<?xml version="1.0" encoding="utf-8"?>
<tool id="sc3_estimate_k" name="SC3 Estimate" version="@TOOL_VERSION@+galaxy0">
  <description>the number of clusters for k-means clustering</description>
  <macros>
    <import>sc3-macros.xml</import>
  </macros>
  <expand macro="requirements" />
  <command detect_errors="exit_code"><![CDATA[
sc3-sc3-estimate-k.R -i '${sc3_prepared}' -t '${sc3_estimated_k}' -o sc3_estimated.rds &&

echo -n "estimated k = " && cat ${sc3_estimated_k}
  ]]></command>

  <inputs>
    <param type="data" name="sc3_prepared" format="rdata" label="Serialised sc3 SingleCellExperiment object"/>
  </inputs>

  <outputs>
    <data name="sc3_estimated_k" format="txt" label="${tool.name} on ${on_string}: txt file containting estimated K value"/>
  </outputs>

  <tests>
    <test>
      <param name="sc3_prepared" value="sc3_prepared.rds"/>
      <output name="sc3_estimated_k" file="sc3-estimated-k.txt"/>
    </test>
  </tests>

  <help><![CDATA[
========================================================================================
Uses Tracy-Widom theory on random matrices to estimate the optimal number of clusters k.
========================================================================================

It creates and populates the k_estimation item of the sc3 slot of the metadata(object).

@HELP@

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