<tool id="gate_finder" name="Perform gating" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>with Vitessce</description>
    <macros>
        <import>main_macros.xml</import>
    </macros>
    <edam_operations>
        <edam_operation>operation_3443</edam_operation>
    </edam_operations>
    <expand macro="vitessce_requirements"/>
    <expand macro="macro_stdio" />
    <version_command>echo "@TOOL_VERSION@"</version_command>
    <expand macro="vitessce_cmd" tool_id="gate_finder" />
    <configfiles>
        <inputs name="inputs" />
    </configfiles>
    <inputs>
        <param name="image" type="data" format="ome.tiff" label="Select the image (OME-TIFF)" />
        <param name="masks" type="data" format="tiff,ome.tiff" optional="true" label="Select masks for the OME Tiff image (Optional)" />
        <section name="do_phenotyping" title=" ">
            <param name="phenotyping_choice" type="hidden" value="add_h5ad"/>
        </section>
        <param name="phenotyping_choice" type="hidden" value="yes" />
        <param name="anndata" type="data" format="h5ad" label="Select the anndata containing marker intensities" />
        <param name="marker" type="text" value=""  label="Marker for which gate is to be defined" help="E.g.: CD45." />
        <param name="from_gate" type="integer" value="6" label="Start value gate of interest" help="Integer. Optional" />
        <param name="to_gate" type="integer" value="8" label="End value of the gate of interest." help="Integer. Optional" />
        <param name="increment" type="float" value="0.1" label="Increments between the start and end values" help="Float." />
        <param name="x_coordinate" type="text" value="X_centroid" optional="true" label="X axis coordinate column name in AnnData object" />
        <param name="y_coordinate" type="text" value="Y_centroid" optional="true" label="X axis coordinate column name in AnnData object" />
    </inputs>
    <outputs>
        <data format="html" name="output" />
        <data format="json" name="vitessce_config" from_work_dir="config.json" hidden="true" label="Vitessce config file on ${on_string}" />
    </outputs>
    <tests>
        <test>
            <param name="image" value="vitessce_image.ome.tiff" ftype="ome.tiff" />
            <param name="masks" value="vitessce_mask.tiff" ftype="tiff" />
            <param name="anndata" value="vitessce_test.h5ad" ftype="h5ad" />
            <param name="marker" value="DNA_1" />
            <param name="from_gate" value="6" />
            <param name="to_gate" value="8" />
            <param name="increment" value=".1" />
            <output name="vitessce_config">
                <assert_contents>
                    <has_json_property_with_text property="name" text="OMETIFF" />
                    <has_json_property_with_text property="name" text="MASKS" />
                    <has_json_property_with_text property="name" text="DNA_1--6.0" />
                    <has_json_property_with_text property="name" text="DNA_1--7.9" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help>
        <![CDATA[
**What it does**
This tool, built on top of vitessce visualization components, mimics the find_gate function from scimap (https://scimap.xyz/) to do manual gating for single cell quantification data.

**Input**

OME-TIFF image.
Segmentation masks (optional).
AnnData with marker intensities.

**Output**

An HTML file with Vitessce component. 


        ]]>
    </help>
    <citations>
        <citation type="doi">10.31219/osf.io/y8thv</citation>
    </citations>
</tool>