<?xml version="1.0" encoding="utf-8"?>
<tool id="monocle3_preprocess" name="Monocle3 preprocess" version="@TOOL_VERSION@+galaxy0">
  <description>a Monocle3 object to an initially dimensionally reduced space</description>
  <macros>
    <import>monocle3-macros.xml</import>
  </macros>
  <expand macro="requirements"/>
  <command detect_errors="exit_code"><![CDATA[
LANG=en_US.UTF-8 monocle3 preprocess
    --method '${method}'
#if $num_dim
    --num-dim '${num_dim}'
#end if
    --norm-method '${norm_method}'
#if $use_genes
    --use-genes '${use_genes}'
#end if
#if $residual_model_formula_str
    --residual-model-formula-str '~${residual_model_formula_str}'
#end if
#if $pseudo_count
    --pseudo-count '${pseudo_count}'
#end if
#if $no_scaling
    --no-scaling
#end if

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

  <inputs>
    <expand macro="input_object_params"/>
    <expand macro="output_object_params"/>
    <param name="method" argument="--method" type="select" label="Initial dimensionality reduction to perform.">
      <option value="PCA" selected="true">PCA</option>
      <option value="LSI">LSI</option>
    </param>
    <param name="num_dim" argument="--num-dim" optional="true" type="integer" value="50" label="The dimensionality of the reduced space."/>
    <param name="norm_method" argument="--norm-method" type="select" label="Determines how to transform expression values prior to reducing dimensionality.">
      <option value="log" selected="true">Size factor correction and log transformation</option>
      <option value="size_only">Size factor correction only</option>
    </param>
    <param name="use_genes" argument="--use-genes" type="text" optional="true" label="Manually subset the gene pool to these genes for dimensionality reduction."/>
    <param name="residual_model_formula_str" argument="--residual-model-formula-str" type="text" optional="true" label="A string model formula specifying effects to subtract from the data (excluding the leading ~)."/>
    <param name="pseudo_count" argument="--pseudo-count" optional="true" type="float" value="1" label="Amount to increase expression values before dimensionality reduction."/>
    <param name="no_scaling" argument="--no-scaling" type="boolean" checked="false" label="When this option is NOT set, scale each gene before running trajectory reconstruction."/>
    <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="method" value="PCA"/>
      <param name="num_dim" value="50"/>
      <param name="norm_method" value="log"/>
      <param name="pseudo_count" value="1"/>
      <param name="output_object_format" value="cds3"/>
      <output name="output_rds" file="output.rds" ftype="rdata" compare="sim_size"/>
    </test>
  </tests>

  <help><![CDATA[
====================================================================================
Preprocess Monocle3 object up to initial dimensionality reduction (`preprocess_cds`)
====================================================================================

Preprocess a Monocle3 object with size factor scaling of the count data, optionally
log transforming, and computing an initial dimensionality reduction. This space is
used as a starting point for a number of subsequent analyses.

@HELP@

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