<tool id="scater_calculate_cpm" name="Scater CalculateCPM" version="@TOOL_VERSION@+galaxy0">
  <description>from raw counts</description>
  <macros>
    <import>scater_macros.xml</import>
  </macros>
  <expand macro="requirements" />
  <command detect_errors="exit_code"><![CDATA[
scater-calculate-cpm.R -i '${R_scater_serialized}'
    -s '$size_factors'
    -o '$R_scater_cpm'
    -t '$cpm_matrix'
  ]]></command>

  <inputs>
    <param name="R_scater_serialized" type="data" format="rdata" label="Serialized SingleCellExperiment in RDS format"
           help="File name in which a serialized R SingleCellExperiment object where object matrix found"/>
    <param name="size_factors" argument="--size-factors" type="boolean" label="Use pre-calculated size factors in the input object if available"/>

  </inputs>

  <outputs>
    <data name="R_scater_cpm" format="rdata" label="${tool.name} on ${on_string}: serialized SingeleCellExperiment object holding CPM"/>
    <data name="cpm_matrix" format="txt" label="${tool.name} on ${on_string}: CPM matrix in text format"/>
  </outputs>

  <tests>
    <test>
      <param name="R_scater_serialized" ftype="rdata" value="R_scater_serialized.rds"/>
      <output name="R_scater_cpm" ftype="rdata" file="R_scater_cpm.rds"/>
      <output name="cpm_matrix" ftype="txt" file="cpm_matrix.txt"/>
    </test>
  </tests>

  <help><![CDATA[
@HELP@

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