view preprocessing.xml @ 0:c84663d92248 draft default tip

planemo upload for repository https://github.com/goeckslab/tools-st/tree/main/tools/spatialge commit 482b2e0e6ca7aaa789ba07b8cd689da9a01532ef

<tool id="cleaning_spatialGE" name="spatialGE Preprocessing" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.01">
    <description>Initial data preparation for downstream spatial transcriptomic analyses</description>
    <macros>
        <import>macros.xml</import>
    </macros>

    <expand macro="spatialge_requirements"/>

    <command detect_errors="aggressive"><![CDATA[

    ##---------------------------------------------------------
    ## VISIUM INPUT HANDLING
    ##---------------------------------------------------------
    
    mkdir counts_dir &&

    #if str($platform) == 'visium':

        ## symlinking metadata file
        #if $visium_metadata
            ln -s '$visium_metadata' '${visium_metadata.name}' &&
        #end if

        ## looping over each visium sample provided
        #for $v in $visium_samples:

            ## create counts_dir with specific visium sample name
            #set current_sample_dir = 'counts_dir/' + str($v.visium_sample_name)

            ## make directory to hold spatial subdir
            mkdir -p '$current_sample_dir/spatial' &&

            ## loop over each file in the visium file collection, if ends with .h5 separate from other files
            #for $f in $v.visium_collection:
                #if f.name.endswith('h5')
                    ln -s '$f' '$current_sample_dir/${f.name}' &&
                #end if
            #end for

            ## other files in visium file collection added to spatial subdir
            #for $f in $v.visium_collection:
                #if f.name.endswith('png') or f.name.endswith('csv') or f.name.endswith('json')
                    ln -s '$f' '$current_sample_dir/spatial/${f.name}' &&
                #end if
            #end for

        #end for
        
        Rscript '$__tool_directory__/spatialGE_multiple_input.R'

        ## counts will now maintain .h5 and spatial subdir structure
        --counts counts_dir

        --meta '${visium_metadata.name}'

        #if str($distribution_plots.plot) == 'raw_plot':
            --distplot
            --plotmeta '${distribution_plots.plotmeta}'
            #if $distribution_plots.samples
                --samples '${distribution_plots.samples}'
            #end if
        #end if

        #if str($spot_filtering.filter) == 'filter':
            --filter
            #if $spot_filtering.spot_min_reads
            --sminreads '${spot_filtering.spot_min_reads}'
            #end if
            #if $spot_filtering.spot_max_reads
            --smaxreads '${spot_filtering.spot_max_reads}'
            #end if
            #if $spot_filtering.spot_min_genes
            --smingenes '${spot_filtering.spot_min_genes}'
            #end if
            #if $spot_filtering.spot_max_genes
            --smaxgenes '${spot_filtering.spot_max_genes}'
            #end if
            #if $spot_filtering.gene_min_reads
            --gminreads '${spot_filtering.gene_min_reads}'
            #end if
            #if $spot_filtering.gene_max_reads
            --gmaxreads '${spot_filtering.gene_max_reads}'
            #end if
            #if $spot_filtering.gene_min_spots
            --gminspots '${spot_filtering.gene_min_spots}'
            #end if
            #if $spot_filtering.gene_max_spots
            --gmaxspots '${spot_filtering.gene_max_spots}'
            #end if
        #end if

        #if str($filtered_distribution_plots.plot) == 'filtered_plot':
            --filterplot
            --plotmeta '${filtered_distribution_plots.plotmeta}'
            #if $filtered_distribution_plots.samples
            --samples '${filtered_distribution_plots.samples}'
            #end if
        #end if

            --type '$transformation';

    #end if

    ##-------------------------------------------
    ## SINGLE COSMX INPUT HANDLING
    ##-------------------------------------------
    
    #if str($platform) == 'cosmx' and str($cosmx_file_quantity) == 'single_cosmx_input':

        ## symlink counts and coords files    
        ln -s '$single_cosmx_counts' '${single_cosmx_counts.name}' &&
        ln -s '$single_cosmx_spotcoords' '${single_cosmx_spotcoords.name}' &&

        Rscript '$__tool_directory__/spatialGE_single_input.R'

        #if $single_cosmx_counts
            --counts '${single_cosmx_counts.name}'
        #end if

        #if $single_cosmx_spotcoords
            --spots '${single_cosmx_spotcoords.name}'
        #end if

        --names '$cosmx_sample_names'

        #if str($distribution_plots.plot) == 'raw_plot':
            --distplot
            --plotmeta '${distribution_plots.plotmeta}'
            #if $distribution_plots.samples
                --samples '${distribution_plots.samples}'
            #end if
        #end if

        #if str($spot_filtering.filter) == 'filter':
            --filter
            #if $spot_filtering.spot_min_reads
            --sminreads '${spot_filtering.spot_min_reads}'
            #end if
            #if $spot_filtering.spot_max_reads
            --smaxreads '${spot_filtering.spot_max_reads}'
            #end if
            #if $spot_filtering.spot_min_genes
            --smingenes '${spot_filtering.spot_min_genes}'
            #end if
            #if $spot_filtering.spot_max_genes
            --smaxgenes '${spot_filtering.spot_max_genes}'
            #end if
            #if $spot_filtering.gene_min_reads
            --gminreads '${spot_filtering.gene_min_reads}'
            #end if
            #if $spot_filtering.gene_max_reads
            --gmaxreads '${spot_filtering.gene_max_reads}'
            #end if
            #if $spot_filtering.gene_min_spots
            --gminspots '${spot_filtering.gene_min_spots}'
            #end if
            #if $spot_filtering.gene_max_spots
            --gmaxspots '${spot_filtering.gene_max_spots}'
            #end if
        #end if

        #if str($filtered_distribution_plots.plot) == 'filtered_plot':
            --filterplot
            --plotmeta '${filtered_distribution_plots.plotmeta}'
            #if $filtered_distribution_plots.samples
            --samples '${filtered_distribution_plots.samples}'
            #end if
        #end if

            --type '$transformation'

    #end if

    ##---------------------------------------------------------
    ## MULTIPLE COSMX INPUT HANDLING
    ##---------------------------------------------------------

    #if str($platform) == 'cosmx' and str($cosmx_file_quantity) == 'multiple_cosmx_input':

        mkdir coords_dir &&

        ## loop over each count and coord file, and symlink
        #if str($cosmx_file_selection.cosmx_file_quantity) == 'multiple_cosmx_input':
            #for $cf in $multiple_cosmx_counts:
                ln -s '$cf' counts_dir/'${cf.name}' &&
            #end for
            #for $sc in $multiple_cosmx_spotcoords:
                ln -s '$sc' coords_dir/'${sc.name}' &&
            #end for
        #end if

        Rscript '$__tool_directory__/spatialGE_multiple_input.R'

        #if $cosmx_file_selection.multiple_cosmx_counts    
            --counts counts_dir/
        #end if

        #if $cosmx_file_selection.multiple_cosmx_spotcoords
            --spots coords_dir/
        #end if

        #if $cosmx_sample_names
            --names '${cosmx_sample_names}'
        #end if

        #if str($distribution_plots.plot) == 'raw_plot':
            --distplot
            --plotmeta '${distribution_plots.plotmeta}'
            #if $distribution_plots.samples
                --samples '${distribution_plots.samples}'
            #end if
        #end if

        #if str($spot_filtering.filter) == 'filter':
            --filter
            #if $spot_filtering.spot_min_reads
            --sminreads '${spot_filtering.spot_min_reads}'
            #end if
            #if $spot_filtering.spot_max_reads
            --smaxreads '${spot_filtering.spot_max_reads}'
            #end if
            #if $spot_filtering.spot_min_genes
            --smingenes '${spot_filtering.spot_min_genes}'
            #end if
            #if $spot_filtering.spot_max_genes
            --smaxgenes '${spot_filtering.spot_max_genes}'
            #end if
            #if $spot_filtering.gene_min_reads
            --gminreads '${spot_filtering.gene_min_reads}'
            #end if
            #if $spot_filtering.gene_max_reads
            --gmaxreads '${spot_filtering.gene_max_reads}'
            #end if
            #if $spot_filtering.gene_min_spots
            --gminspots '${spot_filtering.gene_min_spots}'
            #end if
            #if $spot_filtering.gene_max_spots
            --gmaxspots '${spot_filtering.gene_max_spots}'
            #end if
        #end if

        #if str($filtered_distribution_plots.plot) == 'filtered_plot':
            --filterplot
            --plotmeta '${filtered_distribution_plots.plotmeta}'
            #if $filtered_distribution_plots.samples
            --samples '${filtered_distribution_plots.samples}'
            #end if
        #end if

            --type '$transformation'

    #end if

    ##---------------------------------------------------------
    ## SINGLE RAW INPUT HANDLING
    ##---------------------------------------------------------

    #if str($platform) == 'raw_data' and str($raw_file_selection.raw_file_quantity) == 'single_raw_input':

        ## symlink count, coord, and metadata files
        ln -s '$single_raw_counts' '${single_raw_counts.name}' &&
        ln -s '$single_raw_spotcoords' '${single_raw_spotcoords.name}' &&
        ln -s '$raw_metadata' '${raw_metadata.name}' &&

        Rscript '$__tool_directory__/spatialGE_single_input.R'
    
        #if $single_raw_counts
            --counts '${single_raw_counts.name}'
        #end if

        #if $single_raw_spotcoords
            --spots '${single_raw_spotcoords.name}'
        #end if

        #if $raw_metadata
            --meta '${raw_metadata.name}'
        #end if

        #if str($distribution_plots.plot) == 'raw_plot':
            --distplot
            --plotmeta '${distribution_plots.plotmeta}'
            #if $distribution_plots.samples
                --samples '${distribution_plots.samples}'
            #end if
        #end if

        #if str($spot_filtering.filter) == 'filter':
            --filter
            #if $spot_filtering.spot_min_reads
            --sminreads '${spot_filtering.spot_min_reads}'
            #end if
            #if $spot_filtering.spot_max_reads
            --smaxreads '${spot_filtering.spot_max_reads}'
            #end if
            #if $spot_filtering.spot_min_genes
            --smingenes '${spot_filtering.spot_min_genes}'
            #end if
            #if $spot_filtering.spot_max_genes
            --smaxgenes '${spot_filtering.spot_max_genes}'
            #end if
            #if $spot_filtering.gene_min_reads
            --gminreads '${spot_filtering.gene_min_reads}'
            #end if
            #if $spot_filtering.gene_max_reads
            --gmaxreads '${spot_filtering.gene_max_reads}'
            #end if
            #if $spot_filtering.gene_min_spots
            --gminspots '${spot_filtering.gene_min_spots}'
            #end if
            #if $spot_filtering.gene_max_spots
            --gmaxspots '${spot_filtering.gene_max_spots}'
            #end if
        #end if

        #if str($filtered_distribution_plots.plot) == 'filtered_plot':
            --filterplot
            --plotmeta '${filtered_distribution_plots.plotmeta}'
            #if $filtered_distribution_plots.samples
            --samples '${filtered_distribution_plots.samples}'
            #end if
        #end if

            --type '$transformation'

    #end if

    ##---------------------------------------------------------
    ## MULTIPLE RAW INPUT HANDLING
    ##---------------------------------------------------------

    #if str($platform) == 'raw_data' and str($raw_file_selection.raw_file_quantity) == 'multiple_raw_input':

        mkdir coords_dir &&

        ## loop over each count and coord file, and symlink
        #if str($raw_file_selection.raw_file_quantity) == 'multiple_raw_input':
            #for $cf in $multiple_raw_counts:
                ln -s '$cf' counts_dir/'${cf.name}' &&
            #end for
            #for $sc in $multiple_raw_spotcoords:
                ln -s '$sc' coords_dir/'${sc.name}' &&
            #end for
        #end if

        ln -s '$raw_metadata' '${raw_metadata.name}' &&

        Rscript '$__tool_directory__/spatialGE_multiple_input.R'

        #if $raw_file_selection.multiple_raw_counts    
            --counts counts_dir/
        #end if

        #if $raw_file_selection.multiple_raw_spotcoords
            --spots coords_dir/
        #end if

        #if $raw_metadata
            --meta '${raw_metadata.name}'
        #end if

        #if str($distribution_plots.plot) == 'raw_plot':
            --distplot
            --plotmeta '${distribution_plots.plotmeta}'
            #if $distribution_plots.samples
                --samples '${distribution_plots.samples}'
            #end if
        #end if

        #if str($spot_filtering.filter) == 'filter':
            --filter
            #if $spot_filtering.spot_min_reads
            --sminreads '${spot_filtering.spot_min_reads}'
            #end if
            #if $spot_filtering.spot_max_reads
            --smaxreads '${spot_filtering.spot_max_reads}'
            #end if
            #if $spot_filtering.spot_min_genes
            --smingenes '${spot_filtering.spot_min_genes}'
            #end if
            #if $spot_filtering.spot_max_genes
            --smaxgenes '${spot_filtering.spot_max_genes}'
            #end if
            #if $spot_filtering.gene_min_reads
            --gminreads '${spot_filtering.gene_min_reads}'
            #end if
            #if $spot_filtering.gene_max_reads
            --gmaxreads '${spot_filtering.gene_max_reads}'
            #end if
            #if $spot_filtering.gene_min_spots
            --gminspots '${spot_filtering.gene_min_spots}'
            #end if
            #if $spot_filtering.gene_max_spots
            --gmaxspots '${spot_filtering.gene_max_spots}'
            #end if
        #end if

        #if str($filtered_distribution_plots.plot) == 'filtered_plot':
            --filterplot
            --plotmeta '${filtered_distribution_plots.plotmeta}'
            #if $filtered_distribution_plots.samples
            --samples '${filtered_distribution_plots.samples}'
            #end if
        #end if

            --type '$transformation'

    #end if

    ]]></command>
    <inputs>
        <conditional name="platform_type">
            <param name="platform" type="select" label="Select Input Type" >
                <option value="visium">Visium</option>
                <option value="cosmx">CosMX-SMI</option>
                <option value="raw_data">Raw Counts and Coordinates</option>
            </param>
            <when value="visium">
                <repeat name="visium_samples" title="Visium Sample" min="1">
                    <param name="visium_sample_name" type="text" optional="false" label="Sample Name (sample ID/name in metadata file)" />
                    <param name="visium_collection" type="data_collection" multiple="true" label="Visium Files (h5, png, json, csv)" />
                </repeat>
                <param name="visium_metadata" type="data" format="csv,tsv" label="Metadata" />
            </when>
            <when value="cosmx">
                <conditional name="cosmx_file_selection">
                    <param name="cosmx_file_quantity" type="select" label="Choose Input Quantity" >
                        <option value="single_cosmx_input">Single Sample Input</option>
                        <option value="multiple_cosmx_input">Multiple Sample Input</option>
                    </param>
                    <when value="single_cosmx_input">
                        <param name="single_cosmx_counts" type="data" format="csv,tsv" label="Expression Matrix" />
                        <param name="single_cosmx_spotcoords" type="data" format="csv,tsv" label="Metadata File" />
                    </when>
                    <when value="multiple_cosmx_input">
                        <param name="multiple_cosmx_counts" type="data_collection" format="csv,tsv" label="Collection of Expression Matrices (one file per sample)" />
                        <param name="multiple_cosmx_spotcoords" type="data_collection" format="csv,tsv" label="Collection of Metadata Files (one file per sample)" />
                    </when>
                </conditional>
                <param name="cosmx_sample_names" type="text" optional="false" label="Sample Name(s)" />
            </when>
            <when value="raw_data">
                <conditional name="raw_file_selection">
                    <param name="raw_file_quantity" type="select" label="Choose Input Quantity" >
                        <option value="single_raw_input">Single Sample Input</option>
                        <option value="multiple_raw_input">Multiple Sample Input</option>
                    </param>
                    <when value="single_raw_input">
                        <param name="single_raw_counts" type="data" format="csv,tsv" label="Counts" />
                        <param name="single_raw_spotcoords" type="data" format="csv,tsv" label="Spot Coordinates" />
                    </when>
                    <when value="multiple_raw_input">
                        <param name="multiple_raw_counts" type="data_collection" format="csv,tsv" label="Collection of Counts Files (one per sample)" />
                        <param name="multiple_raw_spotcoords" type="data_collection" format="csv,tsv" label="Collection of spot coord files (one per sample)" />
                    </when>
                </conditional>
                <param name="raw_metadata" type="data" format="csv,tsv" label="Metadata" />
            </when>
        </conditional>
        <conditional name="distribution_plots">
            <param name="plot" type="select" label="Optional: Generate Distribution Plot of Raw Data" >
                <option value="no_plot" selected="true">Do not generate distribution plot</option>
                <option value="raw_plot">Generate distribution plot</option>
            </param>
            <when value="no_plot">
            </when>
            <when value="raw_plot">
                <param name="plotmeta" type="select" label="Plot counts per cell or genes per cell" >
                    <option value="total_counts">Total counts</option>
                    <option value="total_genes">Total genes</option>
                </param>
                <param name="samples" type="text" optional="true" label="Optional subset of samples for distribution plotting (defaults to all)" />
            </when>
        </conditional>
        <conditional name="spot_filtering">
            <param name="filter" type="select" label="Optional: Perform Quality Control with Spot Filtering">
                <option value="no_filter" selected="true">Do not perform filtering</option>
                <option value="filter">Filter spots/cells</option>
            </param>
            <when value="no_filter">
            </when>
            <when value="filter">
                <param name="spot_min_reads" type="integer" min="0" optional="true" label="Minimum number of total reads for a spot to be retained" />
                <param name="spot_max_reads" type="integer" min="0" optional="true" label="Maximum number of total reads for a spot to be retained" />
                <param name="spot_min_genes" type="integer" min="0" optional="true" label="Minimum number of genes expressed in a spot" />
                <param name="spot_max_genes" type="integer" min="0" optional="true" label="Maximum number of genes expressed in a spot" />
                <param name="gene_min_reads" type="integer" min="0" optional="true" label="Minimum number of total reads for a gene to be retained" />
                <param name="gene_max_reads" type="integer" min="0" optional="true" label="Maximum number of total reads for a gene to be retained" />
                <param name="gene_min_spots" type="integer" min="0" optional="true" label="Minimum number of spots present in a gene" />
                <param name="gene_max_spots" type="integer" min="0" optional="true" label="Maximum number of spots present in a gene" />
            </when>
        </conditional>
        <conditional name="filtered_distribution_plots">
            <param name="plot" type="select" label="Optional: Generate Distribution Plot of Filtered Data" >
                <option value="no_plot" selected="true">Do not generate distribution plot</option>
                <option value="filtered_plot">Generate distribution plot</option>
            </param>
            <when value="no_plot">
            </when>
            <when value="filtered_plot">
                <param name="plotmeta" type="select" label="Plot counts per cell or genes per cell" >
                    <option value="total_counts">Total counts</option>
                    <option value="total_genes">Total genes</option>
                </param>
                <param name="samples" type="text" optional="true" label="Optional subset of samples for distribution plotting (defaults to all)" />
            </when>
        </conditional>
        <param name="transformation" type="select"  label="Data Transformation" >
            <option value="log" selected="true">log</option>
            <option value="sct">sct</option>
        </param>
    </inputs>
    <outputs>
        <collection name="raw_distribution_plot" type="list" label="Raw Data Distribution Plot">
            <discover_datasets pattern="__name_and_ext__" directory="./unfiltered_distribution_plots" ext="png" />
            <filter>distribution_plots['plot'] == "raw_plot"</filter>
        </collection>
        <collection name="filtered_dist_plot" type="list" label="Filtered Data Distribution Plot">
            <discover_datasets pattern="__name_and_ext__" directory="./filtered_distribution_plots" ext="png" />
            <filter>filtered_distribution_plots['plot'] == "filtered_plot"</filter>
        </collection>
        <data name="STlist_obj" format="rds" label="STlist.rds" from_work_dir="STobj.rds">
        </data>
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <conditional name="platform_type">
                <param name="platform" value="raw_data" />
                    <conditional name="raw_file_selection">
                        <param name="raw_file_quantity" value="single_raw_input" />
                            <param name="single_raw_counts" value="ST_mel3_rep1_counts.tsv" />
                            <param name="single_raw_spotcoords" value="ST_mel3_rep1_mapping.tsv" />
                    </conditional>
                <param name="raw_metadata" ftype="csv" value="thrane_clinical.csv" />
            </conditional>
            <output name="STlist_obj" file="STobj_raw.rds" compare="sim_size">
            </output>
        </test>
        <test expect_num_outputs="2">
            <conditional name="platform_type">
                <param name="platform" value="raw_data" />
                    <conditional name="raw_file_selection">
                        <param name="raw_file_quantity" value="single_raw_input" />
                            <param name="single_raw_counts" value="ST_mel3_rep1_counts.tsv" />
                            <param name="single_raw_spotcoords" value="ST_mel3_rep1_mapping.tsv" />
                    </conditional>
                <param name="raw_metadata" ftype="csv" value="thrane_clinical.csv" />
            </conditional>
            <conditional name="distribution_plots">
                <param name="plot" value="raw_plot" />
                    <param name="plotmeta" value="total_counts" />
            </conditional>
            <output name="STlist_obj" file="STobj_raw.rds" compare="sim_size">
            </output>
            <output_collection name="raw_distribution_plot">
                <element name="unfiltered_ST_mel3_rep1_counts" file="unfiltered_ST_mel3_rep1_counts.png" compare="sim_size" />
            </output_collection>
        </test>
        <test expect_num_outputs="3">
            <conditional name="platform_type">
                <param name="platform" value="raw_data" />
                    <conditional name="raw_file_selection">
                        <param name="raw_file_quantity" value="single_raw_input" />
                            <param name="single_raw_counts" value="ST_mel3_rep1_counts.tsv" />
                            <param name="single_raw_spotcoords" value="ST_mel3_rep1_mapping.tsv" />
                    </conditional>
                <param name="raw_metadata" ftype="csv" value="thrane_clinical.csv" />
            </conditional>
            <conditional name="distribution_plots">
                <param name="plot" value="raw_plot" />
                    <param name="plotmeta" value="total_counts" />
            </conditional>
            <conditional name="spot_filtering">
                <param name="filter" value="filter" />
                    <param name="spot_min_reads" value="2000" />
            </conditional>
            <conditional name="filtered_distribution_plots">
                <param name="plot" value="filtered_plot" />
                    <param name="plotmeta" value="total_counts" />
            </conditional>
            <output name="STlist_obj" file="STobj_filtered.rds" compare="sim_size">
            </output>
            <output_collection name="raw_distribution_plot">
                <element name="unfiltered_ST_mel3_rep1_counts" file="unfiltered_ST_mel3_rep1_counts.png" compare="sim_size" />
            </output_collection>
            <output_collection name="filtered_dist_plot">
                <element name="filtered_ST_mel3_rep1_counts" file="filtered_ST_mel3_rep1_counts.png" compare="sim_size" />
            </output_collection>
        </test>
    </tests>    
    <help>
        <![CDATA[
    **What it does**

    spatialGE is a tool designed for the analysis and visualization of spatially-resolved transcriptomics data.

    spatialGE Preprocessing is built for data reorganization and filtering with exploratory analysis. Input data will be
    transformed into an `STlist` object for downstream spatialGE analyses. Optional quality control can be performed by filtering spots/cells 
    and genes to specific quanitities. Distribution plots of either total counts or total genes can be produced for both raw and filtered data.
    Data transformation will prepare the data for later analysis.

    **Input**

    Visium:

    - Sample Name: Name of Visium sample(s) that matches a sample ID in the associated metadata file.

    - Visium Files: All file outputs from `spaceranger count`, must include .h5 file and .csv file from `spatial` subdirectory, and optionally including the .png and .json files (one group of files per sample). For multiple samples, select option "Insert Visium Sample".

    - Metadata: Metadata file including sample ID/names for all input samples.

    CosMX-SMI:

    - Expression Matrix: `exprMat` file from CosMX-SMI output. If running multiple sample input, upload collection of `exprMat` files, one file per sample.

    - Metadata: `metadata` file from CosMX-SMI output. If running multiple sample input, upload collection of `metadata` files, one file per sample.

    - Sample Names: Sample name associated with CosMX-SMI output. If running multiple sample input, create a comma-separated list of sample names with one unique name per sample.

    Raw Data:

    - Counts: Raw count data file(s). If running multiple sample input, upload collection of files, one file per sample.

    - Spot Coordinates: Raw coordinate file(s). If running multiple sample input, upload collection of files, one file per sample.

    - Metadata: Metadata file associated with sample(s).


    **Run modes**

    Optional: Generate Distribution Plot of Raw Data

        - Display violin distribution plot of samples

        - Choose between plotting either total counts per spot/cell or total genes per spot/cell

        - Can manually enter specific sample names to subset plot (will automatically plot all provided samples)

    Optional: Perform Quality Control with Spot Filtering

        - Perform quality control by filtering spots/cells

        - Optional input for all filtering parameters, can provide quanitity for one to all parameters

        - Specifying minimum and maximum spots/cells and/or genes will restrict the data

    Optional: Generate Distribution Plot of Filtered Data

        - Display violin distribution plot of samples after filtering data

        - Choose between plotting either total counts per spot/cell or total genes per spot/cell

        - Can manually enter specific sample names to subset plot (will automatically plot all provided samples). If sample names were specified in `Generate Distribution Plot of Raw Data`, same samples will be subset for plotting after filtering.

    **Outputs**

    - STlist Object RDS: saves the STlist object as an .rds file for downstream spatialGE analyses

    - Raw Data Distribution Plot: distribution violin plot of all samples provided, displaying either total counts or total genes

    - Filtered Data Distribution Plot: similar to raw data distribution plot, displaying distribution after quality control filtering

        ]]>
    </help>
    <expand macro="citations"/>
</tool>