<tool id="scimap_phenotyping" name="Single Cell Phenotyping" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>using scimap</description>
    <macros>
        <import>main_macros.xml</import>
    </macros>

    <expand macro="scimap_requirements"/>
    <expand macro="macro_stdio" />
    <version_command>echo "@VERSION@"</version_command>
    <command detect_errors="aggressive">
        <![CDATA[
        python '$__tool_directory__/scimap_phenotyping.py'
            --adata '$anndata'
            #if $log
                --log
            #end if
            #if $manual_gates
                --manual_gates '$manual_gates'
                --manual_gates_ext '${manual_gates.ext}'
            #end if
            --gating_workflow '$gating_workflow'
            --gating_workflow_ext '${gating_workflow.ext}'
            --random_state '$random_state'
            --output '$output'

        ]]>
    </command>
    <configfiles>
        <inputs name="inputs" />
    </configfiles>
    <inputs>
        <param name="anndata" type="data" format="h5ad" label="Select the input anndata" />
        <param name="log" type="boolean" checked="true" label="Whether to log the data prior to rescaling" />
        <param name="manual_gates" type="data" format="tabular,csv" optional="true" label="Select the dataset containing manual gate information" help="First column as markers and second column as the gate values in log1p scale. If a marker is not included, auto gating
        based on gaussian mixture modeling will be executed. Optional."/>
        <param name="gating_workflow" type="data" format="tabular,csv" label="Select the dataset containing gating workflow" />
        <param name="random_state" type="integer" value="0" optional="true" label="Set seed used by the random number generator for GMM" />
    </inputs>
    <outputs>
        <data format="h5ad" name="output" />
    </outputs>
    <tests>
        <test>
            <param name="anndata" value="tutorial_data.h5ad" ftype="h5ad" />
            <param name="manual_gates" value="manual_gates.csv" ftype="csv" />
            <param name="gating_workflow" value="phenotype_workflow.csv" ftype="csv" />
            <output name="output">
                <assert_contents>
                    <has_h5_keys keys="obs/phenotype" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help>
        <![CDATA[
**What it does**

This tool generates single cell phenotyping using either manual gating or auto gating (gaussian mixture modeling) implemented in Scimap.

**Input**

AnnData.

**Important Note**

If adata.raw.X exists, it will be used. If adata.raw.X does not exist, adata.X is used 

**Output**

Anndata with "obs/phenotype" added.


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