--- a/macros.xml	Fri Jan 28 16:27:30 2022 +0000
+++ b/macros.xml	Mon Jun 26 13:55:44 2023 +0000
@@ -1,74 +1,144 @@
 <macros>
-    <token name="@TOOL_VERSION@">0.9.0</token>
-    <xml name="requirements">
-        <requirements>
-            <requirement type="package" version="0.9.0">r-recetox-xmsannotator</requirement>
-        </requirements>
-    </xml>
-    <xml name="creator">
-        <creator>
-            <person
-                givenName="Jiří"
-                familyName="Novotný"
-                url="https://github.com/xtracko"
-                identifier="0000-0001-5449-3523" />
-            <person
-                givenName="Martin"
-                familyName="Čech"
-                url="https://github.com/martenson"
-                identifier="0000-0002-9318-1781" />
-            <organization
-                url="https://www.recetox.muni.cz/"
-                email="GalaxyToolsDevelopmentandDeployment@space.muni.cz"
-                name="RECETOX MUNI" />
-        </creator>
-    </xml>
-    <xml name="inputs">
-        <param name="peak_table" type="data" format="csv,h5,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>.
-            ]]></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>
+<token name="@TOOL_VERSION@">0.10.0</token>
+
+<xml name="requirements">
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">r-recetox-xmsannotator</requirement>
+    </requirements>
+</xml>
+
+<xml name="creator">
+    <creator>
+        <person
+            givenName="Jiří"
+            familyName="Novotný"
+            url="https://github.com/xtracko"
+            identifier="0000-0001-5449-3523" />
+        <person
+            givenName="Martin"
+            familyName="Čech"
+            url="https://github.com/martenson"
+            identifier="0000-0002-9318-1781" />
+        <person
+            givenName="Matej"
+            familyName="Troják"
+            url="https://github.com/xtrojak"
+            identifier="0000-0003-0841-2707" />
+        <organization
+            url="https://www.recetox.muni.cz/"
+            email="GalaxyToolsDevelopmentandDeployment@space.muni.cz"
+            name="RECETOX MUNI" />
+    </creator>
+</xml>
+
+<xml name="inputs">
+    <param name="metadata_table" type="data" format="parquet,csv">
+        <label>Metadata table</label>
+        <help><![CDATA[
+            Peak metadata table*.
+        ]]></help>
+    </param>
+    <param name="intensity_table" type="data" format="parquet,csv">
+        <label>Intensity table</label>
+        <help><![CDATA[
+            Table with intensities** for features (rows) across samples (columns).
+        ]]></help>
+    </param>
+    <param name="compound_table" type="data" format="parquet,csv">
+        <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="parquet,csv" optional="true">
+        <label>Adduct database</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>
+    <param name="adduct_weights" type="data" format="parquet,csv" optional="true">
+        <label>Adduct weights</label>
+        <help>
+            A weight-by-adduct table.
+        </help>
+    </param>
+</xml>
 
-    <xml name="outputs">
-        <data name="annotation_parquet" format="parquet"/>
-    </xml>
+<xml name="outputs">
+    <data name="output_file" format="parquet">
+        <change_format>
+            <when input="metadata_table.ext" value="csv" format="csv" />
+        </change_format>
+    </data>
+</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@">
+Description
+===========
+
+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.
+
+Then, a score and a confidence level is assigned to each match based on peak correlation
+clustering, metabolite pathway associations, adducts expectations, and isotope conformations.
+
+Input tables description
+------------------------
+
+(*) Metadata table
+~~~~~~~~~~~~~~~~~~
 
-    <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 output from recetox-aplcms tool. 
+The `npeaks` column denotes the number of peaks which have been grouped into this feature. 
+The columns with the sample names indicate whether this feature is present in the sample.
+Only id, mz, and rt columns are required to be present.
+
++-------+--------------+--------------+---------------+----------------+---------------+---------------+-----------+------------------------+------------------------+------------------------+
+|  id   | mz           |  mzmin       |  mzmax        |  rt            |  rtmin        |  rtmax        |   npeaks  |  21_qc_no_dil_milliq   |  29_qc_no_dil_milliq   |  8_qc_no_dil_milliq    |
++=======+==============+==============+===============+================+===============+===============+===========+========================+========================+========================+
+|  1    | 70.03707021  |  70.037066   |  70.0370750   |  294.1038014   |  294.0634942  |  294.149985   |   3       |  1                     |  1                     |  1                     |
++-------+--------------+--------------+---------------+----------------+---------------+---------------+-----------+------------------------+------------------------+------------------------+
+|  2    | 70.06505677  |  70.065045   |  70.0650676   |  141.9560055   |  140.5762528  |  143.335758   |   2       |  1                     |  0                     |  1                     |
++-------+--------------+--------------+---------------+----------------+---------------+---------------+-----------+------------------------+------------------------+------------------------+
+|  57   | 78.04643252  |  78.046429   |  78.0464325   |  294.0063397   |  293.9406777  |  294.072001   |   2       |  1                     |  1                     |  0                     |
++-------+--------------+--------------+---------------+----------------+---------------+---------------+-----------+------------------------+------------------------+------------------------+
+|  ...  | ...          |   ...        |  ...          |  ...           |  ...          |  ...          |   ...     |  ...                   |  ...                   |  ...                   |
++-------+--------------+--------------+---------------+----------------+---------------+---------------+-----------+------------------------+------------------------+------------------------+
+
+(**) Intensity table
+~~~~~~~~~~~~~~~~~~~~
 
-        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>
+The output from recetox-aplcms tool.
+This table contains the peak area for aligned features in all samples.
+
++-------+------------------------+------------------------+------------------------+
+|  id   |  21_qc_no_dil_milliq   |  29_qc_no_dil_milliq   |  8_qc_no_dil_milliq    |
++=======+========================+========================+========================+
+|  1    |  13187487.20482895     |  7957395.699119729     |  11700594.397257797    |
++-------+------------------------+------------------------+------------------------+
+|  2    |  2075168.6398983458    |  0                     |  2574362.159289044     |
++-------+------------------------+------------------------+------------------------+
+|  57   |  2934524.4406785755    |  1333044.5065971944    |  0                     |
++-------+------------------------+------------------------+------------------------+
+|  ...  |  ...                   |  ...                   |  ...                   |
++-------+------------------------+------------------------+------------------------+
+</token>
+
+<xml name="citations">
+    <citation type="doi">10.1021/acs.analchem.6b01214</citation>
+</xml>
 </macros>