<?xml version="1.0" encoding="utf-8"?>
<tool id="monocle3_reduceDim" name="Monocle3 reduceDim" version="@TOOL_VERSION@+galaxy0">
  <description>for downstream analysis</description>
  <macros>
    <import>monocle3-macros.xml</import>
  </macros>
  <expand macro="requirements"/>
  <command detect_errors="exit_code"><![CDATA[
LANG=en_US.UTF-8 monocle3 reduceDim
#if $max_components
    --max-components '${max_components}'
#end if
    --reduction-method '${reduction_method}'
    --preprocess-method '${preprocess_method}'

    @INPUT_OPTS@
    @OUTPUT_OPTS@
    
    @VERBOSE@
]]></command>

  <inputs>
    <expand macro="input_object_params"/>
    <expand macro="output_object_params"/>
    <param name="max_components" argument="--max-components" optional="true" type="integer" value="2" label="The dimensionality of the reduced space."/>
    <param name="reduction_method" argument="--reduction-method" type="select" label="The algorithm to use for dimensionality reduction.">
      <option selected="true" value="UMAP">UMAP</option>
      <option value="tSNE">tSNE</option>
      <option value="PCA">PCA</option>
      <option value="LSI">LSI</option>
    </param>
    <param name="preprocess_method" argument="--preprocess-method" type="select" label="The preprocessing method used on the data.">
      <option value="PCA" selected="true">PCA</option>
      <option value="LSI">LSI</option>
    </param>
    <expand macro="verbose_flag"/>
  </inputs>

  <outputs>
    <data name="output_rds" format="rdata" from_work_dir="output.RDS" label="${tool.name} on ${on_string}: ${output_object_format}"/>
  </outputs>

  <tests>
    <test>
      <param name="input_object_file" value="input.RDS"/>
      <param name="input_object_format" value="cds3"/>
      <param name="max_components" value="2"/>
      <param name="reduction_method" value="UMAP"/>
      <param name="preprocess_method" value="PCA"/>
      <param name="output_object_format" value="cds3"/>
      <output name="output_rds" file="output.rds" ftype="rdata" compare="sim_size"/>
    </test>
  </tests>

  <help><![CDATA[
==============================================================
Primary Monocle3 dimensionality reduction (`reduce_dimension`)
==============================================================

Use the results of preprocessing to propose a primary dimensionally reduced space for use
in downstream analysis.

@HELP@

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