<tool id="scater_filter" name="Scater: filter SCE" version="@TOOL_VERSION@" profile="@PROFILE@">
    <description>with user-defined parameters or PCA</description>
    <expand macro="bio_tools"/>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements">
        <requirement type="package" version="0.93_9">r-robustbase</requirement>
    </expand>
    <command detect_errors="exit_code"><![CDATA[
#if $filter_type.filter_type_selector == 'manual':
    Rscript '$__tool_directory__/scater-manual-filter.R'
    -i '$input_loom'
    #if str($filter_type.library_size):
        --library-size ${filter_type.library_size}
    #end if
    #if str($filter_type.percent_counts_MT):
        --percent-counts-MT ${filter_type.percent_counts_MT}
    #end if
    #if str($filter_type.expressed_features):
        --expressed-features ${filter_type.expressed_features}
    #end if
    #if str($filter_type.detection_limit):
        --detection-limit ${filter_type.detection_limit}
    #end if
    #if str($filter_type.min_cells_expressed):
        --min-cells-expressed ${filter_type.min_cells_expressed}
    #end if
#else:
    Rscript '$__tool_directory__/scater-pca-filter.R'
    -i '$input_loom'
#end if
-o '$output_loom'
    ]]></command>
    <inputs>
        <param name="input_loom" type="data" format="loom" label="Input SingleCellLoomExperiment dataset" />
        <conditional name="filter_type">
            <param name="filter_type_selector" type="select" label="Type of filter">
                <option value="manual">manual</option>
                <option value="pca">PCA</option>
            </param>
            <when value="manual">
                <param name="library_size" argument="--library-size" type="integer" optional="true" label="Minimum library size (mapped reads) to filter cells on" help="Raising this number will raise the stringency and may lower the number of included cells" />
                <param name="percent_counts_MT" argument="--percent-counts-MT" type="float" min="0" max="100" optional="true" label="Maximum % of mitochondrial genes expressed per cell" help="Cells that exceed this value will be filtered out" />
                <param name="expressed_features" type="integer" value="100" optional="true" label="Remove cells that have less than the given number of expressed features" />
                <param name="detection_limit" argument="--detection-limit" type="float" optional="true" label="Number of reads mapped to a feature above which it to be deemed as expressed" help="Raising this number will raise the stringency and may lower the number of expressed genes" />
                <param name="min_cells_expressed" argument="---min-cells-expressed" type="integer" optional="true" label="Remove features that occur in less than the given number of cells" help="Features that exceed this value will be filtered out" />
            </when>
            <when value="pca" />
        </conditional>
    </inputs>
    <outputs>
        <data name="output_loom" format="loom" label="${tool.name} on ${on_string}" />
    </outputs>
    <tests>
        <test>
            <param name="input_loom" value="scater_qcready.loom" ftype="loom" />
            <param name="filter_type_selector" value="manual" />
            <param name="detection_limit" value="4" />
            <param name="library_size" value="100000" />
            <param name="percent_counts_MT" value="33.0" />
            <param name="min_cells_expressed" value="3" />
            <output name="output_loom" file="scater_manual_filtered.loom" compare="sim_size" />
        </test>
        <test>
            <param name="input_loom" value="scater_qcready.loom" ftype="loom" />
            <param name="filter_type_selector" value="pca" />
            <output name="output_loom" file="scater_pca_filtered.loom" compare="sim_size" />
        </test>
    </tests>
    <help><![CDATA[
Filter a SingleCellLoomExperiment object with Scater using one of the following methods:

- user-defined parameters
- PCA to automatically removes outliers.
    ]]></help>
    <expand macro="citations" />
</tool>