annotate matchms_metadata_export.xml @ 8:8ff29dee9f26 draft

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author recetox
date Thu, 23 Nov 2023 09:53:16 +0000
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1 <tool id="matchms_metadata_export" name="matchms metadata export" version="@TOOL_VERSION@+galaxy0" profile="21.09">
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2 <description>extract all metadata from mass spectra file to tabular format</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 <import>help.xml</import>
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6 </macros>
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7 <expand macro="creator"/>
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8 <expand macro="bio.tools"/>
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9
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10 <requirements>
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11 <requirement type="package" version="@TOOL_VERSION@">matchms</requirement>
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12 </requirements>
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14 <command detect_errors='aggressive'><![CDATA[
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15 python ${matchms_python_cli}
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16 ]]></command>
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18 <configfiles>
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19 <configfile name="matchms_python_cli">
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20 from matchms.importing import load_from_msp, load_from_mgf
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21 from matchms.exporting.metadata_export import export_metadata_as_csv
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23 spectra_list = list(load_from_${input_file.ext}("${input_file}", $harmonize_metadata))
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25 export_metadata_as_csv(spectra_list, "${output_file}")
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26 </configfile>
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27 </configfiles>
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29 <inputs>
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30 <param label="Spectra file" name="input_file" type="data" format="msp,mgf" help="Mass spectral library file."/>
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31 <param label="Harmonize metadata" name="harmonize_metadata" type="boolean" truevalue="True" falsevalue="False"
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32 checked="false" help="Apply harmonization process on the metadata keys (e.g. parse numeric values, derive precursor mass)."/>
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33 </inputs>
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35 <outputs>
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36 <data label="matchms extract metadata on ${on_string}" name="output_file" format="csv"/>
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37 </outputs>
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39 <tests>
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40 <test>
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41 <param name="input_file" value="convert/mgf_out.mgf" ftype="mgf"/>
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42 <output name="output_file" file="convert/metadata.csv" ftype="csv" compare="sim_size" delta="0"/>
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43 </test>
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44 <test>
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45 <param name="input_file" value="similarity/RECETOX_Exposome_pesticides_HR_MS_20220323.msp" ftype="msp"/>
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46 <output name="output_file" file="convert/metadata.csv" ftype="csv" compare="sim_size" delta="0"/>
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47 </test>
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48 </tests>
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49
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50 <help>
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51 Documentation
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52 Mass spectral libraries are often stored in various formats, such as `msp`, `mgf` or `json`.
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53 This tool can be used to export the metadata accompanying the actual spectral to a tabular file,
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54 creating a column for each attribute and a row for each spectrum.
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55 All keys which are present in at least one spectrum are contained in the output.
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57 @HELP_matchms@
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58 </help>
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60 <expand macro="citations"/>
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61 </tool>