <has_text text="z_layers=[3]"/> + <has_text text="'Test_MERSCOPE_sample_region_polygons': GeoDataFrame shape: (928, 9)"/> + <has_text text="'table': AnnData (928, 130)"/> + </assert_stdout> + <output name="spatialdata_output"> + <assert_contents> + <has_archive_member path="spatialdata/zarr.json"> + <has_text text=""zarr_format": 3"/> + <has_text text=""label": "DAPI""/> + </has_archive_member> + </assert_contents> + </output> + </test> + <!-- test 2: io COSMX full --> + <test> + <conditional name="method_condi"> + <param name="method" value="cosmx"/> + <param name="CellComposite" location="https://zenodo.org/records/18746346/files/cosmx_CellComposite_F001.jpg"/> + <param name="CellLabels" location="https://zenodo.org/records/18746346/files/cosmx_CellLabels_F001.tif"/> + <param name="exprMat_file" location="https://zenodo.org/records/18746346/files/cosmx_dummy_exprMat_file.csv"/> + <param name="fov_positions_file" location="https://zenodo.org/records/18746346/files/cosmx_dummy_fov_positions_file.csv"/> + <param name="metadata_file" location="https://zenodo.org/records/18746346/files/cosmx_dummy_metadata_file.csv"/> + <param name="tx_file" location="https://zenodo.org/records/18746346/files/cosmx_dummy_tx_file.csv"/> + <param name="dataset_id" value="cosmx_dummy"/> + <param name="transcripts_bool" value="True"/> + </conditional> + <output name="spatialdata_output"> + <assert_contents> + <has_archive_member path="spatialdata/zarr.json"> + <has_text text=""zarr_format": 3"/> + <has_text text="images/1_image"/> + </has_archive_member> + </assert_contents> + </output> + </test> + <!-- test 3: io dbit full--> + <test> + <conditional name="method_condi"> + <param name="method" value="dbit"/> + <param name="barcode_positions" location="https://zenodo.org/records/18746346/files/dbit_barcode_positions.txt"/> + <param name="counts" location="https://zenodo.org/records/18746346/files/dbit_counts.h5ad"/> + <param name="tissue_lowres" location="https://zenodo.org/records/18746346/files/dbit_tissue_lowres.png"/> + </conditional> + <assert_stdout> + <has_text text="'Galaxy': GeoDataFrame shape: (500, 1) (2D shapes)"/> + <has_text text="'table': AnnData (500, 1000)"/> + </assert_stdout> + <output name="spatialdata_output"> + <assert_contents> + <has_archive_member path="spatialdata/zarr.json"> + <has_text text=""zarr_format": 3"/> + <has_text text="images/Galaxy_image"/> + </has_archive_member> + </assert_contents> + </output> + </test> + <!-- test 4: io macsima full--> + <test> + <conditional name="method_condi"> + <param name="method" value="macsima"/> + <param name="tiff_files" location="https://zenodo.org/records/18746346/files/macima_C-001_S-000_S_APC_R-01_W-D01_ROI-01_A-CD3_C-REA1151.tif,https://zenodo.org/records/18746346/files/macima_C-002_S-000_S_PE_R-01_W-D01_ROI-01_A-CD279_C-REA1165.tif,https://zenodo.org/records/18746346/files/macima_C-015_S-000_B_DAPI_R-01_W-D01_ROI-01_A-DAPI.tif,https://zenodo.org/records/18746346/files/macima_C-001_S-000_S_DAPI_R-01_W-D01_ROI-01_A-DAPI.tif,https://zenodo.org/records/18746346/files/macima_C-004_S-000_S_FITC_R-01_W-D01_ROI-01_A-CD66b_C-REA306.tif"/> + </conditional> + <assert_stdout> + <has_text text="'input_image': DataTree"/> + <has_text text="'input_table': AnnData (0, 5)"/> + </assert_stdout> + <output name="spatialdata_output"> + <assert_contents> + <has_archive_member path="spatialdata/zarr.json"> + <has_text text=""zarr_format": 3"/> + <has_text text="images/input_image"/> + </has_archive_member> + </assert_contents> + </output> + </test> + <!-- test 5: io VISIUM full --> + <test> + <conditional name="method_condi"> + <param name="method" value="visium"/> + <param name="dataset_id" value="Test_Visium"/> + <param name="feature_bc_matrix" location="https://zenodo.org/records/18746346/files/visium_CytAssist_FFPE_Protein_Expression_Human_Tonsil_filtered_feature_bc_matrix.h5"/> + <param name="matrix_bool" value="false"/> + <param name="scalefactors_json" location="https://zenodo.org/records/18746346/files/visium_scalefactors_json.json"/> + <param name="fullres_image_file" location="https://zenodo.org/records/18746346/files/visium_CytAssist_FFPE_Protein_Expression_Human_Tonsil_image.tif"/> + <param name="tissue_hires_image" location="https://zenodo.org/records/18746346/files/visium_tissue_hires_image.png"/> + <param name="tissue_lowres_image" location="https://zenodo.org/records/18746346/files/visium_tissue_lowres_image.png"/> + <param name="tissue_positions_list" location="https://zenodo.org/records/18746346/files/visium_tissue_positions.csv"/> + </conditional> + <assert_stdout> + <has_text text="'Test_Visium': GeoDataFrame shape: (4194, 2)"/> + <has_text text="'table': AnnData (4194, 18085)"/> + </assert_stdout> + <output name="spatialdata_output"> + <assert_contents> + <has_archive_member path="spatialdata/zarr.json"> + <has_text text=""zarr_format": 3"/> + <has_text text="images/Test_Visium_full_image"/> + </has_archive_member> + </assert_contents> + </output> + </test> + <!-- test 6: io Visium HD full --> + <test> + <conditional name="method_condi"> + <param name="method" value="visium_hd"/> + <param name="dataset_id" value="Test_VisiumHD"/> + <param name="matrix_bool" value="false"/> + <param name="feature_slice" location="https://zenodo.org/records/18746346/files/visiumhd_feature_slice.h5"/> + <conditional name="include_binned_condi"> + <param name="include_binned" value="yes"/> + <section name="bin008"> + <param name="feature_bc_matrix_008" location="https://zenodo.org/records/18746346/files/visiumhd_filtered_feature_bc_matrix_008.h5"/> + <param name="tissue_positions_008" location="https://zenodo.org/records/18746346/files/visiumhd_tissue_positions_008.parquet"/> + <param name="scalefactors_json_008" location="https://zenodo.org/records/18746346/files/visiumhd_scalefactors_json_008.json"/> + </section> + <section name="bin016"> + <param name="feature_bc_matrix_016" location="https://zenodo.org/records/18746346/files/visiumhd_filtered_feature_bc_matrix_016.h5"/> + <param name="tissue_positions_016" location="https://zenodo.org/records/18746346/files/visiumhd_tissue_positions_016.parquet"/> + <param name="scalefactors_json_016" location="https://zenodo.org/records/18746346/files/visiumhd_scalefactors_json_016.json"/> + </section> + <conditional name="include_nucleus_seg_condi"> + <param name="include_nucleus_seg" value="yes"/> + <section name="bin002"> + <param name="feature_bc_matrix_002" location="https://zenodo.org/records/18746346/files/visiumhd_filtered_feature_bc_matrix_002.h5"/> + <param name="tissue_positions_002" location="https://zenodo.org/records/18746346/files/visiumhd_tissue_positions_002.parquet"/> + <param name="scalefactors_json_002" location="https://zenodo.org/records/18746346/files/visiumhd_scalefactors_json_002.json"/> + </section> + <param name="nucleus_segmentation" location="https://zenodo.org/records/18746346/files/visiumhd_nucleus_segmentations.geojson"/> + <param name="barcode_mappings" location="https://zenodo.org/records/18746346/files/visiumhd_barcode_mappings.parquet"/> + </conditional> + </conditional> + <conditional name="segmentation_conditional"> + <param name="enable_segmentation" value="yes"/> + <param name="feature_bc_matrix_seg" location="https://zenodo.org/records/18746346/files/visiumhd_filtered_feature_cell_matrix_seg.h5"/> + <param name="cell_segmentation" location="https://zenodo.org/records/18746346/files/visiumhd_cell_segmentations.geojson"/> + <param name="scalefactors_json_seg" location="https://zenodo.org/records/18746346/files/visiumhd_scalefactors_json_seg.json"/> + </conditional> + <section name="images"> + <param name="tissue_hires" location="https://zenodo.org/records/18746346/files/visiumhd_tissue_hires_image.png"/> + <param name="tissue_lowres" location="https://zenodo.org/records/18746346/files/visiumhd_tissue_lowres_image.png"/> + <conditional name="cytassist_image_condi"> + <param name="include_cytassist" value="yes"/> + <param name="cytassist_image" location="https://zenodo.org/records/18746346/files/visiumhd_cytassist_image.tiff"/> + </conditional> + </section> + <param name="bins_as_squares_bool" value="true"/> + <param name="annotate_table_by_labels_bool" value="false"/> + <param name="var_names_make_unique_bool" value="true"/> + </conditional> + <assert_stdout> + <has_text text="'Test_VisiumHD"/> + <has_text text="Tables"/> + <has_text text="'cell_segmentations': AnnData"/> + </assert_stdout> + <output name="spatialdata_output"> + <assert_contents> + <has_archive_member path="spatialdata/zarr.json"> + <has_text text=""zarr_format": 3"/> + </has_archive_member> + </assert_contents> + </output> + </test> + <!-- test 7: io XENIUM full --> + <test> + <conditional name="method_condi"> + <param name="method" value="xenium"/> + <param name="cell_feature_matrix" location="https://zenodo.org/records/18746346/files/xenium_cell_feature_matrix.h5"/> + <param name="cells" location="https://zenodo.org/records/18746346/files/xenium_cells.parquet"/> + <param name="cells_zarr" location="https://zenodo.org/records/18746346/files/xenium_cells.zarr.zip"/> + <param name="experiment_xenium" location="https://zenodo.org/records/18746346/files/xenium_experiment.xenium"/> + <param name="morphology_focus" location="https://zenodo.org/records/18746346/files/ch0000_dapi.ome.tif,https://zenodo.org/records/18746346/files/ch0006_yellow_background.ome.tif,https://zenodo.org/records/18746346/files/ch0001_atp1a1_cd45_e-cadherin.ome.tif,https://zenodo.org/records/18746346/files/ch0007_red_background.ome.tif,https://zenodo.org/records/18746346/files/ch0002_18s.ome.tif,https://zenodo.org/records/18746346/files/ch0008_pd-1.ome.tif,https://zenodo.org/records/18746346/files/ch0003_alphasma_vimentin.ome.tif,https://zenodo.org/records/18746346/files/ch0009_vista.ome.tif,https://zenodo.org/records/18746346/files/ch0004_blue_background.ome.tif,https://zenodo.org/records/18746346/files/ch0010_pd-l1.ome.tif,https://zenodo.org/records/18746346/files/ch0005_green_background.ome.tif,https://zenodo.org/records/18746346/files/ch0011_lag-3.ome.tif"/> + <param name="cell_boundaries" location="https://zenodo.org/records/18746346/files/xenium_cell_boundaries.parquet"/> + <param name="nucleus_boundaries" location="https://zenodo.org/records/18746346/files/xenium_nucleus_boundaries.parquet"/> + <param name="transcripts" location="https://zenodo.org/records/18746346/files/xenium_transcripts.parquet"/> + <conditional name="add_hne_condi"> + <param name="add_hne" value="yes"/> + <param name="hne_image" location="https://zenodo.org/records/18746346/files/xenium_he_image.ome.tif"/> + </conditional> + </conditional> + <assert_stdout> + <has_text text="'cell_labels': DataTree"/> + <has_text text="'table': AnnData (358, 405)"/> + </assert_stdout> + <output name="spatialdata_output"> + <assert_contents> + <has_archive_member path="spatialdata/zarr.json"> + <has_text text=""zarr_format": 3"/> + <has_text text="images/morphology_focus"/> + </has_archive_member> + </assert_contents> + </output> + </test> + <!-- test 8: io XENIUM full accurate--> + <test> + <conditional name="method_condi"> + <param name="method" value="xenium"/> + <param name="cell_feature_matrix" location="https://zenodo.org/records/18746346/files/xenium_cell_feature_matrix.h5"/> + <param name="cells" location="https://zenodo.org/records/18746346/files/xenium_cells.parquet"/> + <param name="cells_zarr" location="https://zenodo.org/records/18746346/files/xenium_cells.zarr.zip"/> + <param name="experiment_xenium" location="https://zenodo.org/records/18746346/files/xenium_experiment.xenium"/> + <param name="morphology_focus" location="https://zenodo.org/records/18746346/files/ch0000_dapi.ome.tif,https://zenodo.org/records/18746346/files/ch0006_yellow_background.ome.tif,https://zenodo.org/records/18746346/files/ch0001_atp1a1_cd45_e-cadherin.ome.tif,https://zenodo.org/records/18746346/files/ch0007_red_background.ome.tif,https://zenodo.org/records/18746346/files/ch0002_18s.ome.tif,https://zenodo.org/records/18746346/files/ch0008_pd-1.ome.tif,https://zenodo.org/records/18746346/files/ch0003_alphasma_vimentin.ome.tif,https://zenodo.org/records/18746346/files/ch0009_vista.ome.tif,https://zenodo.org/records/18746346/files/ch0004_blue_background.ome.tif,https://zenodo.org/records/18746346/files/ch0010_pd-l1.ome.tif,https://zenodo.org/records/18746346/files/ch0005_green_background.ome.tif,https://zenodo.org/records/18746346/files/ch0011_lag-3.ome.tif"/> + <param name="cell_boundaries" location="https://zenodo.org/records/18746346/files/xenium_cell_boundaries.parquet"/> + <param name="nucleus_boundaries" location="https://zenodo.org/records/18746346/files/xenium_nucleus_boundaries.parquet"/> + <param name="transcripts" location="https://zenodo.org/records/18746346/files/xenium_transcripts.parquet"/> + <conditional name="add_hne_condi"> + <param name="add_hne" value="yes_accurate"/> + <param name="hne_image" location="https://zenodo.org/records/18746346/files/xenium_he_image.ome.tif"/> + <param name="image_alignment" location="https://zenodo.org/records/18746346/files/xenium_he_image_alignment.csv"/> + </conditional> + </conditional> + <assert_stdout> + <has_text text="'cell_labels': DataTree"/> + <has_text text="'table': AnnData (358, 405)"/> + <has_text text="xenium_aligned_image"/> + </assert_stdout> + <output name="spatialdata_output"> + <assert_contents> + <has_archive_member path="spatialdata/zarr.json"> + <has_text text=""zarr_format": 3"/> + <has_text text="images/morphology_focus"/> + </has_archive_member> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ +**What it does** + +This tool loads common spatial omics data formats into the SpatialData framework, a unified data structure for spatial omics data. It supports multiple spatial transcriptomics and proteomics technologies, converting their native output formats into a standardized SpatialData object stored as a Zarr archive. + +----- + +**Supported Technologies** + +- **10x Genomics Visium**: Standard Visium spatial gene expression data +- **10x Genomics Visium HD**: High-definition Visium with multiple bin sizes and segmentation data +- **10x Genomics Xenium**: In situ spatial transcriptomics with subcellular resolution +- **CosMx SMI (Nanostring)**: Spatial molecular imaging platform +- **MERSCOPE (Vizgen)**: Multiplexed error-robust fluorescence in situ hybridization +- **MACSima (Miltenyi)**: Multiplexed antibody-based imaging for cyclic staining +- **DBiT-seq**: Deterministic Barcoding in Tissue for spatial omics + +----- + +**Output** + +The tool produces a SpatialData object saved as a compressed Zarr archive (.spatialdata.zip). This archive contains: + +- **Images**: H&E, staining images +- **Labels**: Pixel-level segmentation +- **Shapes**: Cell/nucleus boundaries, subcellular structures, anatomical annotations, regions of interest (ROIs) +- **Points**: Transcripts locations with gene information, landmarks points +- **Tables**: AnnData objects with gene expression matrices and metadata + +The SpatialData format enables downstream analysis with tools like squidpy, spatialdata-plot, and napari for interactive visualization. + +----- + +**More Information** + +- `SpatialData documentation <https://spatialdata.scverse.org/projects/io/en/stable/>`__ + + + ]]></help> + <expand macro="citations" /> +</tool> \ No newline at end of file