<macros>
  <token name="@TOOL_VERSION@">0.1.4</token>
  <token name="@PROFILE@">18.01</token>
  <token name="@HELP@">More information can be found at https://cole-trapnell-lab.github.io/monocle3/ and https://github.com/ebi-gene-expression-group/monocle-scripts</token>
  <token name="@VERSION_HISTORY@"><![CDATA[
**Version history**
0.1.5+galaxy1: Updated to monocle3-cli 0.0.9 for plot cells to allow for multiple genes plotting.

0.1.5+galaxy0: Updated to monocle3-cli 0.0.8 to add top marker genes and fix container plots for plotCells (only those two modules upgraded).

0.1.4+galaxy0: Updated to monocle3-cli 0.0.7 to fix bug with column headers in tsv.

0.1.3+galaxy0: Updated to monocle3-cli 0.0.5 to fix bug with tsv inputs.

0.1.2+galaxy0: Initial version based on monocle3-cli 0.0.3 and monocle3 0.1.2
    ]]></token>
  <token name="@INPUT_OPTS@">
    --input-object-format '${input_object_format}' '${input_object_file}'
  </token>
  <token name="@OUTPUT_OPTS@">
    --output-object-format '${output_object_format}' output.RDS
#if $introspective
    --introspective
#end if
  </token>
  <token name="@VERBOSE@">
#if $verbose
    --verbose
#end if
  </token>

  <xml name="requirements">
    <requirements>
      <requirement type="package" version="0.0.7">monocle3-cli</requirement>
      <yield/>
    </requirements>
  </xml>

  <xml name="citations">
    <citations>
      <yield />
      <citation type="doi">10.1038/nmeth.4402</citation>
      <citation type="bibtex">
	@misc{githubscanpy-scripts,
	author = {Ni Huang, Krzysztof Polanski, EBI Gene Expression Team},
	year = {2019},
	title = {Monocle3-cli: command line interface for Monocle3},
	publisher = {GitHub},
	journal = {GitHub repository},
	url = {https://github.com/ebi-gene-expression-group/monocle-scripts},
      }</citation>
      <citation type="doi">10.1101/2020.04.08.032698</citation>
    </citations>
  </xml>

  <xml name="input_object_params">
    <param name="input_object_file" argument="input-object-file" type="data" format="rdata" label="Input object in RDS format"/>
    <param name="input_object_format" argument="--input-object-format" type="select" label="Format of input object">
      <option value="cds3" selected="true">Monocle3 object in RDS</option>
    </param>
  </xml>

  <xml name="output_object_params">
    <param name="output_object_format" argument="--output-object-format" type="select" label="Format of output object">
      <option value="cds3" selected="true">Monocle3 object in RDS</option>
    </param>
    <param name="introspective" argument="--introspective" type="boolean" checked="true" label="Print introspective information of output object"/>
  </xml>

  <xml name="verbose_flag">
  	<param name="verbose" argument="--verbose" type="boolean" checked="false" label="Emit verbose output"/>
  </xml>
</macros>