<tool id="immuneml_simulation" name="Simulate immune events into an existing repertoire dataset" version="@VERSION@.0">
  <description></description>
    <macros>
        <import>prod_macros.xml</import>
    </macros>
    <expand macro="requirements" />
  <command><![CDATA[
 
      #if $iml_input
         cp -r ${iml_input.extra_files_path}/result/* . &&
	 (mv repertoires/* . &>/dev/null || :) &&
	 rm -rf repertoires &&
      #end if
      
      cp "$yaml_input" yaml_copy &&
      immune-ml ./yaml_copy ${html_outfile.files_path} --tool GalaxySimulationTool &&

      mv ${html_outfile.files_path}/index.html ${html_outfile} && 
      mv ${html_outfile.files_path}/immuneML_output.zip $archive 

      ]]>
  </command>
  <inputs>
      <param name="iml_input" type="data" format="immuneml_receptors" label="Dataset input" optional="true" help="This field accepts datasets ithe ImmuneML format, as created by the Create Dataset tool."/>
      <param name="yaml_input" type="data" format="txt" label="YAML specification" multiple="false"/>
  </inputs>
    <outputs>
        <data format="zip" name="archive" label="Archive: immune signal simulation"/>
        <data format="immuneml_receptors" name="html_outfile" label="ImmuneML dataset (simulated immune signals)"/>
    </outputs>


  <help><![CDATA[

        This Galaxy tool can be used to implant short disease-associated motifs into an existing Repertoire dataset.
        Such a dataset with simulated immune signals can be used to benchmark different ML methods.
        Any type of repertoire dataset (experimental or simulated) can be used as a starting point for an immune event simulation, as long as it contains amino acid sequences.

        If you instead want to simulate a synthetic dataset from scratch, start with the
        tool `Simulate a synthetic immune receptor or repertoire dataset <root?tool_id=immuneml_simulate_dataset>`_.

        For the exhaustive documentation of this tool and an example YAML specification, see the tutorial `How to simulate immune events into an existing AIRR dataset in Galaxy <https://docs.immuneml.uio.no/latest/galaxy/galaxy_simulate_signals.html>`_.

        **Tool output**

        This Galaxy tool will produce the following history elements:

        - ImmuneML dataset (simulated immune signals): a repertoire dataset which can be used as an input to other immuneML tools. The history element contains a summary HTML page describing general characteristics of the dataset, including the name of the dataset
          (which is used in the dataset definition of a yaml specification), the dataset type and size, available labels, and a link to download the raw data files.

        - Archive: immune signal simulation: a .zip file containing the complete output folder as it was produced by immuneML. This folder
          contains the output of the Simulation instruction including all raw data files.
          Furthermore, the folder contains the complete YAML specification file for the immuneML run, the HTML output and a log file.


    ]]>
  </help>

</tool>