<tool id="scmap_scmap_cell" name="Scmap cell projection" version="@TOOL_VERSION@+galaxy2" 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 '$n_nearest_neighbours'
            --nearest-neighbours-threshold '$nearest_neighbours_threshold'
            --threshold '$threshold'
            --cluster-col '${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 $cluster_projection
            --output-clusters-text-file '$clusters_text_file'
            #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" />
      <param name="nearest_neighbours_threshold" type="integer" label="Nearest neighbour threshold" value='3' help="A positive integer specifying the number of matching nearest neighbours required to label a cell." />
      <param name="threshold" type="float" label="Similarity threshold" value='0.7' help="Threshold on similarity (or probability for SVM and RF)." />
     <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="clusters_text_file" 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_processed.rds" ftype="rdata"/>
            <conditional name="cluster_projection">
                <param name="do_cluster_projection" value="true" />
                <param name="cluster_col" value="cell_type1" />
            </conditional>
            <output name="output_single_cell_experiment" file="closest_cells_clusters.rds" compare="sim_size"/>
            <output name="clusters_text_file">
                <assert_contents>
                    <has_n_lines n="91" delta="1"/>
                    <has_text_matching expression="Oocyte..1.RPKM.\tzygote\t0\.974.*\tzygote"/>
                    <has_text_matching expression="Zygote..3.RPKM.\tunassigned\tNA\tunassigned"/>
                    <has_text_matching expression="X2.cell.embryo.1..Cell.1.RPKM.\t2cell\t0\.976.*\t2cell"/>
                    <has_text_matching expression="X4.cell.embryo.3..Cell.4.RPKM.\t4cell\t0\.979.*\t4cell"/>
                    <has_text_matching expression="X8.cell.embryo.3..Cell.8.RPKM.\t8cell\t0\.973.*\t8cell"/>
                    <has_text_matching expression="Morulae..2..Cell.8.RPKM.\t16cell\t0\.967.*\t16cell"/>
                    <has_text_matching expression="Late.blastocyst..3..Cell.8.RPKM.\tblast\t0\.938.*\tblast"/>
                </assert_contents>
            </output>
            <output name="closest_cells_text_file" file="closest_cells.tsv"/>
            <output name="closest_cells_similarities_text_file">
                <assert_contents>
                    <has_n_lines n="6"/>
                    <has_text_matching expression="1\t0\.974.*\t0\.974.*\t0\.726.*\t0\.922.*\t0\.909.*"/>
                    <has_text_matching expression="2\t0\.974.*\t0\.973.*\t0\.726.*\t0\.922.*\t0\.938.*"/>
                    <has_text_matching expression="3\t0\.974.*\t0\.973.*\t0\.724.*\t0\.911.*\t0\.903.*"/>
                    <has_text_matching expression="4\t0\.969.*\t0\.968.*\t0\.768.*\t0\.947.*\t0\.919.*"/>
                    <has_text_matching expression="5\t0\.969.*\t0\.968.*\t0\.769.*\t0\.925.*\t0\.917.*"/>
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="index_single_cell_experiment" value="index_cell.rds" ftype="rdata"/>
            <param name="project_single_cell_experiment" value="test_sce_processed.rds" ftype="rdata"/>
            <conditional name="cluster_projection">
                <param name="do_cluster_projection" value="true" />
                <param name="cluster_col" value="cell_type1" />
            </conditional>
            <param name="nearest_neighbours_threshold" value="1" />
            <param name="threshold" value="0.2" />
            <output name="output_single_cell_experiment" file="closest_cells_clusters.rds" compare="sim_size"/>
            <output name="clusters_text_file">
                <assert_contents>
                    <has_n_lines n="91" delta="1"/>
                    <has_text_matching expression="Oocyte..1.RPKM.\tzygote\t0\.974.*\tzygote"/>
                    <has_text_matching expression="Zygote..3.RPKM.\tzygote\t0\.980.*\tzygote"/>
                    <has_text_matching expression="X2.cell.embryo.1..Cell.1.RPKM.\t2cell\t0\.976.*\t2cell"/>
                    <has_text_matching expression="X4.cell.embryo.3..Cell.4.RPKM.\t4cell\t0\.979.*\t4cell"/>
                    <has_text_matching expression="X8.cell.embryo.3..Cell.8.RPKM.\t8cell\t0\.973.*\t8cell"/>
                    <has_text_matching expression="Morulae..2..Cell.8.RPKM.\t16cell\t0\.967.*\t16cell"/>
                    <has_text_matching expression="Late.blastocyst..3..Cell.8.RPKM.\tblast\t0\.938.*\tblast"/>
                </assert_contents>
            </output>
            <output name="closest_cells_text_file" file="closest_cells.tsv"/>
            <output name="closest_cells_similarities_text_file">
                <assert_contents>
                    <has_n_lines n="6"/>
                    <has_text_matching expression="1\t0\.974.*\t0\.974.*\t0\.726.*\t0\.922.*\t0\.909.*"/>
                    <has_text_matching expression="2\t0\.974.*\t0\.973.*\t0\.726.*\t0\.922.*\t0\.938.*"/>
                    <has_text_matching expression="3\t0\.974.*\t0\.973.*\t0\.724.*\t0\.911.*\t0\.903.*"/>
                    <has_text_matching expression="4\t0\.969.*\t0\.968.*\t0\.768.*\t0\.947.*\t0\.919.*"/>
                    <has_text_matching expression="5\t0\.969.*\t0\.968.*\t0\.769.*\t0\.925.*\t0\.917.*"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
    @HELP@

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