<tool id="scmap_scmap_cell" name="Scmap cell projection" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
    <description>searches each cell in a query dataset for the nearest neighbours by cosine distance within a collection of reference datasets.</description>
    <macros>
        <import>scmap_macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
        scmap-scmap-cell.R 
            -i '$index_single_cell_experiment' 
            -p '$project_single_cell_experiment' 
            --number-nearest-neighbours '$n_nearest_neighbours' 
            --cluster-col '${cluster_projection.cluster_col}' 
            --output-object-file '$output_single_cell_experiment' 
            --closest-cells-text-file '$closest_cells_text_file' 
            --closest-cells-similarities-text-file '$closest_cells_similarities_text_file'  
            #if $cluster_projection
            --output-clusters-text-file '$closest_cells_clusters_csv' 
            #end if      
      ]]></command>
    <inputs>
      <param type="data" name="index_single_cell_experiment" label="Index SingleCellExperiment object" format="rdata" help="File with serialized SingleCellExperiment object as produced by 'scmap select features' and 'scmap index clusters', onto which another dataset will be projected." />
      <param type="data" name="project_single_cell_experiment" label="SingleCellExperiment object to project" format="rdata" help="File with serialized SingleCellExperiment object to project onto the index'" />
      <param name="n_nearest_neighbours" type="integer" label="Number of nearest neighbours" value='5' help="A positive integer specifying the number of nearest neighbours to find" />
      
     <conditional name="cluster_projection">
        <param name="do_cluster_projection" type="boolean" checked="false" label="Annotate cells of the projection dataset using labels of the reference?" help="If cell cluster annotation is available for the reference datasets, in addition to finding top 10 nearest neighbours scmap-cell also allows to annotate cells of the projection dataset using labels of the reference."/>
        <when value="true" >
          <param name="cluster_col" type="text" label="Cluster column" value="cell_type1" help="Column name in the 'colData' slot of the SingleCellExperiment object containing the cell classification information." />
        </when>
        <when value="false" >
          <param name="cluster_col" type="hidden" value="NULL" />
        </when>
      </conditional>
    </inputs>
    <outputs>
      <data name="output_single_cell_experiment" format="rdata" />
      <data name="closest_cells_text_file" format="tabular" />
      <data name="closest_cells_similarities_text_file" format="tabular" />
      <data name="closest_cells_clusters_csv" format="tabular">
        <filter>cluster_projection['do_cluster_projection']</filter>
      </data>
    </outputs>
    <tests>
        <test>
            <param name="index_single_cell_experiment" value="index_cell.rds" ftype="rdata"/>
            <param name="project_single_cell_experiment" value="test_sce.rds" ftype="rdata"/>
            <param name="cluster_projection" value="true" ftype="rdata"/>
            <output name="output_single_cell_experiment" file="closest_cells_clusters.rds" compare="sim_size"/>
            <output name="closest_cells_clusters_csv" file="closest_cells_clusters.csv" compare="sim_size" />
            <output name="closest_cells_text_file" file="closest_cells.csv" compare="sim_size"/>
            <output name="closest_cells_similarities_text_file" file="closest_cells_similarities.csv" compare="sim_size"/>
        </test>
    </tests>
    <help><![CDATA[
    @HELP@
    
    @VERSION_HISTORY@
    ]]></help>
    <expand macro="citations" />
</tool>