<tool id="signac_umap" name="Calculate UMAP" version="0.1.0" python_template_version="3.5">
<description> embedding of scATAC-seq data.</description>
<macros>
    <import>signac_macros.xml</import>
</macros>
<expand macro="requirements"/>
<stdio>
    <exit_code range="1:" />
</stdio>
<command><![CDATA[
    Rscript '${__tool_directory__}'/signac-umap.R --signac-object $signac_object --reduction $reduction_use --dims-use $dims_use --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="text" name="reduction_use" value='lsi' label="Dimensional reduction to use for UMAP (default:lsi)." help='Which dimensional reduction (PCA or ICA) to use for the UMAP input.'/>
    <param type="text" name="dims_use" value='2,30' label="Dimensional reduction to use for UMAP (default:lsi)." help='How many dimensions to use for UMAP.'/>
</inputs>
<outputs>
    <data name="rds_signac_seurat_file" format="rdata" label="Signac Object RDS (UMAP)"/>
</outputs>
<help><![CDATA[
This tool runs the second step in the Signac pipeline, which will add gene annotations to the Signac object.
    ]]></help>
</tool>