<tool id="signac_createAssayObject" name="Create Assay Object" version="0.1.0" python_template_version="3.5">
<description> Create Assay Object and Normalize Data</description>
<macros>
    <import>signac_macros.xml</import>
</macros>
<expand macro="requirements"/>
<stdio>
    <exit_code range="1:" />
</stdio>
<command><![CDATA[
    Rscript '${__tool_directory__}'/signac-createAssayObject.R --signac-object $signac_object --counts $counts --name $name --min-cells $min_cells --min-features $min_features --method $method --scale-factor $scale_factor --margin $margin --output-object-file $rds_signac_seurat_file 
]]></command>
<inputs>
    <param type="data" name="signac_object" label="Signac object." format="rdata" multiple="false" optional="false"/>
    <param type="data" name="counts" label="Counts Matrix (Output of Gene Activity)" format="rdata" multiple="false" optional="true"/>
    <param type="text" name="name" label="Assay Name." multiple="false" optional="true" value="RNA"/>    
    <param type="integer" name="min_cells" label="Min Cells." multiple="false" optional="false" value="0"/>
    <param type="integer" name="min_features" label="Min Features." multiple="false" optional="false" value="0"/>
    <param type="select" name="method" label="Method for normalization." value="LogNormalize">
        <option value="LogNormalize">LogNormalize</option>
        <option value="CLR">CLR</option>
        <option value="RC">RC</option>
    </param>
    <param type="float" name="scale_factor" value='10000' label="Sets the scale factor for cell-level normalization."/>
    <param type="select" name="margin" label="If performing CLR normalization, normalize across features (1) or cells (2)." value="1">
        <option value="1">1</option>
        <option value="2">2</option>
    </param>
</inputs>
<outputs>
    <data name="rds_signac_seurat_file" format="rdata" label="Signac Object RDS (Create Assay Object - Normalized)"/>
</outputs>
<help><![CDATA[
This tool creates a new assay and runs the NormalizeData function.
    ]]></help>
</tool>