Mercurial > repos > recetox > matchms_remove_key
changeset 5:8a8a58be3929 draft
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f14275bfdc2caa760d71d307ca1803eab1adde76
| author | recetox |
|---|---|
| date | Wed, 13 Mar 2024 10:13:07 +0000 |
| parents | 51ac25987e83 |
| children | dd1b4515c5cd |
| files | matchms_remove_key.xml test-data/add_key/add_key_test2_out.msp test-data/out_matchms_remove_key.msp test-data/remove_key/out2_matchms_remove_key.msp test-data/remove_key/out_matchms_remove_key.msp |
| diffstat | 5 files changed, 399 insertions(+), 197 deletions(-) [+] |
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--- a/matchms_remove_key.xml Thu Feb 22 12:30:20 2024 +0000 +++ b/matchms_remove_key.xml Wed Mar 13 10:13:07 2024 +0000 @@ -1,4 +1,4 @@ -<tool id="matchms_remove_key" name="matchms remove key" version="@TOOL_VERSION@+galaxy0" profile="21.09"> +<tool id="matchms_remove_key" name="matchms remove key" version="@TOOL_VERSION@+galaxy1" profile="21.09"> <description>Remove metadata entry for all spectra in a library</description> <macros> @@ -26,15 +26,19 @@ import matchms @init_logger@ + +#set keys_list = ([str($k.key) for $k in $attribute_repeat]) + matchms.Metadata.set_key_replacements({}) -key = "${key}".lower() spectra = list(matchms.importing.load_from_msp("${spectral_library}", metadata_harmonization = "False")) new_spectra = [] for spectrum in spectra: - if spectrum.get(key) is not None: - metadata = spectrum.metadata - del metadata[key] - spectrum.metadata = metadata + for key in $keys_list: + key = key.lower() + if spectrum.get(key) is not None: + metadata = spectrum.metadata + del metadata[key] + spectrum.metadata = metadata new_spectra.append(spectrum) matchms.exporting.save_as_msp(new_spectra, "${output}") </configfile> @@ -43,8 +47,9 @@ <inputs> <param label="Spectra file" name="spectral_library" type="data" format="msp" help="Mass spectral library file to add key." /> - - <param label="Attribute Name" name="key" type="text" value="" help="Name of the attribute which will be removed from all spectra records in the MSP." /> + <repeat name="attribute_repeat" title="Keys to remove"> + <param label="Attribute Name" name="key" type="text" value="" help="Name of the attribute which will be removed from all spectra records in the MSP." /> + </repeat> </inputs> <outputs> @@ -56,7 +61,17 @@ <test> <param name="spectral_library" value="filtering/input.msp" ftype="msp"/> <param name="key" value="ionmode"/> - <output name="output" file="out_matchms_remove_key.msp" ftype="msp" compare="sim_size"/> + <output name="output" file="remove_key/out_matchms_remove_key.msp" ftype="msp"/> + </test> + <test> + <param name="spectral_library" value="filtering/input.msp" ftype="msp"/> + <repeat name="attribute_repeat"> + <param name="key" value="ionmode"/> + </repeat> + <repeat name="attribute_repeat"> + <param name="key" value="spectrumtype"/> + </repeat> + <output name="output" file="remove_key/out2_matchms_remove_key.msp" ftype="msp"/> </test> </tests>
--- a/test-data/add_key/add_key_test2_out.msp Thu Feb 22 12:30:20 2024 +0000 +++ b/test-data/add_key/add_key_test2_out.msp Wed Mar 13 10:13:07 2024 +0000 @@ -16,6 +16,7 @@ CHARGE: 1 PARENT_MASS: 251.08595400000002 ADDUCT: [M]+ +TOOL_USED: matchms NUM PEAKS: 3 250.07765 0.3282529462971431 252.09323 1.0 @@ -39,6 +40,7 @@ CHARGE: 1 PARENT_MASS: 177.070224 ADDUCT: [M]+ +TOOL_USED: matchms NUM PEAKS: 5 152.0619 0.1657993569424221 176.062 0.24558560966311757
--- a/test-data/out_matchms_remove_key.msp Thu Feb 22 12:30:20 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,188 +0,0 @@ -NAME:C001 -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 6150799 -550.6949 6104789 -426.7772 5431633 -566.5977 5171811 -510.763 4989757 -486.7743 4886062 -460.7076 4528973 -484.7242 4273989 -518.7415 4243468 -334.849 4178412 -413.2664 3965867 -436.8161 3705247 -502.7832 3567833 -342.8093 3285552 -366.8281 3253770 -306.9914 3169316 -268.8537 3090354 -800.4451 2792137 -186.1095 2675456 -234.0134 2550129 -462.7862 2123666 -349.9455 2050695 -612.6927 2005587 -676.6436 1982714 -351.941 1965882 -148.9337 1008656 - -NAME:C002 -RETENTIONTIME:520.25 -RETENTIONINDEX: 1234.5 -SPECTRUMTYPE:Centroid -Num Peaks:35 -525.375 1073323842 -310.1623 295359836 -526.3783 181668883 -1047.7378 150394804 -551.3321 111616808 -1048.7399 90978863 -289.6491 46498377 -312.0296 38757284 -1075.1968 33352763 -1049.7432 29946438 -552.3348 28340614 -813.5403 25060147 -527.3812 23642795 -309.1649 18045974 -301.1565 15185412 -311.1658 13124727 -330.6757 12666597 -624.296 11790213 -1076.2004 10417953 -578.2905 7578406 -562.3269 7538206 -1050.7453 6807767 -267.2688 6103973 -814.5336 5865975 -1069.7158 5074652 -619.3008 4742103 -1216.8041 4439324 -1206.3127 3738816 -1217.807 3565334 -1074.1979 3402288 -553.3314 2609936 -955.1171 2322927 -1101.6535 2023916 -131.1733 1971789 -279.0196 1946255 - -NAME:C003 -RETENTIONTIME:483.67 -SPECTRUMTYPE:Centroid -Num Peaks:26 -522.3565 4089569222 -523.354 1201714423 -288.6414 202172046 -1043.7028 144351468 -1044.7068 83271854 -549.3267 63300808 -279.6362 29849749 -1045.706 27998321 -1058.1594 20718345 -1071.1639 15461047 -378.2093 15309961 -796.9808 13576738 -809.9883 12596682 -265.2529 11366224 -280.6546 8848921 -576.2749 7386007 -1059.1626 6608764 -810.9916 6601055 -1046.7131 6505178 -797.9841 6368973 -1072.1671 5096642 -625.4543 4040374 -379.1966 2902366 -577.3074 2354251 -617.2778 2323470 -266.2564 1420444 - -NAME:C004 -RETENTIONTIME:473.48 -SPECTRUMTYPE:Centroid -Num Peaks:24 -496.34 12577588056 -497.3442 3337125302 -991.6726 1420557258 -992.6749 763118028 -498.3462 532285213 -993.6787 239161906 -296.147 190395687 -1017.6897 168186952 -482.3247 145772322 -1018.6656 120599518 -499.3493 68176083 -1019.6555 57647644 -994.6801 53549573 -770.964 49250157 -483.3283 36245876 -275.6336 28001849 -771.9675 22666873 -1020.6591 12469103 -783.9721 9839299 -949.6233 8009033 -124.1405 6517662 -950.6274 3674694 -784.9749 3622908 -170.2437 1237313 - -NAME:C005 -RETENTIONTIME:41.72 -SPECTRUMTYPE:Centroid -Num Peaks:20 -337.0623 88672453 -359.0443 48435582 -353.0361 37061354 -375.018 29159485 -218.1386 14009249 -417.0027 13822994 -381.0261 13522755 -438.9851 11307111 -396.9999 10317665 -454.9592 9820452 -432.9764 9779399 -338.0654 8770055 -360.0459 5025128 -418.9966 4386311 -512.8989 4072570 -456.9603 3774845 -470.9263 3632486 -572.871 3485486 -440.9796 3364168 -376.0216 2740193
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/remove_key/out_matchms_remove_key.msp Wed Mar 13 10:13:07 2024 +0000 @@ -0,0 +1,189 @@ +NAME: C001 +RETENTIONTIME: 38.74 +RETENTIONINDEX: -1 +SPECTRUMTYPE: Centroid +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 + +NAME: C002 +RETENTIONTIME: 520.25 +RETENTIONINDEX: 1234.5 +SPECTRUMTYPE: Centroid +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 + +NAME: C003 +RETENTIONTIME: 483.67 +SPECTRUMTYPE: Centroid +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 + +NAME: C004 +RETENTIONTIME: 473.48 +SPECTRUMTYPE: Centroid +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 + +NAME: C005 +RETENTIONTIME: 41.72 +SPECTRUMTYPE: Centroid +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 +