--- a/matchms_formatter.xml	Thu May 25 09:06:00 2023 +0000
+++ b/matchms_formatter.xml	Tue Jun 27 14:25:59 2023 +0000
@@ -1,10 +1,15 @@
-<tool id="matchms_formatter" name="matchms output formatter" version="0.1.4" python_template_version="3.5">
-    <description>reformat output tables of matchms</description>
+<tool id="matchms_formatter" name="matchms scores formatter" version="@TOOL_VERSION@+galaxy0" profile="21.09">
+    <description>reformat scores object of matchms to long format table</description>
 
     <macros>
         <import>macros.xml</import>
+        <import>help.xml</import>
     </macros>
     <expand macro="creator"/>
+    <edam_operations>
+        <edam_operation>operation_0335</edam_operation>
+    </edam_operations>
+    <expand macro="bio.tools"/>
 
     <requirements>
         <requirement type="package" version="@TOOL_VERSION@">matchms</requirement>
@@ -24,61 +29,32 @@
     <configfiles>
         <configfile name="matchms_formatter_cli">
             python3 ${__tool_directory__}/formatter.py \
-            --sf "$scores" \
-            --o "$output" \
-            $method.selection \
-            #if $method.selection == "get-thresholded-data"
-            --st $method.scores_threshold \
-            --mt $method.matches_threshold
-            #else
-            --k $method.k
-            #end if
+            --sf '$scores' \
+            --o '$output'
         </configfile>
     </configfiles>
 
     <inputs>
-        <param label="Scores object" name="scores" type="data" format="json" help="MatchMS Scores json file." />
-
-        <conditional name="method">
-            <param name="selection" type="select" label="Formatting method">
-                <option value="get-thresholded-data" selected="true">Thresholding</option>
-                <option value="get-top-k-data">Top K Matches</option>
-            </param>
-            <when value="get-thresholded-data">
-                <param label="Scores Threshold" name="scores_threshold" type="float" value="0.6" min="0.0" max="1.0"
-                       help="Threshold for matching score."/>
-                <param label="Matches Threshold" name="matches_threshold" type="integer" value="3" min="0"
-                       help="Threshold for number of matches ions."/>
-            </when>
-            <when value="get-top-k-data">
-                <param label="Top K" name="k" type="integer" value="5" help="K for top k match selection."/>
-            </when>
-        </conditional>
-
+        <param label="Scores object" name="scores" type="data" format="json" help="matchms Scores json file." />
     </inputs>
     <outputs>
-        <data label="${tool.name} (${method.selection}) on ${on_string}" name="output" format="tsv"/>
+        <data label="${tool.name} on ${on_string}" name="output" format="tsv"/>
     </outputs>
 
     <tests>
         <test>
-            <param name="scores" value="similarity/scores_test2_out.json" ftype="json"/>
-            <param name="selection" value="get-thresholded-data"/>
-            <param name="scores_threshold" value="0.4"/>
-            <param name="matches_threshold" value="2"/>
-            <output name="output" file="formatter/test2_threshold_formatting.tsv" ftype="tsv"
-                checksum="md5$db18b3f3dd5d8dea4db0fc1d59d3db3b"/>
+            <param name="scores" value="formatter/fill2_trunc_scores_with_metadata_match.json" ftype="json"/>
+            <output name="output" value="formatter/fill2_formatted.tsv" ftype="tsv"
+                checksum="md5$4f0d83da381b8a403d807d26a9dd0f34"/>
         </test>
         <test>
-            <param name="scores" value="similarity/scores_test2_out.json" ftype="json"/>
-            <param name="selection" value="get-top-k-data"/>
-            <param name="k" value="3"/>
-            <output name="output" file="formatter/test2_topk_formatting.tsv" ftype="tsv"
-                checksum="md5$ff827ec7413acac3d2394330935ace99"/>
+            <param name="scores" value="similarity/scores_test4_out.json" ftype="json"/>
+            <output name="output" file="formatter/test4_formatted.tsv" ftype="tsv"/>
         </test>
     </tests>
 
-    <help><![CDATA[
+    <help>
         @HELP_formatter@
-    ]]></help>
+        @HELP_matchms@
+    </help>
 </tool>