Merge pull request #502 from zargham-ahmad/issue490

matchms add key, matchms remove key: Added multiple keys handling
RECETOX · Mar 13, 2024 · f14275b · f14275b
2 parents 4018b84 + 297231b
commit f14275b
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Showing 6 changed files with 423 additions and 213 deletions.
diff --git a/tools/matchms/matchms_add_key.xml b/tools/matchms/matchms_add_key.xml
@@ -1,4 +1,4 @@
-<tool id="matchms_add_key" name="matchms add key" version="@TOOL_VERSION@+galaxy1" profile="21.09">
+<tool id="matchms_add_key" name="matchms add key" version="@TOOL_VERSION@+galaxy2" profile="21.09">
     <description>Set metadata key in MSP to static value</description>
 
     <macros>
@@ -29,13 +29,14 @@ import matchms
 from matchms.importing import load_from_msp
 from matchms.exporting import save_as_msp
 
-
+#set keys_dict = ({str($k.key): str($k.value) for $k in $attribute_repeat})
 matchms.Metadata.set_key_replacements({})
 
 spectra = list(load_from_msp("${spectral_library}", metadata_harmonization = "False"))
 new_spectra = []
 for spectrum in spectra:
-    spectrum.set("${key}", "${value}")
+    for key, value in ($keys_dict).items():
+        spectrum.set(key, value)
     new_spectra.append(spectrum)
 save_as_msp(new_spectra, "${output}")
 </configfile>
@@ -44,17 +45,18 @@ save_as_msp(new_spectra, "${output}")
     <inputs>
         <param label="Spectra file" name="spectral_library" type="data" format="msp"
             help="Mass spectral library file to add key." />
-
-        <param label="Attribute Name" name="key" type="text" value="" help="Name of the attribute which will be assigned to all spectra records in the MSP." />
-        <param label="Value" name="value" type="text" value="" help="Value of the attribute which will be assigned to all spectra records in the MSP." >
-            <sanitizer>
-                <valid initial="default">
-                    <add value="{}" />
-                    <add value="[]" />
-                    <add value="\" />
-                </valid>
-            </sanitizer>
-        </param>
+        <repeat name="attribute_repeat" title="Keys to add">
+            <param label="Attribute Name" name="key" type="text" value="" help="Name of the attribute which will be assigned to all spectra records in the MSP." />
+            <param label="Value" name="value" type="text" value="" help="Value of the attribute which will be assigned to all spectra records in the MSP." >
+                <sanitizer>
+                    <valid initial="default">
+                        <add value="{}" />
+                        <add value="[]" />
+                        <add value="\" />
+                    </valid>
+                </sanitizer>
+            </param>
+        </repeat>
     </inputs>
 
     <outputs>
@@ -71,8 +73,14 @@ save_as_msp(new_spectra, "${output}")
         </test>
         <test>
             <param name="spectral_library" value="add_key/add_key_test2.msp" ftype="msp"/>
-            <param name="key" value="adduct"/>
-            <param name="value" value="[M]+"/>
+            <repeat name="attribute_repeat">
+                <param name="key" value="adduct"/>
+                <param name="value" value="[M]+"/>
+            </repeat>
+            <repeat name="attribute_repeat">
+                <param name="key" value="tool_used"/>
+                <param name="value" value="matchms"/>
+            </repeat>
             <output name="output" file="add_key/add_key_test2_out.msp" ftype="msp"/>
         </test>
     </tests>

diff --git a/tools/matchms/matchms_remove_key.xml b/tools/matchms/matchms_remove_key.xml
@@ -1,4 +1,4 @@
-<tool id="matchms_remove_key" name="matchms remove key" version="@TOOL_VERSION@+galaxy0" profile="21.09">
+<tool id="matchms_remove_key" name="matchms remove key" version="@TOOL_VERSION@+galaxy1" profile="21.09">
     <description>Remove metadata entry for all spectra in a library</description>
 
     <macros>
@@ -26,15 +26,19 @@
 import matchms
 @init_logger@
 
+
+#set keys_list = ([str($k.key) for $k in $attribute_repeat])
+
 matchms.Metadata.set_key_replacements({})
-key = "${key}".lower()
 spectra = list(matchms.importing.load_from_msp("${spectral_library}", metadata_harmonization = "False"))
 new_spectra = []
 for spectrum in spectra:
-    if spectrum.get(key) is not None:
-        metadata = spectrum.metadata
-        del metadata[key]
-        spectrum.metadata = metadata
+    for key in $keys_list:
+        key = key.lower()
+        if spectrum.get(key) is not None:
+            metadata = spectrum.metadata
+            del metadata[key]
+            spectrum.metadata = metadata
     new_spectra.append(spectrum)
 matchms.exporting.save_as_msp(new_spectra, "${output}")
 </configfile>
@@ -43,8 +47,9 @@ matchms.exporting.save_as_msp(new_spectra, "${output}")
     <inputs>
         <param label="Spectra file" name="spectral_library" type="data" format="msp"
             help="Mass spectral library file to add key." />
-
-        <param label="Attribute Name" name="key" type="text" value="" help="Name of the attribute which will be removed from all spectra records in the MSP." />
+        <repeat name="attribute_repeat" title="Keys to remove">
+            <param label="Attribute Name" name="key" type="text" value="" help="Name of the attribute which will be removed from all spectra records in the MSP." />
+        </repeat>
     </inputs>
 
     <outputs>
@@ -56,7 +61,17 @@ matchms.exporting.save_as_msp(new_spectra, "${output}")
         <test>
             <param name="spectral_library" value="filtering/input.msp" ftype="msp"/>
             <param name="key" value="ionmode"/>
-            <output name="output" file="out_matchms_remove_key.msp" ftype="msp" compare="sim_size"/>
+            <output name="output" file="remove_key/out_matchms_remove_key.msp" ftype="msp"/>
+        </test>
+        <test>
+            <param name="spectral_library" value="filtering/input.msp" ftype="msp"/>
+            <repeat name="attribute_repeat">
+                <param name="key" value="ionmode"/>
+            </repeat>
+            <repeat name="attribute_repeat">
+                <param name="key" value="spectrumtype"/>
+            </repeat>
+            <output name="output" file="remove_key/out2_matchms_remove_key.msp" ftype="msp"/>
         </test>
     </tests>
 

diff --git a/tools/matchms/test-data/add_key/add_key_test2_out.msp b/tools/matchms/test-data/add_key/add_key_test2_out.msp
@@ -16,6 +16,7 @@ INSTRUMENT_TYPE: GC-EI-Orbitrap
 CHARGE: 1
 PARENT_MASS: 251.08595400000002
 ADDUCT: [M]+
+TOOL_USED: matchms
 NUM PEAKS: 3
 250.07765   0.3282529462971431
 252.09323   1.0
@@ -39,6 +40,7 @@ INSTRUMENT_TYPE: GC-EI-Orbitrap
 CHARGE: 1
 PARENT_MASS: 177.070224
 ADDUCT: [M]+
+TOOL_USED: matchms
 NUM PEAKS: 5
 152.0619    0.1657993569424221
 176.062     0.24558560966311757

diff --git a/tools/matchms/test-data/out_matchms_remove_key.msp b/tools/matchms/test-data/out_matchms_remove_key.msp