<tool id="signac_subset" name="Subset" version="0.1.0" python_template_version="3.5">
<description> a Signac object based on user defined thresholds.</description>
<macros>
    <import>signac_macros.xml</import>
</macros>
<expand macro="requirements"/>
<stdio>
    <exit_code range="1:" />
</stdio>
<command><![CDATA[
    Rscript '${__tool_directory__}'/signac-subset.R --signac-object $signac_object --peak-region-fragments-min $peak_region_fragments_min --peak-region-fragments-max $peak_region_fragments_max --pct-reads-in-peaks $pct_reads_in_peaks --blacklist-ratio $blacklist_ratio --nucleosome-signal $nucleosome_signal --tss-enrichment $tss_enrichment --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="integer" name="peak_region_fragments_min" value='3000' label="Peak region format minimum." help=''/>
    <param type="integer" name="peak_region_fragments_max" value='20000' label="Peak region format maximum." help=''/>
    <param type="integer" name="pct_reads_in_peaks" value='15' label="Minimum percent of reads in peaks." help=''/>
    <param type="float" name="blacklist_ratio" value='0.05' label="Blacklist ratio." help=''/>
    <param type="integer" name="nucleosome_signal" value='4' label="Nucleosome signal threshold." help=''/>
    <param type="integer" name="tss_enrichment" value='2' label="TSS enrichment signal threshold." help=''/>
</inputs>
<outputs>
    <data name="rds_signac_seurat_file" format="rdata" label="Signac RDS (subset)"/>
</outputs>
<help><![CDATA[
This tool runs the second step in the Signac pipeline, which will add gene annotations to the Signac object.
    ]]></help>
</tool>