diff help.xml @ 0:9ff95a1a2705 draft

planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e

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+<macros>
+    <token name="@HELP_matchms@">
+        Documentation
+            The Python library matchms provides functions to convert, filter and compare mass spectrometry data.
+            For an overview of the different galaxy modules, see the figure below.
+            For detailed documentation on the tool, see https://github.com/matchms/matchms/blob/master/README.rst
+            and https://matchms.readthedocs.io/en/latest/ for the Python API.
+
+            To get more familiar with the library, there is a `tutorial`_ available which explains how to build a mass spectrometry data processing
+            pipeline with matchms.
+                
+            .. _tutorial: https://medium.com/escience-center/build-your-own-mass-spectrometry-analysis-pipeline-in-python-using-matchms-part-i-d96c718c68ee
+
+        Overview
+            .. image:: https://github.com/RECETOX/galaxytools/raw/29e54e69dab6ab1263f56d35ea19f5d7f284d728/tools/matchms/images/matchms_galaxytools.png
+               :width: 3120
+               :height: 1686
+               :scale: 30
+               :alt: Overview of different matchms galaxytools and how they are connected.
+    </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>
+</macros>
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