Mercurial > repos > recetox > matchms

diff matchms_similarity.xml @ 4:ba5e9bd05d5b draft

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5661cf2406e0616d7b2f4bee1b57ec43716088de
author recetox
date Tue, 18 Oct 2022 11:00:55 +0000
parents 9f8532c99845
children 28f7f2e60331
line wrap: on
line diff
--- a/matchms_similarity.xml	Wed Sep 21 15:28:55 2022 +0000
+++ b/matchms_similarity.xml	Tue Oct 18 11:00:55 2022 +0000
@@ -1,4 +1,4 @@
-<tool id="matchms" name="matchMS similarity" version="@TOOL_VERSION@+galaxy2" python_template_version="3.8">
+<tool id="matchms" name="matchMS similarity" version="@TOOL_VERSION@+galaxy0" python_template_version="3.8">
     <description>calculate the similarity score and matched peaks</description>
 
     <macros>
@@ -39,7 +39,6 @@
             "$algorithm.mz_power" \
             "$algorithm.intensity_power" \
             "$similarity_scores" \
-            "$similarity_matches"
         </configfile>
     </configfiles>
 
@@ -82,80 +81,52 @@
     </inputs>
 
     <outputs>
-        <data label="$similarity_metric scores of ${on_string}" name="similarity_scores" format="tsv"/>
-        <data label="$similarity_metric matches of ${on_string}" name="similarity_matches" format="tsv"/>
+        <data label="$similarity_metric scores of ${on_string}" name="similarity_scores" format="json"/>
     </outputs>
 
     <tests>
-        <test>
+        <test> <!-- TEST #1: Test scoring of different file formats. -->
             <param name="references" value="similarity/fill.mgf" ftype="mgf"/>
-            <param name="queries" value="similarity/fill.msp" ftype="msp"/>
+            <param name="queries" value="similarity/fill2.msp" ftype="msp"/>
             <param name="similarity_metric" value="CosineGreedy"/>
-            <output name="similarity_scores" file="similarity/scores_test1_out.tsv" ftype="tsv"
-                    checksum="md5$1aff8d0777e2f4e565be2b1b393547ef"/>
-            <output name="similarity_matches" file="similarity/matches_test1_out.tsv" ftype="tsv"
-                    checksum="md5$aab26ef4a0e80a53699832db72c06340"/>
-        </test>
-        <test>
-            <param name="references" value="similarity/recetox_gc-ei_ms_20201028.msp" ftype="msp"/>
-            <param name="queries" value="similarity/fill.msp" ftype="msp"/>
-            <param name="similarity_metric" value="CosineGreedy"/>
-            <output name="similarity_scores" file="scores_test2_out.tsv" ftype="tsv"
-                    checksum="md5$d2a5a01d9980636ce6a246d68834b84e"/>
-            <output name="similarity_matches" file="matches_test2_out.tsv" ftype="tsv"
-                    checksum="md5$28dc16ce45105234437e53d59e240046"/>
+            <output name="similarity_scores" file="similarity/scores_test1_out.json" ftype="json"
+                checksum="md5$72f96c48f8c34cf2a7c37d3aede33ca0"/>
         </test>
-        <test>
-            <param name="references" value="similarity/recetox_gc-ei_ms_20201028.msp" ftype="msp"/>
-            <param name="queries" value="similarity/fill.msp" ftype="msp"/>
-            <param name="similarity_metric" value="CosineHungarian"/>
-            <output name="similarity_scores" file="similarity/scores_test3_out.tsv" ftype="tsv"
-                    checksum="md5$1341369778036e0a267ff723f8cfca9c"/>
-            <output name="similarity_matches" file="similarity/matches_test3_out.tsv" ftype="tsv"
-                    checksum="md5$28dc16ce45105234437e53d59e240046"/>
+        <test> <!-- TEST #2: Test scoring of the same file formats. -->
+            <param name="references" value="similarity/RECETOX_Exposome_pesticides_HR_MS_20220323.msp" ftype="msp"/>
+            <param name="queries" value="similarity/fill2.msp" ftype="msp"/>
+            <param name="similarity_metric" value="CosineGreedy"/>
+            <output name="similarity_scores" file="similarity/scores_test2_out.json" ftype="json"
+                checksum="md5$d325a895f74262087553d08cc40a99aa"/>
         </test>
-        <test>
-            <param name="references" value="similarity/recetox_gc-ei_ms_20201028.msp" ftype="msp"/>
-            <param name="queries" value="similarity/recetox_gc-ei_ms_20201028.msp" ftype="msp"/>
-            <param name="similarity_metric" value="ModifiedCosine"/>
-            <output name="similarity_scores" file="similarity/scores_test4_out.tsv" ftype="tsv"/>
-            <output name="similarity_matches" file="similarity/matches_test4_out.tsv" ftype="tsv"/>
-        </test>
-        <test>
-            <param name="queries" value="similarity/fill.msp" ftype="msp"/>
-            <param name="similarity_metric" value="CosineHungarian"/>
-            <param name="is_symmetric" value="TRUE"/>
-            <output name="similarity_scores" file="similarity/scores_test5_out.tsv" ftype="tsv"/>
-            <output name="similarity_matches" file="similarity/matches_test5_out.tsv" ftype="tsv"/>
-        </test>
-        <test>
-            <param name="references" value="similarity/recetox_gc-ei_ms_20201028.msp" ftype="msp"/>
+        <test> <!-- TEST #3: Test scoring with applying RI filtering. -->
+            <param name="references" value="similarity/fill.mgf" ftype="mgf"/>
             <param name="queries" value="similarity/fill2.msp" ftype="msp"/>
             <conditional name="ri_filtering">
                 <param name="is_true" value="True"></param>
                 <param name="tolerance" value="60.0" />
             </conditional>
-            <param name="similarity_metric" value="CosineGreedy"/>
-            <output name="similarity_scores" file="similarity/scores_test6_out.tsv" ftype="tsv"/>
-            <output name="similarity_matches" file="similarity/matches_test6_out.tsv" ftype="tsv"/>
+            <param name="similarity_metric" value="CosineHungarian"/>
+            <output name="similarity_scores" file="similarity/scores_test3_out.json" ftype="json"
+                checksum="md5$437c03775ebe978f03b7c63aa09ee52e"/>
         </test>
-        <test>
-            <param name="references" value="similarity/RECETOX_Exposome_pesticides_HR_MS_20220323.msp" ftype="msp"/>
-            <param name="queries" value="similarity/RECETOX_Exposome_pesticides_HR_MS_20220323.msp" ftype="msp"/>
+        <test> <!-- TEST #4: Test symmetric scoring. -->
+            <param name="queries" value="similarity/recetox_gc-ei_ms_20201028.msp" ftype="msp"/>
+            <param name="is_symmetric" value="TRUE"/>
             <param name="similarity_metric" value="NeutralLossesCosine"/>
-            <output name="similarity_scores" file="similarity/scores_test7_out.tsv" ftype="tsv"/>
-            <output name="similarity_matches" file="similarity/matches_test7_out.tsv" ftype="tsv"/>
+            <output name="similarity_scores" file="similarity/scores_test4_out.json" ftype="json"
+                checksum="md5$951b3bad2207d8301e0c60397533e607"/>
         </test>
-        <test>
+        <test> <!-- TEST #5: Test symmetric scoring with applying RI filtering. -->
             <param name="queries" value="similarity/recetox_gc-ei_ms_20201028.msp" ftype="msp"/>
-            <param name="similarity_metric" value="CosineGreedy"/>
+            <param name="similarity_metric" value="ModifiedCosine"/>
             <param name="is_symmetric" value="TRUE" />
             <conditional name="ri_filtering">
                 <param name="is_true" value="True"></param>
                 <param name="tolerance" value="60.0" />
             </conditional>
-            <output name="similarity_scores" file="similarity/scores_test8_out.tsv" ftype="tsv"/>
-            <output name="similarity_matches" file="similarity/matches_test8_out.tsv" ftype="tsv"/>
+            <output name="similarity_scores" file="similarity/scores_test5_out.json" ftype="json"
+                checksum="md5$31f83451443a1996fbd7fbc204803481"/>
         </test>
     </tests>
 
@@ -166,7 +137,7 @@
     </help>
 
     <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>