<tool id="scater_filter" name="Scater Filter" version="@TOOL_VERSION@+galaxy0">
  <description>cells and genes based on pre-calculated stats and QC metrics</description>
  <macros>
    <import>scater_macros.xml</import>
  </macros>
  <expand macro="requirements" />
  <command detect_errors="exit_code"><![CDATA[
scater-filter.R -i '${R_scater_qc}' -o '$R_scater_filtered'
#if $cell_parameters
    #set cell_pars = ','.join([str($p['name']) for $p in $cell_parameters])
    -s '${cell_pars}'
    #set cell_mins = ','.join([str($p['min']) for $p in $cell_parameters])
    -l '${cell_mins}'
    #set cell_maxs = ','.join([str($p['max']) for $p in $cell_parameters])
    -j '${cell_maxs}'
#end if
#if $feature_parameters
    #set ft_pars = ','.join([str($p['name']) for $p in $feature_parameters])
    -t '${ft_pars}'
    #set ft_mins = ','.join([str($p['min']) for $p in $feature_parameters])
    -m '${ft_mins}'
    #set ft_maxs = ','.join([str($p['max']) for $p in $feature_parameters])
    -n '${ft_maxs}'
#end if
#if $cells_use:
    -c '$cells_use'
#end if
#if $cells_discard:
    -C '$cells_discard'
#end if
#if $features_use:
    -f '$features_use'
#end if
#if $output_selected_cells:
    -u '$selected_cells'
#end if
#if $output_selected_features:
    -v '$selected_featuers'
#end if

  ]]></command>

  <inputs>
    <param name="R_scater_qc" type="data" format="rdata"
           help="A serialized SingleCellExperiment object file in RDS format."/>

    <repeat name="cell_parameters" title="Parameters used to filter cells" min="0">
      <param name="name" type="text" value="total_features_by_counts" label="Name of the parameter to filter on" help="for example: total_features_by_counts, total_counts">
        <option value="total_features_by_counts">total_features_by_counts</option>
        <option value="total_counts">total_counts</option>
      </param>
      <param name="min" type="float" value="-1e9" label="Min value"/>
      <param name="max" type="float" value="1e9" label="Max value"/>
    </repeat>

    <repeat name="feature_parameters" title="Parameters used to filter features" min="0">
      <param name="name" type="text" value="n_cells_by_counts" label="Name of the parameter to filter on" help="for example: n_cells_by_counts, total_counts">
        <option value="n_cells_by_counts">n_cells_by_counts</option>
        <option value="total_counts">total_counts</option>
      </param>
      <param name="min" type="float" value="-1e9" label="Min value"/>
      <param name="max" type="float" value="1e9" label="Max value"/>
    </repeat>

    <param name="cells_use" argument="--cells-use" type="data" format="txt" optional="true"
           label="List of cells to include (optional)"
           help="Text file with one cell per line providing cell names to use as a subset."/>

    <param name="cells_discard" argument="--cells-discard" type="data" format="txt" optional="true"
           label="List of cells to exclude (optional)"
           help="Text file with one cell per line providing cell names to discard as a subset."/>

    <param name="features_use" argument="--features-use" type="data" format="txt" optional="true"
           label="List of features to include (optional)"
           help="Text file with one features per line providing feature names to use as a subset."/>

    <param name="output_selected_cells" label="Output lists of pass-filter cells" type="boolean" checked="false"/>

    <param name="output_selected_features" label="Output lists of pass-filter features" type="boolean" checked="false"/>

  </inputs>

  <outputs>
    <data name="R_scater_filtered" format="rdata" label="${tool.name} on ${on_string}: serialized SingleCellExperiment object"/>

    <data name="selected_cells" format="tsv" label="${tool.name} on ${on_string}: pass-filter cells">
      <filter>output_selected_cells</filter>
    </data>
    <data name="selected_featuers" format="tsv" label="${tool.name} on ${on_string}: pass-filter features">
      <filter>output_selected_features</filter>
    </data>
  </outputs>

  <tests>
    <test>
      <param name="R_scater_qc" value="R_scater_qc.rds"/>
      <output name="R_scater_filtered" file="R_scater_filtered.rds"/>
    </test>
  </tests>

  <help><![CDATA[
@HELP@

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