annotate macros.xml @ 0:8001319743c0 draft

planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/celesta commit 0ec46718dfd00f37ccae4e2fa133fa8393fe6d92

<macros>
    <token name="@TOOL_VERSION@">0.0.0.9</token>
    <token name="@VERSION_SUFFIX@">0</token>
    <token name="@PROFILE@">20.01</token>

    <xml name="celesta_requirements">
        <requirements>
            <container type="docker">quay.io/goeckslab/celesta:@TOOL_VERSION@</container>
            <yield />
        </requirements>
    </xml>

    <xml name="macro_stdio">
        <stdio>
            <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error" />
        </stdio>
    </xml>
    <xml name="citations">
        <citations>
            <citation type="doi">10.1038/s41592-022-01498-z</citation>
        </citations>
    </xml>
    <xml name="celesta_base_options" token_label="celesta_base_options">
        <param name="x_coord" type="text" value="X_centroid" optional="false" label="Name of anndata.obs key containing cell or nucleus centroid X position" />
        <param name="y_coord" type="text" value="Y_centroid" optional="false" label="Name of anndata.obs key containing cell or nucleus centroid Y position" />
        <conditional name="filter_cells">
            <param name="filter" type="select" label="Choose whether to filter cells" help="FilterCells">
                <option value="no_filter" selected="true">Do not filter cells</option>
                <option value="filter">Filter cells based on marker intensity</option>
            </param>
            <when value="no_filter">
            </when>
            <when value="filter">
                <param name="low_threshold" type="float" value="0.4" optional="false" label="Set the low threshold for filtering cells" help="Cells below low threshold will be filtered out" />
                <param name="high_threshold" type="float" value="0.9" optional="false" label="Set the high threshold for filtering cells" help="Cells above high threshold will be filtered out" />
            </when>
        </conditional>
    </xml>
</macros>