--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/immuneml_simulate_events.xml	Thu Jul 01 11:36:43 2021 +0000
@@ -0,0 +1,59 @@
+<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="yaml_input" type="data" format="txt" label="YAML specification" multiple="false"/>
+      <param name="iml_input" type="data" format="iml_dataset" label="Dataset input" optional="true" help="This field accepts datasets in iml_dataset format, as created by the Create Dataset tool."/>
+  </inputs>
+    <outputs>
+        <data format="zip" name="archive" label="Archive: immune signal simulation"/>
+        <data format="iml_dataset" 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 <https://galaxy.immuneml.uio.no/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/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>