<?xml version="1.0" encoding="utf-8"?>
<tool id="sc3_kmeans" name="SC3 K-Means" version="@TOOL_VERSION@+galaxy0">
  <description>perform k-means clustering</description>
  <macros>
    <import>sc3-macros.xml</import>
  </macros>
  <expand macro="requirements" />
  <command detect_errors="exit_code"><![CDATA[
sc3-sc3-kmeans.R -i '${sc3_transformed}'
#if $choose.method == "file":
    -k '${choose.sc3_estimated_k}'
#else
    -k '${choose.input_k}'
#end if
    -o '${sc3_kmeans}'
]]></command>

  <inputs>
    <param name="sc3_transformed" type="data" format="rdata" label="Serialised sc3 SingleCellExperiment object with transformed distances"/>

    <conditional name="choose">
      <param name="method" type="select" label="Method to supply K">
        <option value="input">Enter K as an integer</option>
        <option value="file">Provide a text file containing K</option>
      </param>
      <when value="input">
        <param name="input_k" type="integer" value="0" label="Integer K as the number of clusters for kmeans"/>
      </when>
      <when value="file">
        <param name="sc3_estimated_k" type="data" format="txt" label="Text file containing estimated K"/>
      </when>
    </conditional>
  </inputs>

  <outputs>
    <data name="sc3_kmeans" format="rdata" label="${tool.name} on ${on_string}: serialised sc3 SingleCellExperiment object storing the k-means clusters"/>
  </outputs>

  <tests>
    <test>
      <param name="sc3_transformed" value="sc3_transformed.rds"/>
      <param name="sc3_estimated_k" value="K_size"/>
      <output name="sc3_kmeans" file="sc3_kmeans.rds"/>
    </test>
  </tests>

  <help><![CDATA[
=========================================
This function performs kmeans clustering.
=========================================

It uses transformed distance matrix contained in the transformations item of the
sc3 slot of the metadata(object).  It then creates and populates the following
items of the sc3 slot:

- kmeans: contains a list of kmeans clusterings.

@HELP@

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