--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/immuneml_yaml.xml	Thu Jul 01 11:36:43 2021 +0000
@@ -0,0 +1,74 @@
+<tool id="immune_ml" name="Run immuneML with any YAML specification" 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
+
+      #set $input_orig_names = []
+      #if $data_input
+          #for $input in $data_input
+             #set input_orig_names += [str($input.element_identifier)]
+             ([ -e ./"$input.element_identifier" ] && echo "File '$input.element_identifier' already exists in the input folder, skipping." || ln -s $input "$input.element_identifier") &&
+          #end for#
+      #end if
+
+      cp "$yaml_input" yaml_copy &&
+      immune-ml ./yaml_copy ${html_outfile.files_path} --tool GalaxyYamlTool &&
+      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="data_input" type="data" multiple="true" label="Additional files" optional="true" help="This field should include individual repertoire files, metadata files, receptor data and others."/>
+      <param name="iml_input" type="data"  format="iml_dataset" label="ImmuneML dataset" optional="true" help="This field accepts ImmuneML datasets, as created by the Create Dataset tool."/>
+  </inputs>
+    <outputs>
+        <data format="zip" name="archive" label="Archive: immuneML Analysis"/>
+        <data format="html" name="html_outfile" label="Summary: immuneML analysis"/>
+    </outputs>
+
+
+      <help><![CDATA[
+
+
+        This Galaxy tool can be used to run any possible YAML-based immuneML analysis in Galaxy.
+
+        It is typically recommended to use the analysis-specific Galaxy tools for
+        `creating datasets <https://galaxy.immuneml.uio.no/root?tool_id=immune_ml_dataset>`_,
+        `simulating synthetic data <https://galaxy.immuneml.uio.no/root?tool_id=immuneml_simulate_dataset>`_,
+        `implanting synthetic immune signals <https://galaxy.immuneml.uio.no/root?tool_id=immuneml_simulation>`_ or
+        `training <https://galaxy.immuneml.uio.no/root?tool_id=immuneml_train_ml_model>`_ and
+        `applying <https://galaxy.immuneml.uio.no/root?tool_id=immuneml_apply_ml_model>`_ ML models instead of this tool.
+        These other tools are able to export the relevant output files to Galaxy history elements.
+
+        However, when you want to run the `ExploratoryAnalysis <https://docs.immuneml.uio.no/specification.html#exploratoryanalysis>`_ instruction,
+        or other analyses that do not have a corresponding Galaxy tool, this generic tool can be used.
+
+        For the exhaustive documentation of this tool and an example YAML specification for exploratory analysis, see the tutorial `How to run any AIRR ML analysis in Galaxy <https://docs.immuneml.uio.no/galaxy/galaxy_general_yaml.html>`_.
+
+
+        **Tool output**
+
+        This Galaxy tool will produce the following history elements:
+
+        - Summary: immuneML analysis: a HTML page that allows you to browse through all results.
+
+        - ImmuneML Analysis Archive: a .zip file containing the complete output folder as it was produced by immuneML. This folder
+          contains the output of the instruction that was used, 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>