--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Tue Mar 22 16:08:45 2022 +0000
@@ -0,0 +1,70 @@
+<macros>
+    <token name="@TOOL_VERSION@">0.14.0</token>
+
+    <xml name="creator">
+        <creator>
+            <person
+                givenName="Helge"
+                familyName="Hecht"
+                url="https://github.com/hechth"
+                identifier="0000-0001-6744-996X" />
+            <organization
+                url="https://www.recetox.muni.cz/"
+                email="GalaxyToolsDevelopmentandDeployment@space.muni.cz"
+                name="RECETOX MUNI" />
+        </creator>
+    </xml>
+
+    <token name="@HELP_matchms@">
+        <![CDATA[
+            Documentation
+                For documentation on the tool see https://github.com/matchms/matchms/blob/master/README.rst
+                and https://matchms.readthedocs.io/en/latest/.
+
+            Upstream Tools
+                +-----------+---------------+--------+-----------+
+                | Name      | Output File   | Format | Parameter |
+                +===========+===============+========+===========+
+                | RAMClustR | Mass spectra  | msp    | references|
+                +-----------+---------------+--------+-----------+
+                | RAMClustR | Mass spectra  | msp    | queries   |
+                +-----------+---------------+--------+-----------+
+
+            Downstream Tools
+                The outputs are two tsv datasets. One containing the similarity scores and the other number of matched peaks.
+        ]]>
+    </token>
+
+    <token name="@HELP_formatter@">
+        <![CDATA[
+            Usage
+                This tool creates user friendly tables from the data matrices produces by matchms.
+                The tool can be operated on two modes based on (i) thresholds or (ii) top k matches.
+
+            Input Table Format
+                The tool expects two data matrices with the format as depicted below.
+                The tool assumes the reference compound labels as row labels and the query labels as column labels (as naturally outputted by matchms).
+
+                +----------+------+------+-----+
+                |          | C001 | C002 | ... |
+                +==========+======+======+=====+
+                | Perylene | 0.1  | 0.0  | ... |
+                +----------+------+------+-----+
+                | Glycine  | 0.5  | 0.34 | ... |
+                +----------+------+------+-----+
+                |   ...    | ...  | ...  | ... |
+                +----------+------+------+-----+
+
+            Output Table Format
+                +----------+-----------+---------+--------+
+                | query    | reference | matches | scores |
+                +==========+===========+=========+========+
+                | C001     | Glycine   |      6  | 0.5    |
+                +----------+-----------+---------+--------+
+                | C002     | Glycine   |     3   | 0.34   |
+                +----------+-----------+---------+--------+
+                |   ...    | ...       | ...     | ...    |
+                +----------+-----------+---------+--------+
+        ]]>
+    </token>
+</macros>