comparison scmap_scmap_cell.xml @ 12:65b719530dd5 draft

"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit a1ad1ddd9b8e4db5bb82c3accae8311e0e488b19"

11:1543a50e08c9

      ]]></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>

      </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@
    

12:65b719530dd5

      ]]></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>

      </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"/>
            <param name="cluster_projection" value="true" />
            <output name="output_single_cell_experiment" file="closest_cells_clusters.rds" compare="sim_size"/>
            <output name="closest_cells_clusters_csv" file="closest_cells_clusters.tsv" compare="sim_size" />
            <output name="closest_cells_text_file" file="closest_cells.tsv" compare="sim_size"/>
            <output name="closest_cells_similarities_text_file" file="closest_cells_similarities.tsv" compare="sim_size"/>
        </test>
    </tests>
    <help><![CDATA[
    @HELP@