Mercurial > repos > recetox > matchms_filtering
changeset 2:b8bf66da7e6f draft
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit c32f579c38aef4c2c5d088e6c1c9e522bc0a1a12"
| author | recetox |
|---|---|
| date | Thu, 17 Mar 2022 12:26:57 +0000 |
| parents | 2f9c19fa4346 |
| children | 21aef8443d78 |
| files | macros.xml matchms_filtering.xml test-data/filtering/clean_metadata.msp test-data/filtering/default_filters.msp test-data/filtering/input.msp test-data/filtering/mz_range.msp test-data/filtering/normalise_intensities.msp test-data/filtering/relative_intensity.msp |
| diffstat | 8 files changed, 673 insertions(+), 711 deletions(-) [+] |
line wrap: on
line diff
--- a/macros.xml Fri Jan 28 16:22:45 2022 +0000 +++ b/macros.xml Thu Mar 17 12:26:57 2022 +0000 @@ -1,5 +1,5 @@ <macros> - <token name="@TOOL_VERSION@">0.11.0</token> + <token name="@TOOL_VERSION@">0.14.0</token> <xml name="creator"> <creator>
--- a/matchms_filtering.xml Fri Jan 28 16:22:45 2022 +0000 +++ b/matchms_filtering.xml Thu Mar 17 12:26:57 2022 +0000 @@ -111,9 +111,6 @@ </test> <test> <param name="spectra" value="filtering/input.msp" ftype="msp"/> - <section name="normalise_intensities"> - <param name="is_true" value="TRUE"/> - </section> <section name="relative_intensity"> <param name="is_true" value="TRUE"/> <param name="from_intensity" value="0.3"/>
--- a/test-data/filtering/clean_metadata.msp Fri Jan 28 16:22:45 2022 +0000 +++ b/test-data/filtering/clean_metadata.msp Thu Mar 17 12:26:57 2022 +0000 @@ -1,212 +1,197 @@ -NAME: C001 -IONMODE: Negative -RETENTIONTIME: 38.74 -RETENTIONINDEX: +IONMODE: negative SPECTRUMTYPE: Centroid COMPOUND_NAME: C001 +RETENTION_TIME: 38.74 RETENTION_INDEX: None -RETENTION_TIME: 38.74 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 +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 -NAME: C002 -IONMODE: Negative -RETENTIONTIME: 520.25 -RETENTIONINDEX: +IONMODE: negative SPECTRUMTYPE: Centroid COMPOUND_NAME: C002 -RETENTION_INDEX: None 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 +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 -NAME: C003 -IONMODE: Negative -RETENTIONTIME: 483.67 -RETENTIONINDEX: +IONMODE: negative SPECTRUMTYPE: Centroid COMPOUND_NAME: C003 +RETENTION_TIME: 483.67 RETENTION_INDEX: None -RETENTION_TIME: 483.67 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 +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 -NAME: C004 -IONMODE: Negative -RETENTIONTIME: 473.48 -RETENTIONINDEX: +IONMODE: negative SPECTRUMTYPE: Centroid COMPOUND_NAME: C004 +RETENTION_TIME: 473.48 RETENTION_INDEX: None -RETENTION_TIME: 473.48 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 +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 -NAME: C005 -IONMODE: Negative -RETENTIONTIME: 41.72 -RETENTIONINDEX: +IONMODE: negative SPECTRUMTYPE: Centroid COMPOUND_NAME: C005 +RETENTION_TIME: 41.72 RETENTION_INDEX: None -RETENTION_TIME: 41.72 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 +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
--- a/test-data/filtering/default_filters.msp Fri Jan 28 16:22:45 2022 +0000 +++ b/test-data/filtering/default_filters.msp Thu Mar 17 12:26:57 2022 +0000 @@ -1,207 +1,199 @@ -NAME: C001 IONMODE: negative -RETENTIONTIME: 38.74 -RETENTIONINDEX: 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 +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 -NAME: C002 IONMODE: negative -RETENTIONTIME: 520.25 -RETENTIONINDEX: 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 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 +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 -NAME: C003 IONMODE: negative -RETENTIONTIME: 483.67 -RETENTIONINDEX: SPECTRUMTYPE: Centroid COMPOUND_NAME: C003 +RETENTION_TIME: 483.67 CHARGE: -1 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 +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 -NAME: C004 IONMODE: negative -RETENTIONTIME: 473.48 -RETENTIONINDEX: SPECTRUMTYPE: Centroid 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 +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 -NAME: C005 IONMODE: negative -RETENTIONTIME: 41.72 -RETENTIONINDEX: 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 +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
--- a/test-data/filtering/input.msp Fri Jan 28 16:22:45 2022 +0000 +++ b/test-data/filtering/input.msp Thu Mar 17 12:26:57 2022 +0000 @@ -1,7 +1,7 @@ NAME:C001 IONMODE:Negative RETENTIONTIME:38.74 -RETENTIONINDEX: +RETENTIONINDEX: -1 SPECTRUMTYPE:Centroid Num Peaks:57 216.9205 32607700 @@ -65,7 +65,7 @@ NAME:C002 IONMODE:Negative RETENTIONTIME:520.25 -RETENTIONINDEX: +RETENTIONINDEX: 1234.5 SPECTRUMTYPE:Centroid Num Peaks:35 525.375 1073323842 @@ -107,7 +107,6 @@ NAME:C003 IONMODE:Negative RETENTIONTIME:483.67 -RETENTIONINDEX: SPECTRUMTYPE:Centroid Num Peaks:26 522.3565 4089569222 @@ -140,7 +139,6 @@ NAME:C004 IONMODE:Negative RETENTIONTIME:473.48 -RETENTIONINDEX: SPECTRUMTYPE:Centroid Num Peaks:24 496.34 12577588056 @@ -171,7 +169,6 @@ NAME:C005 IONMODE:Negative RETENTIONTIME:41.72 -RETENTIONINDEX: SPECTRUMTYPE:Centroid Num Peaks:20 337.0623 88672453
--- a/test-data/filtering/mz_range.msp Fri Jan 28 16:22:45 2022 +0000 +++ b/test-data/filtering/mz_range.msp Thu Mar 17 12:26:57 2022 +0000 @@ -1,132 +1,129 @@ -NAME: C001 -IONMODE: Negative -RETENTIONTIME: 38.74 -RETENTIONINDEX: +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 +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 -NAME: C002 -IONMODE: Negative -RETENTIONTIME: 520.25 -RETENTIONINDEX: +IONMODE: negative SPECTRUMTYPE: Centroid +COMPOUND_NAME: C002 +RETENTION_TIME: 520.25 +RETENTION_INDEX: 1234.5 NUM PEAKS: 16 -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 +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 -NAME: C003 -IONMODE: Negative -RETENTIONTIME: 483.67 -RETENTIONINDEX: +IONMODE: negative SPECTRUMTYPE: Centroid +COMPOUND_NAME: C003 +RETENTION_TIME: 483.67 NUM PEAKS: 11 -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 +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 -NAME: C004 -IONMODE: Negative -RETENTIONTIME: 473.48 -RETENTIONINDEX: +IONMODE: negative SPECTRUMTYPE: Centroid +COMPOUND_NAME: C004 +RETENTION_TIME: 473.48 NUM PEAKS: 10 -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 +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 -NAME: C005 -IONMODE: Negative -RETENTIONTIME: 41.72 -RETENTIONINDEX: +IONMODE: negative SPECTRUMTYPE: Centroid +COMPOUND_NAME: C005 +RETENTION_TIME: 41.72 NUM PEAKS: 19 -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 +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
--- a/test-data/filtering/normalise_intensities.msp Fri Jan 28 16:22:45 2022 +0000 +++ b/test-data/filtering/normalise_intensities.msp Thu Mar 17 12:26:57 2022 +0000 @@ -1,197 +1,194 @@ -NAME: C001 -IONMODE: Negative -RETENTIONTIME: 38.74 -RETENTIONINDEX: +IONMODE: negative SPECTRUMTYPE: Centroid +COMPOUND_NAME: C001 +RETENTION_TIME: 38.74 +RETENTION_INDEX: None NUM PEAKS: 57 -138.9121 0.31238713555387226 -148.9337 0.03093306182282099 -175.0641 0.8212827951680125 -186.1095 0.08204982258791635 -196.8658 0.6559932163262051 -198.8647 0.6651371915222478 -200.8848 0.23744477531380626 -206.9034 0.8013745219687375 -216.9205 1.0 -234.0134 0.0782063439003671 -254.8252 0.7282800074828951 -256.8215 0.9622769161885076 -258.8237 0.4763537140000675 -266.8652 0.30071259242448867 -268.8537 0.09477374975849262 -306.9914 0.09719532503059093 -312.7841 0.30826464301376666 -316.7777 0.3291912033047409 -322.8157 0.1937471210787636 -324.9549 0.2643519782137348 -334.849 0.12814188059875428 -342.8093 0.10076000453880525 -349.9455 0.06288990023828728 -350.9875 0.18863026217733847 -351.941 0.06028888882073866 -366.8281 0.09978532677864431 -370.7418 0.29948334289140294 -372.7383 0.5941806076478868 -382.8218 0.3930228749651156 -384.8177 0.2548937827568335 -392.7685 0.33468631642219476 -413.2664 0.1216236349083192 -426.7772 0.1665751647616974 -428.7834 0.262351377128715 -434.7287 0.3049380667756389 -436.8161 0.11363104420121628 -440.7322 0.32516890182380237 -442.7401 0.25367480687076976 -450.7016 0.268730177228078 -460.7076 0.13889274619185038 -462.7862 0.06512774590050817 -484.7242 0.13107299809554185 -486.7743 0.14984380989766222 -488.6825 0.376229111528872 -492.744 0.23498572423077985 -494.8953 0.22046305013846423 -498.8794 0.20888946475832396 -500.8484 0.19997396320500985 -502.7832 0.10941688619559184 -510.763 0.15302388699601627 -518.7415 0.13013699218282798 -546.6093 0.2201034418250904 -550.6949 0.18721924576097057 -566.5977 0.15860704680182902 -612.6927 0.061506545999871196 -676.6436 0.06080508591528995 -800.4451 0.08562814917948829 +138.9121 0.31238713555387226 +148.9337 0.03093306182282099 +175.0641 0.8212827951680125 +186.1095 0.08204982258791635 +196.8658 0.6559932163262051 +198.8647 0.6651371915222478 +200.8848 0.23744477531380626 +206.9034 0.8013745219687375 +216.9205 1.0 +234.0134 0.0782063439003671 +254.8252 0.7282800074828951 +256.8215 0.9622769161885076 +258.8237 0.4763537140000675 +266.8652 0.30071259242448867 +268.8537 0.09477374975849262 +306.9914 0.09719532503059093 +312.7841 0.30826464301376666 +316.7777 0.3291912033047409 +322.8157 0.1937471210787636 +324.9549 0.2643519782137348 +334.849 0.12814188059875428 +342.8093 0.10076000453880525 +349.9455 0.06288990023828728 +350.9875 0.18863026217733847 +351.941 0.06028888882073866 +366.8281 0.09978532677864431 +370.7418 0.29948334289140294 +372.7383 0.5941806076478868 +382.8218 0.3930228749651156 +384.8177 0.2548937827568335 +392.7685 0.33468631642219476 +413.2664 0.1216236349083192 +426.7772 0.1665751647616974 +428.7834 0.262351377128715 +434.7287 0.3049380667756389 +436.8161 0.11363104420121628 +440.7322 0.32516890182380237 +442.7401 0.25367480687076976 +450.7016 0.268730177228078 +460.7076 0.13889274619185038 +462.7862 0.06512774590050817 +484.7242 0.13107299809554185 +486.7743 0.14984380989766222 +488.6825 0.376229111528872 +492.744 0.23498572423077985 +494.8953 0.22046305013846423 +498.8794 0.20888946475832396 +500.8484 0.19997396320500985 +502.7832 0.10941688619559184 +510.763 0.15302388699601627 +518.7415 0.13013699218282798 +546.6093 0.2201034418250904 +550.6949 0.18721924576097057 +566.5977 0.15860704680182902 +612.6927 0.061506545999871196 +676.6436 0.06080508591528995 +800.4451 0.08562814917948829 -NAME: C002 -IONMODE: Negative -RETENTIONTIME: 520.25 -RETENTIONINDEX: +IONMODE: negative SPECTRUMTYPE: Centroid +COMPOUND_NAME: C002 +RETENTION_TIME: 520.25 +RETENTION_INDEX: 1234.5 NUM PEAKS: 35 -131.1733 0.0018370867419900284 -267.2688 0.005686981655625982 -279.0196 0.0018132970906277511 -289.6491 0.04332185234360982 -301.1565 0.014148024487841387 -309.1649 0.01681316793110052 -310.1623 0.2751824048272655 -311.1658 0.012228114653210135 -312.0296 0.03610959011940033 -330.6757 0.011801281686240601 -525.375 1.0 -526.3783 0.16925822001818533 -527.3812 0.022027643545069038 -551.3321 0.10399173449088443 -552.3348 0.026404532249270578 -553.3314 0.00243163889393971 -562.3269 0.0070232353973927655 -578.2905 0.007060689144739971 -619.3008 0.004418147454139941 -624.296 0.010984767633625341 -813.5403 0.023348169508005768 -814.5336 0.005465242427736922 -955.1171 0.0021642368399005527 -1047.7378 0.1401206216753359 -1048.7399 0.08476366539149328 -1049.7432 0.027900654796038715 -1050.7453 0.006342696149667753 -1069.7158 0.004727978454800783 -1074.1979 0.0031698615710057058 -1075.1968 0.03107427758042852 -1076.2004 0.009706253222314986 -1101.6535 0.0018856526994021623 -1206.3127 0.003483399747305716 -1216.8041 0.004136052723591693 -1217.807 0.0033217691254826334 +131.1733 0.0018370867419900284 +267.2688 0.005686981655625982 +279.0196 0.0018132970906277511 +289.6491 0.04332185234360982 +301.1565 0.014148024487841387 +309.1649 0.01681316793110052 +310.1623 0.2751824048272655 +311.1658 0.012228114653210135 +312.0296 0.03610959011940033 +330.6757 0.011801281686240601 +525.375 1.0 +526.3783 0.16925822001818533 +527.3812 0.022027643545069038 +551.3321 0.10399173449088443 +552.3348 0.026404532249270578 +553.3314 0.00243163889393971 +562.3269 0.0070232353973927655 +578.2905 0.007060689144739971 +619.3008 0.004418147454139941 +624.296 0.010984767633625341 +813.5403 0.023348169508005768 +814.5336 0.005465242427736922 +955.1171 0.0021642368399005527 +1047.7378 0.1401206216753359 +1048.7399 0.08476366539149328 +1049.7432 0.027900654796038715 +1050.7453 0.006342696149667753 +1069.7158 0.004727978454800783 +1074.1979 0.0031698615710057058 +1075.1968 0.03107427758042852 +1076.2004 0.009706253222314986 +1101.6535 0.0018856526994021623 +1206.3127 0.003483399747305716 +1216.8041 0.004136052723591693 +1217.807 0.0033217691254826334 -NAME: C003 -IONMODE: Negative -RETENTIONTIME: 483.67 -RETENTIONINDEX: +IONMODE: negative SPECTRUMTYPE: Centroid +COMPOUND_NAME: C003 +RETENTION_TIME: 483.67 NUM PEAKS: 26 -265.2529 0.0027793206039538215 -266.2564 0.00034733340430054716 -279.6362 0.0072989959038771346 -280.6546 0.002163778266032735 -288.6414 0.049436024927126176 -378.2093 0.0037436610481220017 -379.1966 0.0007096996877780199 -522.3565 1.0 -523.354 0.29384865685493955 -549.3267 0.015478600450010918 -576.2749 0.0018060599048590942 -577.3074 0.0005756721239330571 -617.2778 0.0005681454143142512 -625.4543 0.0009879705613649104 -796.9808 0.0033198455052339984 -797.9841 0.0015573701420036753 -809.9883 0.0030801977705220513 -810.9916 0.0016141198844341264 -1043.7028 0.035297475152995465 -1044.7068 0.020362011126266247 -1045.706 0.0068462763386867055 -1046.7131 0.0015906756058816994 -1058.1594 0.00506614361447774 -1059.1626 0.0016160049240511426 -1071.1639 0.0037806052815603864 -1072.1671 0.0012462539997079428 +265.2529 0.0027793206039538215 +266.2564 0.00034733340430054716 +279.6362 0.0072989959038771346 +280.6546 0.002163778266032735 +288.6414 0.049436024927126176 +378.2093 0.0037436610481220017 +379.1966 0.0007096996877780199 +522.3565 1.0 +523.354 0.29384865685493955 +549.3267 0.015478600450010918 +576.2749 0.0018060599048590942 +577.3074 0.0005756721239330571 +617.2778 0.0005681454143142512 +625.4543 0.0009879705613649104 +796.9808 0.0033198455052339984 +797.9841 0.0015573701420036753 +809.9883 0.0030801977705220513 +810.9916 0.0016141198844341264 +1043.7028 0.035297475152995465 +1044.7068 0.020362011126266247 +1045.706 0.0068462763386867055 +1046.7131 0.0015906756058816994 +1058.1594 0.00506614361447774 +1059.1626 0.0016160049240511426 +1071.1639 0.0037806052815603864 +1072.1671 0.0012462539997079428 -NAME: C004 -IONMODE: Negative -RETENTIONTIME: 473.48 -RETENTIONINDEX: +IONMODE: negative SPECTRUMTYPE: Centroid +COMPOUND_NAME: C004 +RETENTION_TIME: 473.48 NUM PEAKS: 24 -124.1405 0.0005181964913289414 -170.2437 9.837442556482469e-05 -275.6336 0.002226328996889195 -296.147 0.015137694616192635 -482.3247 0.011589847063758851 -483.3283 0.00288178272643532 -496.34 1.0 -497.3442 0.2653231515567137 -498.3462 0.04232013408533278 -499.3493 0.005420441717160338 -770.964 0.003915707588825487 -771.9675 0.0018021637295703144 -783.9721 0.0007822882222085712 -784.9749 0.0002880447335267696 -949.6233 0.0006367701791743273 -950.6274 0.00029216205711611197 -991.6726 0.11294353509394345 -992.6749 0.06067284320350776 -993.6787 0.01901492598860482 -994.6801 0.004257539105397458 -1017.6897 0.013371955835345416 -1018.6656 0.00958844553208827 -1019.6555 0.004583362385803359 -1020.6591 0.0009913747329363162 +124.1405 0.0005181964913289414 +170.2437 9.837442556482469e-05 +275.6336 0.002226328996889195 +296.147 0.015137694616192635 +482.3247 0.011589847063758851 +483.3283 0.00288178272643532 +496.34 1.0 +497.3442 0.2653231515567137 +498.3462 0.04232013408533278 +499.3493 0.005420441717160338 +770.964 0.003915707588825487 +771.9675 0.0018021637295703144 +783.9721 0.0007822882222085712 +784.9749 0.0002880447335267696 +949.6233 0.0006367701791743273 +950.6274 0.00029216205711611197 +991.6726 0.11294353509394345 +992.6749 0.06067284320350776 +993.6787 0.01901492598860482 +994.6801 0.004257539105397458 +1017.6897 0.013371955835345416 +1018.6656 0.00958844553208827 +1019.6555 0.004583362385803359 +1020.6591 0.0009913747329363162 -NAME: C005 -IONMODE: Negative -RETENTIONTIME: 41.72 -RETENTIONINDEX: +IONMODE: negative SPECTRUMTYPE: Centroid +COMPOUND_NAME: C005 +RETENTION_TIME: 41.72 NUM PEAKS: 20 -218.1386 0.15798873862212878 -337.0623 1.0 -338.0654 0.09890394032518758 -353.0361 0.4179579198062785 -359.0443 0.5462303157441691 -360.0459 0.0566706776455141 -375.018 0.3288449119592981 -376.0216 0.03090241565776916 -381.0261 0.15250232222627247 -396.9999 0.1163570494660839 -417.0027 0.1558882553976487 -418.9966 0.049466444781898614 -432.9764 0.11028677643551825 -438.9851 0.12751548668671656 -440.9796 0.037939268467062706 -454.9592 0.11074974998154162 -456.9603 0.042570661713847026 -470.9263 0.04096521385282981 -512.8989 0.04592824335196862 -572.871 0.03930742730214083 +218.1386 0.15798873862212878 +337.0623 1.0 +338.0654 0.09890394032518758 +353.0361 0.4179579198062785 +359.0443 0.5462303157441691 +360.0459 0.0566706776455141 +375.018 0.3288449119592981 +376.0216 0.03090241565776916 +381.0261 0.15250232222627247 +396.9999 0.1163570494660839 +417.0027 0.1558882553976487 +418.9966 0.049466444781898614 +432.9764 0.11028677643551825 +438.9851 0.12751548668671656 +440.9796 0.037939268467062706 +454.9592 0.11074974998154162 +456.9603 0.042570661713847026 +470.9263 0.04096521385282981 +512.8989 0.04592824335196862 +572.871 0.03930742730214083
--- a/test-data/filtering/relative_intensity.msp Fri Jan 28 16:22:45 2022 +0000 +++ b/test-data/filtering/relative_intensity.msp Thu Mar 17 12:26:57 2022 +0000 @@ -1,54 +1,51 @@ -NAME: C001 -IONMODE: Negative -RETENTIONTIME: 38.74 -RETENTIONINDEX: +IONMODE: negative SPECTRUMTYPE: Centroid +COMPOUND_NAME: C001 +RETENTION_TIME: 38.74 +RETENTION_INDEX: None NUM PEAKS: 16 -138.9121 0.31238713555387226 -175.0641 0.8212827951680125 -196.8658 0.6559932163262051 -198.8647 0.6651371915222478 -206.9034 0.8013745219687375 -254.8252 0.7282800074828951 -258.8237 0.4763537140000675 -266.8652 0.30071259242448867 -312.7841 0.30826464301376666 -316.7777 0.3291912033047409 -372.7383 0.5941806076478868 -382.8218 0.3930228749651156 -392.7685 0.33468631642219476 -434.7287 0.3049380667756389 -440.7322 0.32516890182380237 -488.6825 0.376229111528872 +138.9121 10186226.0 +175.0641 26780143.0 +196.8658 21390430.0 +198.8647 21688594.0 +206.9034 26130980.0 +254.8252 23747536.0 +258.8237 15532799.0 +266.8652 9805546.0 +312.7841 10051801.0 +316.7777 10734168.0 +372.7383 19374863.0 +382.8218 12815572.0 +392.7685 10913351.0 +434.7287 9943329.0 +440.7322 10603010.0 +488.6825 12267966.0 -NAME: C002 -IONMODE: Negative -RETENTIONTIME: 520.25 -RETENTIONINDEX: +IONMODE: negative SPECTRUMTYPE: Centroid +COMPOUND_NAME: C002 +RETENTION_TIME: 520.25 +RETENTION_INDEX: 1234.5 NUM PEAKS: 0 -NAME: C003 -IONMODE: Negative -RETENTIONTIME: 483.67 -RETENTIONINDEX: +IONMODE: negative SPECTRUMTYPE: Centroid +COMPOUND_NAME: C003 +RETENTION_TIME: 483.67 NUM PEAKS: 0 -NAME: C004 -IONMODE: Negative -RETENTIONTIME: 473.48 -RETENTIONINDEX: +IONMODE: negative SPECTRUMTYPE: Centroid +COMPOUND_NAME: C004 +RETENTION_TIME: 473.48 NUM PEAKS: 0 -NAME: C005 -IONMODE: Negative -RETENTIONTIME: 41.72 -RETENTIONINDEX: +IONMODE: negative SPECTRUMTYPE: Centroid +COMPOUND_NAME: C005 +RETENTION_TIME: 41.72 NUM PEAKS: 3 -353.0361 0.4179579198062785 -359.0443 0.5462303157441691 -375.018 0.3288449119592981 +353.0361 37061354.0 +359.0443 48435582.0 +375.018 29159485.0