Mercurial > repos > recetox > matchms_remove_key

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit a57d984a9850c1faa44b6948981eb1303881ba9c
author recetox
date Thu, 14 Aug 2025 12:43:54 +0000
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1 <tool id="matchms_remove_key" name="matchms remove key" version="@TOOL_VERSION@+galaxy0" profile="23.0" license="MIT">
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2 <description>Remove metadata entry for all spectra in a library</description>
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4 <macros>
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5 <import>macros.xml</import>
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6 <import>help.xml</import>
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7 </macros>
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9 <expand macro="creator"/>
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11 <edam_operations>
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12 <edam_operation>operation_3695</edam_operation>
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13 </edam_operations>
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14 <expand macro="bio.tools"/>
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16 <requirements>
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17 <requirement type="package" version="@TOOL_VERSION@">matchms</requirement>
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18 </requirements>
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20 <command detect_errors='aggressive'><![CDATA[
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21 python3 '${matchms_python_cli}'
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22 ]]></command>
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24 <configfiles>
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25 <configfile name="matchms_python_cli">
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26 import matchms
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27 @init_logger@
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30 #set keys_list = ([str($k.key) for $k in $attribute_repeat])
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31
0
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32 matchms.Metadata.set_key_replacements({})
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33 spectra = list(matchms.importing.load_from_msp("${spectral_library}", metadata_harmonization = "False"))
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34 new_spectra = []
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35 for spectrum in spectra:
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36 for key in $keys_list:
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37 key = key.lower()
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38 if spectrum.get(key) is not None:
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39 metadata = spectrum.metadata
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40 del metadata[key]
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41 spectrum.metadata = metadata
0
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42 new_spectra.append(spectrum)
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43 matchms.exporting.save_as_msp(new_spectra, "${output}")
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44 </configfile>
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45 </configfiles>
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47 <inputs>
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48 <param label="Spectra file" name="spectral_library" type="data" format="msp"
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49 help="Mass spectral library file to add key." />
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50 <repeat name="attribute_repeat" title="Keys to remove">
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51 <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." />
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52 </repeat>
0
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53 </inputs>
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54
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55 <outputs>
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56 <data label="${tool.name} on ${on_string}" name="output" format="msp">
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57 </data>
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58 </outputs>
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60 <tests>
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61 <test>
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62 <param name="spectral_library" value="filtering/input.msp" ftype="msp"/>
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63 <repeat name="attribute_repeat">
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64 <param name="key" value="ionmode"/>
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65 </repeat>
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66 <output name="output" file="remove_key/out_matchms_remove_key.msp" ftype="msp"/>
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67 </test>
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68 <test>
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69 <param name="spectral_library" value="filtering/input.msp" ftype="msp"/>
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70 <repeat name="attribute_repeat">
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71 <param name="key" value="ionmode"/>
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72 </repeat>
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73 <repeat name="attribute_repeat">
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74 <param name="key" value="spectrumtype"/>
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75 </repeat>
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76 <output name="output" file="remove_key/out2_matchms_remove_key.msp" ftype="msp"/>
0
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77 </test>
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78 </tests>
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79
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80 <help><![CDATA[
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81 Description
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82 The tool take MSP file as an input and take as parameters the name of the
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83 attribute which will be removed from all spectra records in the MSP.
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84 ]]></help>
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85
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86 <citations>
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87 <citation type="doi">10.5281/zenodo.6035335</citation>
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88 </citations>
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89 </tool>