removed param

tools/matchms/matchms_export_skyline_transition_list.ipynb

@@ -0,0 +1,112 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from matchms.importing import load_from_msp\n",
+    "from matchms.exporting.metadata_export import get_metadata_as_array\n",
+    "\n",
+    "import pandas as pd"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "spectra_file = \"test-data/filtering/reduce_to_top_n_peaks.msp\"\n",
+    "name_key = 'compound_name'\n",
+    "cols_to_include = [name_key, 'retention_index', 'mz', 'intensity']"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 40,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "2024-11-06 14:26:01,189:WARNING:matchms:add_precursor_mz:No precursor_mz found in metadata.\n",
+      "2024-11-06 14:26:01,190:WARNING:matchms:add_retention:None can't be converted to float.\n",
+      "2024-11-06 14:26:01,191:WARNING:matchms:add_precursor_mz:No precursor_mz found in metadata.\n",
+      "2024-11-06 14:26:01,192:WARNING:matchms:add_precursor_mz:No precursor_mz found in metadata.\n",
+      "2024-11-06 14:26:01,193:WARNING:matchms:add_precursor_mz:No precursor_mz found in metadata.\n",
+      "2024-11-06 14:26:01,194:WARNING:matchms:add_precursor_mz:No precursor_mz found in metadata.\n"
+     ]
+    }
+   ],
+   "source": [
+    "spectra = list(load_from_msp(spectra_file))\n",
+    "spectra_dict = {}\n",
+    "for spectrum in spectra:\n",
+    "    spectra_dict[spectrum.get(name_key)] = spectrum"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 41,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "spectra_metadata, cols = get_metadata_as_array(spectra)\n",
+    "spectra_metadata_df = pd.DataFrame(spectra_metadata)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 42,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "spectra_metadata_df['peaks'] = spectra_metadata_df[name_key].transform(lambda x: spectra_dict[x].peaks)\n",
+    "spectra_metadata_df['mz'] = spectra_metadata_df['peaks'].transform(lambda x: x.mz)\n",
+    "spectra_metadata_df['intensity'] = spectra_metadata_df['peaks'].transform(lambda x: x.intensities)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 43,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "spectra_metadata_df = spectra_metadata_df.explode(['mz', 'intensity']).reset_index(drop=True)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 45,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "result = spectra_metadata_df[cols_to_include].rename(columns={'compound_name': 'precursor name', 'retention_index': 'retention index'})"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "matchms",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.12.7"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}

tools/matchms/matchms_export_skyline_transition_list.xml

@@ -25,14 +25,11 @@ from matchms.exporting.metadata_export import get_metadata_as_array
 name_key = 'compound_name'
 cols_to_include = [name_key, 'mz', 'intensity']
 
-if "$harmonize_metadata" == "False":
-    matchms.Metadata.set_key_replacements({})
-
 #if $metadata_cols != 'None':
 cols_to_include += '$metadata_cols'.split(',')
 #end if
 
-spectra = list(load_from_${input_file.ext}("${input_file}", $harmonize_metadata))
+spectra = list(load_from_${input_file.ext}("${input_file}", True))
 
 spectra_dict = {}
 for spectrum in spectra:
@@ -51,8 +48,6 @@ spectra_metadata_df.to_csv("${output_file}", sep='\t', index=False)
 
     <inputs>
         <param label="Spectra file" name="input_file" type="data" format="msp,mgf" help="Mass spectral library file."/>
-        <param label="Harmonize metadata" name="harmonize_metadata" type="boolean" truevalue="True" falsevalue="False" hidden="True"
-               checked="true" help="Apply harmonization process on the metadata keys (e.g. parse numeric values, derive precursor mass)."/>
         <param name="metadata_cols" type="select" label="Metadata to include" help="Select the metadata attributes to include in the output file." multiple="true">
             <option value="retention_index">Retention Index</option>
             <option value="precursor_mz">Precursor m/z</option>