diff macros.xml @ 0:169c72b2ce79 draft

planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Thu Apr 27 12:02:44 2023 +0000
@@ -0,0 +1,99 @@
+<macros>
+    <token name="@TOOL_VERSION@">0.17.0</token>
+
+    <xml name="creator">
+        <creator>
+            <yield/>
+            <person
+                givenName="Helge"
+                familyName="Hecht"
+                url="https://github.com/hechth"
+                identifier="0000-0001-6744-996X" />
+            <person
+                givenName="Maksym"
+                familyName="Skoryk"
+                url="https://github.com/maximskorik"
+                identifier="0000-0003-2056-8018" />
+            <person
+                givenName="Zargham"
+                familyName="Ahmad"
+                url="https://github.com/zargham-ahmad"
+                identifier="0000-0002-6096-224X" />
+            <person
+                givenName="Wudmir"
+                familyName="Rojas"
+                url="https://github.com/wverastegui"
+                identifier="0000-0001-7036-9987" />
+            <organization
+                url="https://www.recetox.muni.cz/"
+                email="[e-mail]"
+                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 output is a JSON file containing serialized matchMS Scores object. The file can be processed by **matchMS output formatter**. 
+        ]]>
+    </token>
+    
+    <token name="@HELP_matchms_networking@">
+        <![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**
+
+        matchMS similarity
+        
+        **Downstream Tools**
+        
+        The output is a network-graph file that can be visualized using graph visualization software (e.g., Cytoscape).
+        ]]>
+    </token>
+    
+    <token name="@HELP_formatter@">
+        <![CDATA[
+            Usage
+                This tool creates user friendly tables from the similarity scores produced by **matchMS similarity**.
+                The tool can be operated on two modes based on (i) thresholds or (ii) top k matches.
+
+            Input Table Format
+                The tool expects a JSON file containing serialized matchMS Scores object.
+
+            Output Table Format
+                +----------+-----------+---------+--------+
+                | query    | reference | matches | scores |
+                +==========+===========+=========+========+
+                | C001     | Glycine   |      6  | 0.5    |
+                +----------+-----------+---------+--------+
+                | C002     | Glycine   |     3   | 0.34   |
+                +----------+-----------+---------+--------+
+                |   ...    | ...       | ...     | ...    |
+                +----------+-----------+---------+--------+
+        ]]>
+    </token>
+    
+        <xml name="citations">
+            <citations>
+                <citation type="doi">10.5281/zenodo.7178586</citation>
+                <citation type="doi">10.21105/joss.02411</citation>
+            </citations>
+        </xml>
+
+</macros>