--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Fri Oct 29 09:49:13 2021 +0000
@@ -0,0 +1,65 @@
+<macros>
+    <token name="@TOOL_VERSION@">0.9.0</token>
+    <xml name="requirements">
+        <requirements>
+            <container type="docker">recetox/recetox-xmsannotator:october4</container>
+        </requirements>
+    </xml>
+    <xml name="creator">
+        <creator>
+            <organization
+                url="https://www.recetox.muni.cz/"
+                name="RECETOX MUNI" />
+        </creator>
+    </xml>
+    <xml name="inputs">
+        <param name="peak_table" type="data" format="csv,parquet">
+            <label>Peak table</label>
+            <help><![CDATA[
+                A peak-intensity table such as outputted from apLCMS.
+                The file is required to contain the fields <em>mz</em> and <em>rt</em>.
+                Columns for feature intensity in a sample have to start with <em>intensity</em>.
+
+            ]]></help>
+        </param>
+        <param name="compound_table" type="data" format="csv,parquet">
+            <label>Compound database</label>
+            <help><![CDATA[
+                Database of compounds according to which the annotation is performed.
+                The database is required to contain the fields <em>compound_id</em>, <em>monoisotopic_mass</em>, and <em>molecular_formula</em>.
+            ]]></help>
+        </param>
+        <param name="adduct_table" type="data" format="csv,parquet" optional="true">
+            <label>Adduct database (optional)</label>
+            <help><![CDATA[
+                Database of adduct which is combined with the database of compound to form a molecule-adduct pairs.
+                The database is required to contain <em>adduct</em>, <em>charge</em>, <em>mass</em>, and <em>n_molecules</em>.
+            ]]></help>
+        </param>
+    </xml>
+
+    <xml name="outputs">
+        <data name="annotation_parquet" format="parquet"/>
+    </xml>
+
+    <xml name="tolerance">
+        <param name="mass_tolerance_ppm" type="integer" min="0" value="5">
+            <label>Mass tolerance [ppm]</label>
+            <help>Mass tolerance in ppm for database matching.</help>
+        </param>
+        <yield/>
+    </xml>
+    <token name="@HELP@">
+        <![CDATA[
+        Annotate the peak intensity table (e.g. from an apLCMS run) with compounds from the compounds database
+        using advanced methods.
+
+        The annotation process generates all possible compound-adduct pairs and matches those pairs to the measured
+        peaks. A compound-adduct pair is pronounced as a match to a certain peak when the difference of their masses are
+        withing some tolerance.
+        ]]>
+    </token>
+    <xml name="citations">
+        <citation type="doi">10.1021/acs.analchem.6b01214</citation>
+    </xml>
+</macros>