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matchms add key, matchms remove key: Added multiple keys handling #502

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Mar 13, 2024
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matchms add key, matchms remove key: Added multiple keys handling #502

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40 changes: 24 additions & 16 deletions tools/matchms/matchms_add_key.xml
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Original file line number Diff line number Diff line change
@@ -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>
Expand Down Expand Up @@ -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, "${output}")
</configfile>
Expand All @@ -44,17 +45,18 @@ save_as_msp(new_spectra, "${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>
Expand All @@ -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>
Expand Down
33 changes: 24 additions & 9 deletions tools/matchms/matchms_remove_key.xml
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Original file line number Diff line number Diff line change
@@ -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>
Expand Down Expand Up @@ -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>
Expand All @@ -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>
Expand All @@ -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>

Expand Down
2 changes: 2 additions & 0 deletions tools/matchms/test-data/add_key/add_key_test2_out.msp
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Expand Up @@ -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
Expand All @@ -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
Expand Down
188 changes: 0 additions & 188 deletions tools/matchms/test-data/out_matchms_remove_key.msp
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