Mercurial > repos > recetox > matchms_metadata_match

diff matchms_metadata_match.xml @ 19:c86d265f6f5e draft default tip

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit bd80a813fb2f01f22eed0c874f8911ce4d00762a
author recetox
date Mon, 30 Jun 2025 12:59:27 +0000
parents 86e080d81cfb
children
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--- a/matchms_metadata_match.xml	Thu Nov 14 15:11:57 2024 +0000
+++ b/matchms_metadata_match.xml	Mon Jun 30 12:59:27 2025 +0000
@@ -1,4 +1,4 @@
-<tool id="matchms_metadata_match" name="matchms metadata match" version="@TOOL_VERSION@+galaxy0" profile="21.09">
+<tool id="matchms_metadata_match" name="matchms metadata match" version="@TOOL_VERSION@+galaxy0" profile="23.0" license="MIT">
     <description>matchms metadata match calculation for numeric fields based on tolerance</description>
 
     <macros>
@@ -85,45 +85,75 @@
 
     <tests>
         <test>
-            <param name="queries" value="similarity/rcx_gc-ei_ms_subset.msp" ftype="msp"/>
-            <param name="references" value="similarity/rcx_gc-ei_ms_subset.msp" ftype="msp"/>
-            <param name="tolerance" value="60.0" />
+            <conditional name="scores">
+                <param name="use_scores" value="False"/>
+                <param name="queries" value="similarity/rcx_gc-ei_ms_subset.msp" ftype="msp"/>
+                <param name="references" value="similarity/rcx_gc-ei_ms_subset.msp" ftype="msp"/>
+            </conditional>
+            <conditional name="matching">
+                <param name="matching_type" value="difference" />
+                <param name="tolerance" value="60.0" />
+            </conditional>
             <output name="scores_out" value="metadata_match/ri_match_60.json" ftype="json" />
         </test>
         <test>
-            <param name="queries" value="similarity/rcx_gc-ei_ms_subset.msp" ftype="msp"/>
-            <param name="references" value="similarity/rcx_gc-ei_ms_subset.msp" ftype="msp"/>
-            <param name="matching_type" value="equal_match" />
-            <param name="metadata_match_field" value="smiles" />
+            <conditional name="scores">
+                <param name="use_scores" value="False"/>
+                <param name="queries" value="similarity/rcx_gc-ei_ms_subset.msp" ftype="msp"/>
+                <param name="references" value="similarity/rcx_gc-ei_ms_subset.msp" ftype="msp"/>
+            </conditional>
+            <conditional name="matching">
+                <param name="matching_type" value="equal_match" />
+                <param name="metadata_match_field" value="smiles" />
+            </conditional>
             <output name="scores_out" value="metadata_match/smiles.json" ftype="json" />
         </test>
         <test>
-            <param name="use_scores" value="True"/>
-            <param name="scores_in" value="metadata_match/smiles.json" ftype="json"/>
-            <param name="matching_type" value="equal_match" />
-            <param name="metadata_match_field" value="inchikey" />
-            <param name="join_type" value="inner" />
+            <conditional name="scores">     
+                <param name="use_scores" value="True"/>
+                <param name="scores_in" value="metadata_match/smiles.json" ftype="json"/>
+                <param name="join_type" value="inner" />
+            </conditional>
+            <conditional name="matching">
+                <param name="matching_type" value="equal_match" />
+                <param name="metadata_match_field" value="inchikey" />
+            </conditional>
             <output name="scores_out" value="metadata_match/inchi_key_inner.json" ftype="json" />
         </test>
         <test>
-            <param name="use_scores" value="True"/>
-            <param name="scores_in" value="metadata_match/ri_match_60.json" ftype="json"/>
-            <param name="tolerance" value="20.0" />
-            <param name="join_type" value="inner" />
+            <conditional name="scores"> 
+                <param name="use_scores" value="True"/>
+                <param name="scores_in" value="metadata_match/ri_match_60.json" ftype="json"/>
+                <param name="join_type" value="inner" />
+            </conditional>
+            <conditional name="matching">
+                <param name="matching_type" value="difference" />
+                <param name="tolerance" value="20.0" />
+            </conditional>
             <output name="scores_out" value="metadata_match/inner_join_ri_20.json" ftype="json" />
         </test>
         <test>
-            <param name="use_scores" value="True"/>
-            <param name="scores_in" value="metadata_match/ri_match_60.json" ftype="json"/>
-            <param name="tolerance" value="20.0" />
-            <param name="join_type" value="left" />
+            <conditional name="scores"> 
+                <param name="use_scores" value="True"/>
+                <param name="scores_in" value="metadata_match/ri_match_60.json" ftype="json"/>
+                <param name="join_type" value="left" />
+            </conditional>
+            <conditional name="matching">
+                <param name="matching_type" value="difference" />
+                <param name="tolerance" value="20.0" />
+            </conditional>
             <output name="scores_out" value="metadata_match/left_join_ri_20.json" ftype="json" />
         </test>
         <test>
-            <param name="queries" value="similarity/rcx_gc-ei_ms_subset.msp" ftype="msp"/>
-            <param name="references" value="similarity/rcx_gc-ei_ms_subset.msp" ftype="msp"/>
-            <param name="matching_type" value="equal_match" />
-            <param name="metadata_match_field" value="formula" />
+            <conditional name="scores"> 
+                <param name="use_scores" value="False"/>
+                <param name="queries" value="similarity/rcx_gc-ei_ms_subset.msp" ftype="msp"/>
+                <param name="references" value="similarity/rcx_gc-ei_ms_subset.msp" ftype="msp"/>
+            </conditional>
+            <conditional name="matching">
+                <param name="matching_type" value="equal_match" />
+                <param name="metadata_match_field" value="formula" />
+            </conditional>
             <output name="scores_out" value="metadata_match/formula.json" ftype="json" />
         </test>
     </tests>