# HG changeset patch # User recetox # Date 1647965283 0 # Node ID 3d275fbdf741c8b24753ca623b5bfe8f43d0cd1a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122" diff -r 000000000000 -r 3d275fbdf741 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Tue Mar 22 16:08:03 2022 +0000 @@ -0,0 +1,70 @@ + + 0.14.0 + + + + + + + + + + + + + + + + diff -r 000000000000 -r 3d275fbdf741 matchms_filtering.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/matchms_filtering.xml Tue Mar 22 16:08:03 2022 +0000 @@ -0,0 +1,154 @@ + + filter and normalize mass spectrometry data + + macros.xml + + + + matchms + pandas + + + + \$_GALAXY_JOB_TMP_DIR + + + + + + + python3 ${__tool_directory__}/matchms_filtering_wrapper.py \ + --spectra "$spectra" \ + --spectra_format "$spectra.ext" \ + #if $normalise_intensities.is_true + -normalise_intensities \ + #end if + #if $default_filters.is_true + -default_filters \ + #end if + #if $clean_metadata.is_true + -clean_metadata \ + #end if + #if $relative_intensity.is_true + -relative_intensity \ + --from_intensity "$relative_intensity.from_intensity" \ + --to_intensity "$relative_intensity.to_intensity" \ + #end if + #if $mz_range.is_true + -mz_range \ + --from_mz "$mz_range.from_mz" \ + --to_mz "$mz_range.to_mz" \ + #end if + --output "$output" + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ + + + + + + + + 10.5281/zenodo.4589154 + 10.21105/joss.02411 + + diff -r 000000000000 -r 3d275fbdf741 matchms_filtering_wrapper.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/matchms_filtering_wrapper.py Tue Mar 22 16:08:03 2022 +0000 @@ -0,0 +1,77 @@ +import argparse +import sys + +from matchms.exporting import save_as_mgf, save_as_msp +from matchms.filtering import add_compound_name, add_fingerprint, add_losses, add_parent_mass, add_precursor_mz,\ + add_retention_index, add_retention_time, clean_compound_name +from matchms.filtering import default_filters, normalize_intensities, select_by_mz, select_by_relative_intensity +from matchms.importing import load_from_mgf, load_from_msp + + +def main(argv): + parser = argparse.ArgumentParser(description="Compute MSP similarity scores") + parser.add_argument("--spectra", type=str, required=True, help="Mass spectra file to be filtered.") + parser.add_argument("--spectra_format", type=str, required=True, help="Format of spectra file.") + parser.add_argument("--output", type=str, required=True, help="Filtered mass spectra file.") + parser.add_argument("-normalise_intensities", action='store_true', + help="Normalize intensities of peaks (and losses) to unit height.") + parser.add_argument("-default_filters", action='store_true', + help="Collection of filters that are considered default and that do no require any (factory) arguments.") + parser.add_argument("-clean_metadata", action='store_true', + help="Apply all adding and cleaning filters if possible, so that the spectra have canonical metadata.") + parser.add_argument("-relative_intensity", action='store_true', + help="Keep only peaks within set relative intensity range (keep if to_intensity >= intensity >= from_intensity).") + parser.add_argument("--from_intensity", type=float, help="Lower bound for intensity filter") + parser.add_argument("--to_intensity", type=float, help="Upper bound for intensity filter") + parser.add_argument("-mz_range", action='store_true', + help="Keep only peaks between set m/z range (keep if to_mz >= m/z >= from_mz).") + parser.add_argument("--from_mz", type=float, help="Lower bound for m/z filter") + parser.add_argument("--to_mz", type=float, help="Upper bound for m/z filter") + args = parser.parse_args() + + if not (args.normalise_intensities + or args.default_filters + or args.clean_metadata + or args.relative_intensity + or args.mz_range): + raise ValueError('No filter selected.') + + if args.spectra_format == 'msp': + spectra = list(load_from_msp(args.spectra)) + elif args.queries_format == 'mgf': + spectra = list(load_from_mgf(args.spectra)) + else: + raise ValueError(f'File format {args.spectra_format} not supported for mass spectra file.') + + filtered_spectra = [] + for spectrum in spectra: + if args.normalise_intensities: + spectrum = normalize_intensities(spectrum) + + if args.default_filters: + spectrum = default_filters(spectrum) + + if args.clean_metadata: + filters = [add_compound_name, add_precursor_mz, add_fingerprint, add_losses, add_parent_mass, + add_retention_index, add_retention_time, clean_compound_name] + for metadata_filter in filters: + spectrum = metadata_filter(spectrum) + + if args.relative_intensity: + spectrum = select_by_relative_intensity(spectrum, args.from_intensity, args.to_intensity) + + if args.mz_range: + spectrum = select_by_mz(spectrum, args.from_mz, args.to_mz) + + filtered_spectra.append(spectrum) + + if args.spectra_format == 'msp': + save_as_msp(filtered_spectra, args.output) + else: + save_as_mgf(filtered_spectra, args.output) + + return 0 + + +if __name__ == "__main__": + main(argv=sys.argv[1:]) diff -r 000000000000 -r 3d275fbdf741 test-data/filtering/clean_metadata.msp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/filtering/clean_metadata.msp Tue Mar 22 16:08:03 2022 +0000 @@ -0,0 +1,197 @@ +IONMODE: negative +SPECTRUMTYPE: Centroid +COMPOUND_NAME: C001 +RETENTION_TIME: 38.74 +RETENTION_INDEX: None +NUM PEAKS: 57 +138.9121 10186226.0 +148.9337 1008656.0 +175.0641 26780143.0 +186.1095 2675456.0 +196.8658 21390430.0 +198.8647 21688594.0 +200.8848 7742528.0 +206.9034 26130980.0 +216.9205 32607700.0 +234.0134 2550129.0 +254.8252 23747536.0 +256.8215 31377637.0 +258.8237 15532799.0 +266.8652 9805546.0 +268.8537 3090354.0 +306.9914 3169316.0 +312.7841 10051801.0 +316.7777 10734168.0 +322.8157 6317648.0 +324.9549 8619910.0 +334.849 4178412.0 +342.8093 3285552.0 +349.9455 2050695.0 +350.9875 6150799.0 +351.941 1965882.0 +366.8281 3253770.0 +370.7418 9765463.0 +372.7383 19374863.0 +382.8218 12815572.0 +384.8177 8311500.0 +392.7685 10913351.0 +413.2664 3965867.0 +426.7772 5431633.0 +428.7834 8554675.0 +434.7287 9943329.0 +436.8161 3705247.0 +440.7322 10603010.0 +442.7401 8271752.0 +450.7016 8762673.0 +460.7076 4528973.0 +462.7862 2123666.0 +484.7242 4273989.0 +486.7743 4886062.0 +488.6825 12267966.0 +492.744 7662344.0 +494.8953 7188793.0 +498.8794 6811405.0 +500.8484 6520691.0 +502.7832 3567833.0 +510.763 4989757.0 +518.7415 4243468.0 +546.6093 7177067.0 +550.6949 6104789.0 +566.5977 5171811.0 +612.6927 2005587.0 +676.6436 1982714.0 +800.4451 2792137.0 + +IONMODE: negative +SPECTRUMTYPE: Centroid +COMPOUND_NAME: C002 +RETENTION_TIME: 520.25 +RETENTION_INDEX: 1234.5 +NUM PEAKS: 35 +131.1733 1971789.0 +267.2688 6103973.0 +279.0196 1946255.0 +289.6491 46498377.0 +301.1565 15185412.0 +309.1649 18045974.0 +310.1623 295359836.0 +311.1658 13124727.0 +312.0296 38757284.0 +330.6757 12666597.0 +525.375 1073323842.0 +526.3783 181668883.0 +527.3812 23642795.0 +551.3321 111616808.0 +552.3348 28340614.0 +553.3314 2609936.0 +562.3269 7538206.0 +578.2905 7578406.0 +619.3008 4742103.0 +624.296 11790213.0 +813.5403 25060147.0 +814.5336 5865975.0 +955.1171 2322927.0 +1047.7378 150394804.0 +1048.7399 90978863.0 +1049.7432 29946438.0 +1050.7453 6807767.0 +1069.7158 5074652.0 +1074.1979 3402288.0 +1075.1968 33352763.0 +1076.2004 10417953.0 +1101.6535 2023916.0 +1206.3127 3738816.0 +1216.8041 4439324.0 +1217.807 3565334.0 + +IONMODE: negative +SPECTRUMTYPE: Centroid +COMPOUND_NAME: C003 +RETENTION_TIME: 483.67 +RETENTION_INDEX: None +NUM PEAKS: 26 +265.2529 11366224.0 +266.2564 1420444.0 +279.6362 29849749.0 +280.6546 8848921.0 +288.6414 202172046.0 +378.2093 15309961.0 +379.1966 2902366.0 +522.3565 4089569222.0 +523.354 1201714423.0 +549.3267 63300808.0 +576.2749 7386007.0 +577.3074 2354251.0 +617.2778 2323470.0 +625.4543 4040374.0 +796.9808 13576738.0 +797.9841 6368973.0 +809.9883 12596682.0 +810.9916 6601055.0 +1043.7028 144351468.0 +1044.7068 83271854.0 +1045.706 27998321.0 +1046.7131 6505178.0 +1058.1594 20718345.0 +1059.1626 6608764.0 +1071.1639 15461047.0 +1072.1671 5096642.0 + +IONMODE: negative +SPECTRUMTYPE: Centroid +COMPOUND_NAME: C004 +RETENTION_TIME: 473.48 +RETENTION_INDEX: None +NUM PEAKS: 24 +124.1405 6517662.0 +170.2437 1237313.0 +275.6336 28001849.0 +296.147 190395687.0 +482.3247 145772322.0 +483.3283 36245876.0 +496.34 12577588056.0 +497.3442 3337125302.0 +498.3462 532285213.0 +499.3493 68176083.0 +770.964 49250157.0 +771.9675 22666873.0 +783.9721 9839299.0 +784.9749 3622908.0 +949.6233 8009033.0 +950.6274 3674694.0 +991.6726 1420557258.0 +992.6749 763118028.0 +993.6787 239161906.0 +994.6801 53549573.0 +1017.6897 168186952.0 +1018.6656 120599518.0 +1019.6555 57647644.0 +1020.6591 12469103.0 + +IONMODE: negative +SPECTRUMTYPE: Centroid +COMPOUND_NAME: C005 +RETENTION_TIME: 41.72 +RETENTION_INDEX: None +NUM PEAKS: 20 +218.1386 14009249.0 +337.0623 88672453.0 +338.0654 8770055.0 +353.0361 37061354.0 +359.0443 48435582.0 +360.0459 5025128.0 +375.018 29159485.0 +376.0216 2740193.0 +381.0261 13522755.0 +396.9999 10317665.0 +417.0027 13822994.0 +418.9966 4386311.0 +432.9764 9779399.0 +438.9851 11307111.0 +440.9796 3364168.0 +454.9592 9820452.0 +456.9603 3774845.0 +470.9263 3632486.0 +512.8989 4072570.0 +572.871 3485486.0 + diff -r 000000000000 -r 3d275fbdf741 test-data/filtering/default_filters.msp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/filtering/default_filters.msp Tue Mar 22 16:08:03 2022 +0000 @@ -0,0 +1,199 @@ +IONMODE: negative +SPECTRUMTYPE: Centroid +COMPOUND_NAME: C001 +RETENTION_TIME: 38.74 +RETENTION_INDEX: None +CHARGE: -1 +NUM PEAKS: 57 +138.9121 10186226.0 +148.9337 1008656.0 +175.0641 26780143.0 +186.1095 2675456.0 +196.8658 21390430.0 +198.8647 21688594.0 +200.8848 7742528.0 +206.9034 26130980.0 +216.9205 32607700.0 +234.0134 2550129.0 +254.8252 23747536.0 +256.8215 31377637.0 +258.8237 15532799.0 +266.8652 9805546.0 +268.8537 3090354.0 +306.9914 3169316.0 +312.7841 10051801.0 +316.7777 10734168.0 +322.8157 6317648.0 +324.9549 8619910.0 +334.849 4178412.0 +342.8093 3285552.0 +349.9455 2050695.0 +350.9875 6150799.0 +351.941 1965882.0 +366.8281 3253770.0 +370.7418 9765463.0 +372.7383 19374863.0 +382.8218 12815572.0 +384.8177 8311500.0 +392.7685 10913351.0 +413.2664 3965867.0 +426.7772 5431633.0 +428.7834 8554675.0 +434.7287 9943329.0 +436.8161 3705247.0 +440.7322 10603010.0 +442.7401 8271752.0 +450.7016 8762673.0 +460.7076 4528973.0 +462.7862 2123666.0 +484.7242 4273989.0 +486.7743 4886062.0 +488.6825 12267966.0 +492.744 7662344.0 +494.8953 7188793.0 +498.8794 6811405.0 +500.8484 6520691.0 +502.7832 3567833.0 +510.763 4989757.0 +518.7415 4243468.0 +546.6093 7177067.0 +550.6949 6104789.0 +566.5977 5171811.0 +612.6927 2005587.0 +676.6436 1982714.0 +800.4451 2792137.0 + +IONMODE: negative +SPECTRUMTYPE: Centroid +COMPOUND_NAME: C002 +RETENTION_TIME: 520.25 +RETENTION_INDEX: 1234.5 +CHARGE: -1 +NUM PEAKS: 35 +131.1733 1971789.0 +267.2688 6103973.0 +279.0196 1946255.0 +289.6491 46498377.0 +301.1565 15185412.0 +309.1649 18045974.0 +310.1623 295359836.0 +311.1658 13124727.0 +312.0296 38757284.0 +330.6757 12666597.0 +525.375 1073323842.0 +526.3783 181668883.0 +527.3812 23642795.0 +551.3321 111616808.0 +552.3348 28340614.0 +553.3314 2609936.0 +562.3269 7538206.0 +578.2905 7578406.0 +619.3008 4742103.0 +624.296 11790213.0 +813.5403 25060147.0 +814.5336 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+COMPOUND_NAME: C004 +RETENTION_TIME: 473.48 +CHARGE: -1 +NUM PEAKS: 24 +124.1405 6517662.0 +170.2437 1237313.0 +275.6336 28001849.0 +296.147 190395687.0 +482.3247 145772322.0 +483.3283 36245876.0 +496.34 12577588056.0 +497.3442 3337125302.0 +498.3462 532285213.0 +499.3493 68176083.0 +770.964 49250157.0 +771.9675 22666873.0 +783.9721 9839299.0 +784.9749 3622908.0 +949.6233 8009033.0 +950.6274 3674694.0 +991.6726 1420557258.0 +992.6749 763118028.0 +993.6787 239161906.0 +994.6801 53549573.0 +1017.6897 168186952.0 +1018.6656 120599518.0 +1019.6555 57647644.0 +1020.6591 12469103.0 + +IONMODE: negative +SPECTRUMTYPE: Centroid +COMPOUND_NAME: C005 +RETENTION_TIME: 41.72 +CHARGE: -1 +NUM PEAKS: 20 +218.1386 14009249.0 +337.0623 88672453.0 +338.0654 8770055.0 +353.0361 37061354.0 +359.0443 48435582.0 +360.0459 5025128.0 +375.018 29159485.0 +376.0216 2740193.0 +381.0261 13522755.0 +396.9999 10317665.0 +417.0027 13822994.0 +418.9966 4386311.0 +432.9764 9779399.0 +438.9851 11307111.0 +440.9796 3364168.0 +454.9592 9820452.0 +456.9603 3774845.0 +470.9263 3632486.0 +512.8989 4072570.0 +572.871 3485486.0 + diff -r 000000000000 -r 3d275fbdf741 test-data/filtering/input.msp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/filtering/input.msp Tue Mar 22 16:08:03 2022 +0000 @@ -0,0 +1,193 @@ +NAME:C001 +IONMODE:Negative +RETENTIONTIME:38.74 +RETENTIONINDEX: -1 +SPECTRUMTYPE:Centroid +Num Peaks:57 +216.9205 32607700 +256.8215 31377637 +175.0641 26780143 +206.9034 26130980 +254.8252 23747536 +198.8647 21688594 +196.8658 21390430 +372.7383 19374863 +258.8237 15532799 +382.8218 12815572 +488.6825 12267966 +392.7685 10913351 +316.7777 10734168 +440.7322 10603010 +138.9121 10186226 +312.7841 10051801 +434.7287 9943329 +266.8652 9805546 +370.7418 9765463 +450.7016 8762673 +324.9549 8619910 +428.7834 8554675 +384.8177 8311500 +442.7401 8271752 +200.8848 7742528 +492.744 7662344 +494.8953 7188793 +546.6093 7177067 +498.8794 6811405 +500.8484 6520691 +322.8157 6317648 +350.9875 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22 16:08:03 2022 +0000 @@ -0,0 +1,129 @@ +IONMODE: negative +SPECTRUMTYPE: Centroid +COMPOUND_NAME: C001 +RETENTION_TIME: 38.74 +RETENTION_INDEX: None +NUM PEAKS: 41 +306.9914 3169316.0 +312.7841 10051801.0 +316.7777 10734168.0 +322.8157 6317648.0 +324.9549 8619910.0 +334.849 4178412.0 +342.8093 3285552.0 +349.9455 2050695.0 +350.9875 6150799.0 +351.941 1965882.0 +366.8281 3253770.0 +370.7418 9765463.0 +372.7383 19374863.0 +382.8218 12815572.0 +384.8177 8311500.0 +392.7685 10913351.0 +413.2664 3965867.0 +426.7772 5431633.0 +428.7834 8554675.0 +434.7287 9943329.0 +436.8161 3705247.0 +440.7322 10603010.0 +442.7401 8271752.0 +450.7016 8762673.0 +460.7076 4528973.0 +462.7862 2123666.0 +484.7242 4273989.0 +486.7743 4886062.0 +488.6825 12267966.0 +492.744 7662344.0 +494.8953 7188793.0 +498.8794 6811405.0 +500.8484 6520691.0 +502.7832 3567833.0 +510.763 4989757.0 +518.7415 4243468.0 +546.6093 7177067.0 +550.6949 6104789.0 +566.5977 5171811.0 +612.6927 2005587.0 +676.6436 1982714.0 + +IONMODE: 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