comparison scimap_spatial.xml @ 3:472780baf150 draft

planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 49210b00535415865694ddbec16238d8cf5e6bb0

2:d19c068c2490

                    </param>
                    <param argument="radius" type="integer" value="30" optional="true" label="The radius used to define a local neighbhourhood" />
                    <param argument="knn" type="integer" value="10" optional="true" label="Number of cells considered for defining the local neighbhourhood" />
                    <param argument="num_motifs" type="integer" value="10" optional="true" label="The number of requested latent motifs to be extracted from the training corpus" />
                    <param argument="random_state" type="integer" value="0" optional="true" label="The seed number for random state" />
                </expand>
            </when>
            <when value="spatial_pscore">
                <expand macro="scimap_spatial_options" label="spatial_pscore">
                    <param argument="proximity" type="text" value="" optional="false" label="Type in the list of cell-types for which the proximity score needs to calculated" help="Comma delimited. e.g.: CellType-A,CellType-B." />

            </when>
        </conditional>
    </inputs>
    <outputs>
        <data format="h5ad" name="output" label="Scimap.tools.${analyses.selected_tool} on ${on_string}" />
    </outputs>
    <tests>
        <test>
            <param name="anndata" value="tutorial_data_pheno.h5ad" />
            <conditional name="analyses">
                <param name="selected_tool" value="cluster" />
                <param name="method" value="kmeans" />
            </conditional>

                <assert_contents>
                    <has_h5_keys keys="obs/kmeans" />
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="anndata" value="tutorial_data_pheno.h5ad" />
            <conditional name="analyses">
                <param name="selected_tool" value="spatial_aggregate" />
            </conditional>
            <output name="output">
                <assert_contents>
                    <has_h5_keys keys="obs/spatial_aggregate" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help>
        <![CDATA[
**What it does**

3:472780baf150

                    </param>
                    <param argument="radius" type="integer" value="30" optional="true" label="The radius used to define a local neighbhourhood" />
                    <param argument="knn" type="integer" value="10" optional="true" label="Number of cells considered for defining the local neighbhourhood" />
                    <param argument="num_motifs" type="integer" value="10" optional="true" label="The number of requested latent motifs to be extracted from the training corpus" />
                    <param argument="random_state" type="integer" value="0" optional="true" label="The seed number for random state" />
                    <param argument="max_weight_assignment" type="boolean" checked="false" optional="true" label="Assign cells to motifs based on maximum LDA weight" />
                </expand>
            </when>
            <when value="spatial_pscore">
                <expand macro="scimap_spatial_options" label="spatial_pscore">
                    <param argument="proximity" type="text" value="" optional="false" label="Type in the list of cell-types for which the proximity score needs to calculated" help="Comma delimited. e.g.: CellType-A,CellType-B." />

            </when>
        </conditional>
    </inputs>
    <outputs>
        <data format="h5ad" name="output" label="Scimap.tools.${analyses.selected_tool} on ${on_string}" />
        <collection name="tabular_outputs" type="list" label="Tabular outputs from Scimap.tools.${analyses.selected_tool} on ${on_string}">
            <data format="tabular" name="lda_weights" from_work_dir="lda_weights.txt" label="LDA weights from Scimap.tools.${analyses.selected_tool} on ${on_string}" />
            <data format="tabular" name="lda_probabilities" from_work_dir="lda_probabilities.txt" label="LDA probabilites from Scimap.tools.${analyses.selected_tool} on ${on_string}" />
            <filter>analyses['selected_tool'] == 'spatial_lda'</filter>
        </collection>
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <param name="anndata" value="tutorial_data_pheno.h5ad" />
            <conditional name="analyses">
                <param name="selected_tool" value="cluster" />
                <param name="method" value="kmeans" />
            </conditional>

                <assert_contents>
                    <has_h5_keys keys="obs/kmeans" />
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="1">
            <param name="anndata" value="tutorial_data_pheno.h5ad" />
            <conditional name="analyses">
                <param name="selected_tool" value="spatial_aggregate" />
            </conditional>
            <output name="output">
                <assert_contents>
                    <has_h5_keys keys="obs/spatial_aggregate" />
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="4">
            <param name="anndata" value="tutorial_data_pheno.h5ad" />
            <conditional name="analyses">
                <param name="selected_tool" value="spatial_lda" />
                <section name="options">
                    <param name="max_weight_assignment" value="True" />
                </section>
            </conditional>
            <output name="output">
                <assert_contents>
                    <has_h5_keys keys="obs/neighborhood_motif" />
                </assert_contents>
            </output>
            <output_collection name="tabular_outputs" type="list">
                <element name="lda_weights">
                    <assert_contents>
                        <has_n_lines n="500" />
                        <has_n_columns n="12" />
                    </assert_contents>
                </element>
                <element name="lda_probabilities">
                    <assert_contents>
                        <has_n_lines n="11" />
                        <has_n_columns n="15" />
                    </assert_contents>
                </element>
            </output_collection>
        </test>
    </tests>
    <help>
        <![CDATA[
**What it does**