<?xml version="1.0" encoding="utf-8"?>
<tool id="sc3_calc_biology" name="SC3 DiffExp" version="@TOOL_VERSION@+galaxy1">
  <description>calculates DE genes, marker genes and cell outliers</description>
  <macros>
    <import>sc3-macros.xml</import>
  </macros>
  <expand macro="requirements" />
  <command detect_errors="exit_code"><![CDATA[
sc3-sc3-calc-biology.R -i '${sc3_consensus}' -o '${sc3_biology_markers}' -t '${sc3_biology_markers_tsv}' -k '${ks}' -r '${regime}'
  ]]></command>

  <inputs>
    <param name="sc3_consensus" type="data" format="rdata" label="Serialised sc3 SingleCellExperiment object with stored consensus kmeans clustering"/>

    <param name="ks" argument="--ks" type="text" label="An integer or comma-separated list of integers">
      <validator type="regex" message="Please only enter integers or comma-separated list of integers">^[0-9]+(,[0-9]+)*$</validator>
    </param>

    <param name="regime" argument="--regime" type="select" label="Biological analysis to perform">
      <option value="marker" selected="true">Marker gene identification</option>
      <option value="de">Differential expression</option>
      <option value="outl">Outlier identification</option>
    </param>
  </inputs>

  <outputs>
    <data name="sc3_biology_markers" format="rdata" label="${tool.name} on ${on_string}: serialised sc3 SingleCellExperiment storing the DE markers"/>
    <data name="sc3_biology_markers_tsv" format="tsv" label="${tool.name} on ${on_string}: tsv table storing the DE markers"/>
  </outputs>

  <tests>
    <test>
      <param name="sc3_consensus" value="sc3_consensus.rds"/>
      <param name="ks" value="7,8"/>
      <param name="regime" value="marker"/>
      <output name="sc3_biology_markers" file="sc3_bio_sce.rds"/>
      <output name="sc3_biology_markers_tsv" file="sc3_biology_markers.tsv"/>
    </test>
  </tests>

  <help><![CDATA[
========================================================
This function performs differential expression analysis.
========================================================

Calculate differentially expressed (DE) genes, marker genes and cell outliers
based on the consensus SC3 clusterings.

@HELP@

@VERSION_HISTORY@
  ]]></help>
  <expand macro="citations" />
</tool>