<tool id="signac_createObject" name="CreateObject" version="0.1.0" python_template_version="3.5">
<description> reads in output files from CellRanger-ATAC and creates a Seurat object containing a ChromatinAssay assay.</description>
<macros>
    <import>signac_macros.xml</import>
</macros>
<expand macro="requirements"/>
<stdio>
    <exit_code range="1:" />
</stdio>
<command><![CDATA[
    ln -s $fragment_file fragments.tsv.gz &&
    ln -s $fragment_index_file fragments.tsv.gz.tbi &&
    Rscript '${__tool_directory__}'/signac-createObject.R --h5-file $h5_file --metadata $metadata --genome $genome --fragment-file fragments.tsv.gz --output-object-file $rds_signac_seurat_file --min-cells $min_cells --min-features $min_features
]]></command>
<inputs>
    <param type="data" name="h5_file" label="Select the h5 file containing the filtered peak BC matrix." format="h5" multiple="false" optional="false"/>
    <param type="data" name="metadata" label="Select the metadata file." format="csv" multiple="false" optional="false"/> 
    <param type="select" name="genome" label="Select the respective genome." multiple="false" format="text" optional="false">
        <option value="GRCh38">GRCh38/hg38</option>
        <option value="hg19">GRCh37/hg19</option>
		<option value="mm10">GRCm38/mm10</option>
    </param>
    <param type="integer" name="min_cells" value="10" label="Minimum number of cells features needs to be detected in." multiple="false" optional="false"/> 
    <param type="integer" name="min_features" value="200" label="Minimum number of features for a cell to be retained." multiple="false" optional="false"/> 
    <param type="data" name="fragment_file" label="Select the fragment file."  format="bgzip" multiple="false" optional="false"/>
    <param type="data" name="fragment_index_file" label="Select the fragment index file." format="text" multiple="false" optional="false"/>
</inputs>
<outputs>
    <data name="rds_signac_seurat_file" format="rdata" label="Signac Object RDS (CreateObject)"/>
</outputs>
<help><![CDATA[
This tool runs the first step in the Signac pipeline, which is to read in the filtered peak BC matrix, the metadata and the fragment file and create a Seurat object.
    ]]></help>
</tool>