<tool id="scater_create_qcmetric_ready_sce" name="Scater: calculate QC metrics" version="@TOOL_VERSION@" profile="@PROFILE@">
    <description>from single-cell expression matrix</description>
    <expand macro="bio_tools"/>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
Rscript '$__tool_directory__/scater-create-qcmetric-ready-sce.R'
-a '$counts'
#if $col_data:
    -c '$col_data'
#end if
#if $mt_controls:
    -f '$mt_controls'
#end if
#if $ercc_controls:
    -p '$ercc_controls'
#end if
#if $cell_controls:
    -l '$cell_controls'
#end if
-o '$output_loom'
    ]]></command>
    <inputs>
        <param name="counts" type="data" format="tabular" label="Expression matrix in tabular format" help="The first column of all files is assumed to be feature names and the first row is assumed to be sample names" />
        <param name="col_data" type="data" format="tabular" optional="true" label="Format dataset describing the features in tabular format" help="The number of rows (samples) must equal the number of columns in the expression matrix" />
        <param name="mt_controls" type="data" format="txt" optional="true" label="Dataset containing the list of the mitochondrial control genes" />
        <param name="ercc_controls" type="data" format="txt" optional="true" label="Dataset containing the list of the ERCC controls" />
        <param name="cell_controls" type="data" format="txt" optional="true" label="Dataset containing the list of the cell controls" help="Cell (sample) names used to identify cell controls (for example, blank wells or bulk controls)" />
    </inputs>
    <outputs>
        <data name="output_loom" format="loom" label="${tool.name} on ${on_string}" />
    </outputs>
    <tests>
        <test>
            <param name="counts" value="counts.txt" />
            <param name="col_data" value="annotation.txt" />
            <param name="mt_controls" value="mt_controls.txt" />
            <output name="output_loom" file="scater_qcready.loom" compare="sim_size" />
        </test>
    </tests>
    <help><![CDATA[
Calculate QC metrics for single-cell RNA-seq analysis using Scater.
    ]]></help>
    <expand macro="citations" />
</tool>