# HG changeset patch
# User recetox
# Date 1666090750 0
# Node ID 97c4050411164aa2b8cdc994ce2224e745b9aaea
# Parent  a1eb173cab5df2f8a8bbf243b26a9ce79beb0c0b
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5661cf2406e0616d7b2f4bee1b57ec43716088de

diff -r a1eb173cab5d -r 97c405041116 macros.xml
--- a/macros.xml	Fri Jul 22 16:47:00 2022 +0000
+++ b/macros.xml	Tue Oct 18 10:59:10 2022 +0000
@@ -1,5 +1,5 @@
 <macros>
-    <token name="@TOOL_VERSION@">0.15.0</token>
+    <token name="@TOOL_VERSION@">0.17.0</token>
 
     <xml name="creator">
         <creator>
@@ -9,6 +9,11 @@
                 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"
@@ -19,7 +24,7 @@
                 name="RECETOX MUNI" />
         </creator>
     </xml>
-
+    
     <token name="@HELP_matchms@">
         <![CDATA[
             Documentation
@@ -36,29 +41,18 @@
                 +-----------+---------------+--------+-----------+
 
             Downstream Tools
-                The outputs are two tsv datasets. One containing the similarity scores and the other number of matched peaks.
+                The output is a JSON file containing serialized matchMS Scores object. The file can be processed by **matchMS output formatter**. 
         ]]>
     </token>
 
     <token name="@HELP_formatter@">
         <![CDATA[
             Usage
-                This tool creates user friendly tables from the data matrices produces by matchms.
+                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 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 | ... |
-                +----------+------+------+-----+
-                |   ...    | ...  | ...  | ... |
-                +----------+------+------+-----+
+                The tool expects a JSON file containing serialized matchMS Scores object.
 
             Output Table Format
                 +----------+-----------+---------+--------+
diff -r a1eb173cab5d -r 97c405041116 matchms_filtering.xml
--- a/matchms_filtering.xml	Fri Jul 22 16:47:00 2022 +0000
+++ b/matchms_filtering.xml	Tue Oct 18 10:59:10 2022 +0000
@@ -148,7 +148,7 @@
 
 
     <citations>
-        <citation type="doi">10.5281/zenodo.4589154</citation>
+        <citation type="doi">10.5281/zenodo.7178586</citation>
         <citation type="doi">10.21105/joss.02411</citation>
     </citations>
 </tool>