comparison scimap_spatial.xml @ 2:d19c068c2490 draft default tip

planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea

1:fd38e533a54b

    </macros>

    <expand macro="scimap_requirements"/>
    <expand macro="macro_stdio" />
    <version_command>echo "@VERSION@"</version_command>
    <command>
        <![CDATA[
        python '$__tool_directory__/scimap_spatial.py'
            --inputs '$inputs'
            --anndata '$anndata'
            --output '$output'

            <when value="cluster">
                <param name="method" type="select" label="Select the clustering method">
                    <option value="kmeans" selected="true">kmeans</option>
                    <option value="phenograph">phenograph</option>
                    <option value="leiden">leiden</option>
                    <option value="parc">parc</option>
                </param>
                <section name="options" title="Advanced Options" expanded="false">
                    <param argument="subset_genes" type="text" value="" optional="true" label="Type in a list of genes  that should be included for the purpose of clustering" help="Optional. Comma delimited. By default the algorithm uses all genes in the dataset." />
                    <param argument="sub_cluster" type="boolean" checked="false" optional="true" label="Whether to do sub-clustering on existing clustering or phenotyping " />
                    <param argument="sub_cluster_column" type="text" value="phenotype" optional="true" label="Type in the name of a column to be sub-clustered" help="This is only required when sub_cluster is set to True." />
                    <param argument="sub_cluster_group" type="text" value="" optional="true" label="Type in a list of group names within the sub-cluster column" help="Optional. Comma delimited. By default the program will sub-cluster all groups within column passed through the argument sub_cluster_column." />
                    <param argument="parc_small_pop" type="integer" value="50" optional="true" label="Smallest cluster population to be considered a community in PARC clustering" />
                    <param argument="parc_too_big_factor" type="float" value="0.4" optional="true" label="If a cluster exceeds this share of the entire cell population, then the PARC will be run on the large cluster" />
                    <param argument="k" type="integer" value="10" optional="true" label="Number of clusters to return when using K-Means clustering" />
                    <param argument="n_pcs" type="integer" value="" optional="true" label="Number of PC's to be used in leiden clustering" help="By default it uses all PC's" />
                    <param argument="resolution" type="float" value="1" optional="true" label="A parameter value controlling the coarseness of the clustering" help="Higher values lead to more clusters." />
                    <param argument="phenograph_clustering_metric" type="select" label="Distance metric to define nearest neighbors">
                        <option value="euclidean" selected="true">euclidean</option>

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

Anndata with a corresponding key added.


        ]]>
    </help>
    <citations>
    </citations>
</tool>

2:d19c068c2490

    </macros>

    <expand macro="scimap_requirements"/>
    <expand macro="macro_stdio" />
    <version_command>echo "@VERSION@"</version_command>
    <command detect_errors="aggressive">
        <![CDATA[
        python '$__tool_directory__/scimap_spatial.py'
            --inputs '$inputs'
            --anndata '$anndata'
            --output '$output'

            <when value="cluster">
                <param name="method" type="select" label="Select the clustering method">
                    <option value="kmeans" selected="true">kmeans</option>
                    <option value="phenograph">phenograph</option>
                    <option value="leiden">leiden</option>
                </param>
                <section name="options" title="Advanced Options" expanded="false">
                    <param argument="subset_genes" type="text" value="" optional="true" label="Type in a list of genes  that should be included for the purpose of clustering" help="Optional. Comma delimited. By default the algorithm uses all genes in the dataset." />
                    <param argument="sub_cluster" type="boolean" checked="false" optional="true" label="Whether to do sub-clustering on existing clustering or phenotyping " />
                    <param argument="sub_cluster_column" type="text" value="phenotype" optional="true" label="Type in the name of a column to be sub-clustered" help="This is only required when sub_cluster is set to True." />
                    <param argument="sub_cluster_group" type="text" value="" optional="true" label="Type in a list of group names within the sub-cluster column" help="Optional. Comma delimited. By default the program will sub-cluster all groups within column passed through the argument sub_cluster_column." />
                    <param argument="k" type="integer" value="10" optional="true" label="Number of clusters to return when using K-Means clustering" />
                    <param argument="n_pcs" type="integer" value="" optional="true" label="Number of PC's to be used in leiden clustering" help="By default it uses all PC's" />
                    <param argument="resolution" type="float" value="1" optional="true" label="A parameter value controlling the coarseness of the clustering" help="Higher values lead to more clusters." />
                    <param argument="phenograph_clustering_metric" type="select" label="Distance metric to define nearest neighbors">
                        <option value="euclidean" selected="true">euclidean</option>

    <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>
            <output name="output">

Anndata with a corresponding key added.


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