<tool id="signac_runQC" name="Run quality control" version="0.1.0" python_template_version="3.5">
<description> on Signac object and plot results.</description>
<macros>
    <import>signac_macros.xml</import>
</macros>
<expand macro="requirements"/>
<stdio>
    <exit_code range="1:" />
</stdio>
<command><![CDATA[
    cp $fragment_file fragments.tsv.gz &&
    cp $fragment_index_file fragments.tsv.gz.tbi &&
    Rscript '${__tool_directory__}'/signac-runQC.R --signac-object $signac_object --fragment-file fragments.tsv.gz --tss-threshold $tss_threshold --output-object-file $rds_signac_seurat_file --output-tss-plot $output_tss_plot --frag-history-plot $frag_history_plot --png-width $png_width --png-height $png_height
]]></command>
<inputs>
	<param type="data" name="signac_object" label="Signac object." format="rdata" 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"/>
    <param type="integer" name="tss_threshold" value="2" label=" Transcription start site (TSS) enrichment score threshold for considering cells with a high TSS enrichment for the TSS plot." multiple="false" optional="false"/> 
    <param type="integer" name="png_width" value='1000' label="Figure width" help='Width of png in pixels.'/>
    <param type="integer" name="png_height" value='1000' label="Figure height" help='Height of png in pixels.'/>
</inputs>
<outputs>
	<data name="rds_signac_seurat_file" format="rdata" label="Signac Object RDS (QC)"/>
	<data name="output_tss_plot" format="png" from_work_dir="scATACseq.TSS_plot.png" label="scATACseq.TSS_plot.png"/>
	<data name="frag_history_plot" format="png" from_work_dir="scATACseq.fraghist_plot.png" label="scATACseq.fraghist_plot.png"/>
</outputs>
<help><![CDATA[
This tool runs the second step in the Signac pipeline, which will add gene annotations to the Signac object.
    ]]></help>
</tool>