<?xml version="1.0" encoding="utf-8"?>
<tool id="monocle3_create" name="Monocle3 create" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@">
  <description>a Monocle3 object from input data</description>
  <macros>
    <import>monocle3-macros.xml</import>
  </macros>
  <expand macro="requirements"/>
  <command detect_errors="exit_code"><![CDATA[
ln -s '${expression_matrix}' expression_matrix.'${expression_matrix_format}' &&
#if $cell_metadata
ln -s '${cell_metadata}' cell_metadata.'${cell_metadata_format}' &&
#end if
#if $gene_annotation
ln -s '${gene_annotation}' gene_annotation.'${gene_annotation_format}' &&
#end if
LANG=en_US.UTF-8 monocle3 create
    --expression-matrix expression_matrix.'${expression_matrix_format}'
#if $cell_metadata
    --cell-metadata cell_metadata.'${cell_metadata_format}'
#end if
#if $gene_annotation
    --gene-annotation gene_annotation.'${gene_annotation_format}'
#end if
    @OUTPUT_OPTS@
    @VERBOSE@
]]></command>

  <inputs>
    <param name="expression_matrix" argument="--expression-matrix" type="data" format="tabular,tsv,csv,rdata" label="Expression matrix, genes as rows, cells as columns. Required input. Provide as TSV, CSV or RDS."/>
    <param name="expression_matrix_format" type="select" label="Format of expression matrix">
      <option value="rds" selected="true">RDS</option>
      <option value="tsv">TSV</option>
      <option value="mtx">MTX</option>
      <option value="csv">CSV</option>
    </param>
    <param name="cell_metadata" argument="--cell-metadata" optional="true" type="data" format="tabular,tsv,csv,rdata" label="Per-cell annotation, optional. Row names must match the column names of the expression matrix. Provide as TSV, CSV or RDS."/>
    <param name="cell_metadata_format" type="select" label="Format of cell metadata">
      <option value="rds" selected="true">RDS</option>
      <option value="tsv">TSV</option>
      <option value="csv">CSV</option>
    </param>
    <param name="gene_annotation" argument="--gene-annotation" optional="true" type="data" format="tabular,tsv,csv,rdata" label="Per-gene annotation, optional. Row names must match the row names of the expression matrix. Provide as TSV, CSV or RDS."/>
    <param name="gene_annotation_format" type="select" label="Format of gene annotation">
      <option value="rds" selected="true">RDS</option>
      <option value="tsv">TSV</option>
      <option value="csv">CSV</option>
    </param>
    <expand macro="output_object_params"/>
    <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="expression_matrix" value="expression.RDS"/>
      <param name="cell_metadata" value="cells.RDS"/>
      <param name="gene_annotation" value="genes.RDS"/>
      <param name="output_object_format" value="cds3"/>
      <output name="output_rds" file="output.rds" ftype="rdata" compare="sim_size"/>
    </test>
  </tests>

  <help><![CDATA[
===========================================================================
Create Monocle3 object from input expression/metadata (`new_cell_data_set`)
===========================================================================

Create a Monocle3 cds3 object from input expression data and optional metadata.
The expression matrix, with genes as rows and cells as columns, is the only mandatory
input. The cell metadata (with row names matching the column names of the expression
matrix) and gene annotation (with row names matching the row names of the expression
matrix) are optional. These files can be provided as RDS objects, or CSV/TSV. Select the
format of your input files in the corresponding drop-downs.

@HELP@

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