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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
author recetox
date Thu, 12 Oct 2023 13:26:04 +0000
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ea00a749ec1f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
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1 <tool id="matchms_add_key" name="matchms add key" version="@TOOL_VERSION@+galaxy1" profile="21.09">
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2 <description>Set metadata key in MSP to static value</description>
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ea00a749ec1f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
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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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ea00a749ec1f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
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9 <expand macro="creator"/>
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ea00a749ec1f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
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11 <edam_operations>
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12 <edam_operation>operation_2409</edam_operation>
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13 </edam_operations>
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14 <expand macro="bio.tools"/>
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ea00a749ec1f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
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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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ea00a749ec1f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
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20 <command detect_errors='aggressive'><![CDATA[
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21 python ${matchms_python_cli}
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22 ]]></command>
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ea00a749ec1f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
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24 <configfiles>
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25 <configfile name="matchms_python_cli">
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26 @init_logger@
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ea00a749ec1f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
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28 from matchms.importing import load_from_msp
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29 from matchms.exporting import save_as_msp
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30 spectra = list(load_from_msp("${spectral_library}", metadata_harmonization = "False"))
ea00a749ec1f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
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31 new_spectra = []
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32 for spectrum in spectra:
ea00a749ec1f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
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33 spectrum.set("${key}", "${value}")
ea00a749ec1f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
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34 new_spectra.append(spectrum)
ea00a749ec1f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
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35 save_as_msp(new_spectra, "${output}")
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36 </configfile>
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37 </configfiles>
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ea00a749ec1f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
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39 <inputs>
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40 <param label="Spectra file" name="spectral_library" type="data" format="msp"
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41 help="Mass spectral library file to add key." />
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43 <param label="Attribute Name" name="key" type="text" value="" help="Name of the attribute which will be assigned to all spectra records in the MSP." />
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44 <param label="Value" name="value" type="text" value="" help="Value of the attribute which will be assigned to all spectra records in the MSP." />
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45 </inputs>
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47 <outputs>
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48 <data label="${tool.name} on ${on_string}" name="output" format="msp">
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49 </data>
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50 </outputs>
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52 <tests>
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53 <test>
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54 <param name="spectral_library" value="filtering/input.msp" ftype="msp"/>
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55 <param name="key" value="tool_used"/>
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56 <param name="value" value="matchms"/>
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57 <output name="output" file="out_matchms_add_key.msp" ftype="msp"/>
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58 </test>
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59 </tests>
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61 <help><![CDATA[
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62 Description
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63 The tool take MSP file as an input and take as parameters the name of the
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64 attribute and its value which will be assigned to all spectra records in the MSP.
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65 ]]></help>
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66
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67 <citations>
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68 <citation type="doi">https://doi.org/10.5281/zenodo.6035335</citation>
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69 </citations>
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70 </tool>