| Previous changeset 1:4207233ead9c (2019-12-05) Next changeset 3:ccda730c6cf7 (2020-04-09) |
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Commit message:
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 242de155f13acd6cb88946e89b5196ac55578aa8" |
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modified:
combineAnnotations.R createDatabase.R macros.xml test-data/averageFragSpectra_output_all.RData test-data/averageFragSpectra_output_all_only.RData test-data/averageFragSpectra_output_inter.RData test-data/averageFragSpectra_output_intra.RData test-data/combineAnnotations_combined_annotations.sqlite test-data/combineAnnotations_combined_annotations.tsv test-data/createDatabase_output.sqlite test-data/createDatabase_output_eic.sqlite test-data/createMSP_output_av_all_metadata.msp test-data/filterFragSpectra_output.RData test-data/flagRemove_output.tsv test-data/frag4feature_output.RData test-data/purityA_output.RData test-data/spectralMatching_db_with_spectral_matching.sqlite test-data/spectralMatching_db_with_spectral_matching_instrumentTypes.sqlite |
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| diff -r 4207233ead9c -r 96fba93b4c8a combineAnnotations.R --- a/combineAnnotations.R Thu Dec 05 07:37:41 2019 -0500 +++ b/combineAnnotations.R Wed Apr 01 11:05:00 2020 -0400 |
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| @@ -20,7 +20,9 @@ make_option("--probmetab_weight", type="numeric"), make_option("--ms1_lookup_weight", type="numeric"), make_option("--biosim_weight", type="numeric"), - + + make_option("--summaryOutput", action="store_true"), + make_option("--create_new_database", action="store_true"), make_option("--outdir", type="character", default="."), @@ -56,11 +58,21 @@ 'biosim'=opt$biosim_weight ) print(weights) -if (round(!sum(unlist(weights),0)==1)){ + +if (is.null(opt$probmetab_resultPth)){ + opt$probmetab_resultPth = NA +} +if (round(!sum(unlist(weights),0)==1)){ stop(paste0('The weights should sum to 1 not ', sum(unlist(weights)))) } +if (is.null(opt$summaryOutput)){ + summaryOutput = FALSE +}else{ + summaryOutput = TRUE +} + if (opt$compoundDbType=='local_config'){ # load in compound config # Soure local function taken from workflow4metabolomics @@ -76,8 +88,6 @@ compoundDbPass = NA } - - summary_output <- msPurity::combineAnnotations( sm_resultPth = sm_resultPth, compoundDbPth = compoundDbPth, @@ -94,7 +104,12 @@ compoundDbPort = compoundDbPort, compoundDbUser = compoundDbUser, compoundDbPass = compoundDbPass, - weights = weights) + weights = weights, + summaryOutput = summaryOutput) +if (summaryOutput){ + write.table(summary_output, file.path(opt$outdir, 'combined_annotations.tsv'), sep = '\t', row.names = FALSE) +} + write.table(summary_output, file.path(opt$outdir, 'combined_annotations.tsv'), sep = '\t', row.names = FALSE) |
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| diff -r 4207233ead9c -r 96fba93b4c8a createDatabase.R --- a/createDatabase.R Thu Dec 05 07:37:41 2019 -0500 +++ b/createDatabase.R Wed Apr 01 11:05:00 2020 -0400 |
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| @@ -115,10 +115,10 @@ -if(is.null(opt$grp_peaklist)){ +if(is.null(opt$grpPeaklist)){ grpPeaklist = NA }else{ - grpPeaklist = opt$grp_peaklist + grpPeaklist = opt$grpPeaklist } |
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| diff -r 4207233ead9c -r 96fba93b4c8a macros.xml --- a/macros.xml Thu Dec 05 07:37:41 2019 -0500 +++ b/macros.xml Wed Apr 01 11:05:00 2020 -0400 |
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| @@ -1,7 +1,7 @@ <?xml version="1.0"?> <macros> - <token name="@TOOL_VERSION@">1.12.0</token> - <token name="@GALAXY_TOOL_VERSION@">1</token> + <token name="@TOOL_VERSION@">1.12.2</token> + <token name="@GALAXY_TOOL_VERSION@">0</token> <xml name="requirements"> <requirements> |
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| diff -r 4207233ead9c -r 96fba93b4c8a test-data/averageFragSpectra_output_all.RData |
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| Binary file test-data/averageFragSpectra_output_all.RData has changed |
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| diff -r 4207233ead9c -r 96fba93b4c8a test-data/averageFragSpectra_output_all_only.RData |
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| diff -r 4207233ead9c -r 96fba93b4c8a test-data/averageFragSpectra_output_inter.RData |
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| Binary file test-data/averageFragSpectra_output_inter.RData has changed |
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| diff -r 4207233ead9c -r 96fba93b4c8a test-data/averageFragSpectra_output_intra.RData |
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| Binary file test-data/averageFragSpectra_output_intra.RData has changed |
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| diff -r 4207233ead9c -r 96fba93b4c8a test-data/combineAnnotations_combined_annotations.sqlite |
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| Binary file test-data/combineAnnotations_combined_annotations.sqlite has changed |
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| diff -r 4207233ead9c -r 96fba93b4c8a test-data/combineAnnotations_combined_annotations.tsv --- a/test-data/combineAnnotations_combined_annotations.tsv Thu Dec 05 07:37:41 2019 -0500 +++ b/test-data/combineAnnotations_combined_annotations.tsv Wed Apr 01 11:05:00 2020 -0400 |
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| b'@@ -1,107 +1,102 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\t""\t1\t"HMDB0031641"\t"277,343,409,410"\t0.99\tNA\t"0.0"\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.7143\t0.178575\t0.178575\t17\t"[M+H]+"\n+12\t"M116T48"\t116.070597631071\t47.7346706134597\t"MWFMGBPGAXYFAR-UHFFFAOYSA-N"\t"InChI=1S/C4H7NO/c1-4(2,6)3-5/h6H,1-2H3"\t"MWFMGBPGAXYFAR-UHFFFAOYSA-N"\t"MWFMGBPGAXYFAR"\t"UHFFFAOYSA"\t"N"\t"ACETONE CYANOHYDRIN"\t85.05276385\t"C4H7NO"\t"6406"\t"C02659"\t""\t""\t"HMDB0060427"\t"False"\t"False"\t0\t"HMDB0031456"\t"277,343,409,410"\t0.99\tNA\t"0"\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.6923\t0.173075\t0.173075\t18\t"[M+H]+"\n+12\t"M116T48"\t116.070597631071\t47.7346706134597\t"RRUDCFGSUDOHDG-UHFFFAOYSA-N"\t"InChI=1S/C2H5NO2/c1-2(4)3-5/h5H,1H3,(H,3,4)"\t"RRUDCFGSUDOHDG-UHFFFAOYSA-N"\t"RRUDCFGSUDOHDG"\t"UHFFFAOYSA"\t"N"\t"acetohydroxamic acid"\t75.032028405\t"C2H5NO2"\t"1990"\t"C06808"\t"Anatomical Therapeutic Chemical (ATC) classification [BR:br08303]"\t"D00220"\t"HMDB0014691"\t"False"\t"True"\t0\t"HMDB0003338"\t"277,343,409,410"\t0.99\tNA\t"0"\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.5455\t0.136375\t0.136375\t19\t"[M+H]+"\n+27\t"M132T74"\t132.101827517612\t73.554846736017\t"AGPKZVBTJJNPAG-UHFFFAOYSA-N"\t"InChI=1S/C6H13NO2/c1-3-4(2)5(7)6(8)9/h4-5H,3,7H2,1-2H3,(H,8,9)"\t"AGPKZVBTJJNPAG-UHFFFAOYSA-N"\t"AGPKZVBTJJNPAG"\t"UHFFFAOYSA"\t"N"\t"2-ammonio-3-methylpentanoate"\t131.09462866\t"C6H13NO2"\t"791,57397079"\t"C16434"\t""\t""\t"HMDB0033923"\t"True"\t"False"\t18\t"HMDB0000172"\t"478,547,616,475,541,607"\t1\t"CE000616"\t"0"\t0\t0\t0\t0.940890528192141\t0.282267158457642\t0\t0\t0\t0\t1\t0.25\t0.532267158457642\t1\t"[M+H]+"\n' |
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| diff -r 4207233ead9c -r 96fba93b4c8a test-data/createMSP_output_av_all_metadata.msp --- a/test-data/createMSP_output_av_all_metadata.msp Thu Dec 05 07:37:41 2019 -0500 +++ b/test-data/createMSP_output_av_all_metadata.msp Wed Apr 01 11:05:00 2020 -0400 |
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| @@ -10,7 +10,7 @@ CH$LINK: PUBCHEM CID:5328 CH$NAME Unknown XCMS groupid (grpid): 12 -COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_all' msPurity version:1.12.0 +COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_all' msPurity version:1.12.2 PK$NUM_PEAK: 2 PK$PEAK: m/z int. rel.int. 112.050884246826 502873.46875 100 @@ -28,7 +28,7 @@ CH$LINK: PUBCHEM CID:5328 CH$NAME Unknown XCMS groupid (grpid): 12 -COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_all' msPurity version:1.12.0 +COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_all' msPurity version:1.12.2 PK$NUM_PEAK: 2 PK$PEAK: m/z int. rel.int. 112.050884246826 502873.46875 100 |
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| diff -r 4207233ead9c -r 96fba93b4c8a test-data/flagRemove_output.tsv --- a/test-data/flagRemove_output.tsv Thu Dec 05 07:37:41 2019 -0500 +++ b/test-data/flagRemove_output.tsv Wed Apr 01 11:05:00 2020 -0400 |
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| @@ -1,7 +1,7 @@ -"grpid" "ID" "mzmed" "mzmin" "mzmax" "rtmed" "rtmin" "rtmax" "npeaks" "KO" "WT" "ko15" "ko16" "ko18" "wt19" "wt21" "wt22" "KO_median_I" "WT_median_I" "KO_RSD_I" "WT_RSD_I" "KO_coverage" "WT_coverage" "KO_RSD_RT" "WT_RSD_RT" "rsd_all_RT" "grpid.1" "KO_valid" "WT_valid" "all_sample_valid" "mzmin_full" "mzmax_full" "rtmin_full" "rtmax_full" -"1" "1" 205 205 205 2794.024 2793.436 2803.044 3 0 3 NA NA NA 1507943.06947222 1533767.074875 1354004.93486208 NA 1507943.06947222 NA 6.63321894286696 0 1 NA 0.19255594131829 0.19255594131829 1 0 1 1 205 205 2767.512 2816.3 -"2" "2" 231 231 231 2519.839 2504.508 2535.473 6 1 3 NA NA 30766.3350000011 45103.2999999989 104989.362833335 49776.3899999999 30766.3350000011 49776.3899999999 NA 49.9951594827002 0.333333333333333 1 NA 0.360049078987311 0.432545161192324 2 0 1 1 231 231 2507.963 2514.738 -"3" "3" 402.200012207031 402.200012207031 402.200012207031 3598.551 3592.212 3610.036 4 1 3 NA NA 14554.4999999997 37458.7453333329 91785.7281052629 142007.379692308 14554.4999999997 91785.7281052629 NA 57.8293736085665 0.333333333333333 1 NA 0.251337522585405 0.206331444617903 3 0 1 1 402.200012207031 402.200012207031 3563.503 3597.137 -"4" "4" 449.100006103516 449.100006103516 449.100006103516 2667.26 2664.638 2676.652 3 0 3 NA NA NA 6663.76999999991 11221.0499999998 6830.35200000006 NA 6830.35200000006 NA 31.3702198972974 0 1 NA 0.236631537850627 0.236631537850627 4 0 1 1 449.100006103516 449.100006103516 2659.233 2670.393 -"5" "5" 564.200012207031 564.200012207031 564.200012207031 3498.002 3491.993 3507.349 4 0 3 NA NA NA 149980.21 87237.7950000002 160589.344999999 NA 149980.21 NA 29.896461605479 0 1 NA 0.135256683436928 0.135256683436928 5 0 1 1 564.200012207031 564.200012207031 3473.214 3501.034 -"6" "6" 586.299987792969 586.299987792969 586.299987792969 3308.894 3308.249 3310.396 3 0 3 NA NA NA 10504.2799999998 7491.65500000026 12363.4999999997 NA 10504.2799999998 NA 24.294650028749 0 1 NA 0.0332903660058522 0.0332903660058522 6 0 1 1 586.299987792969 586.299987792969 3304.199 3312.024 +"grpid" "ID" "mzmed" "mzmin" "mzmax" "rtmed" "rtmin" "rtmax" "npeaks" "KO" "WT" "ko15" "ko16" "ko18" "wt19" "wt21" "wt22" "KO_median_I" "WT_median_I" "KO_RSD_I" "WT_RSD_I" "KO_coverage" "WT_coverage" "KO_RSD_RT" "WT_RSD_RT" "rsd_all_RT" "grpid.1" "KO_valid" "WT_valid" "all_sample_valid" "mzmin_full" "mzmax_full" "rtmin_full" "rtmax_full" "grp_names" +"1" "1" "205" "205" "205" "2794.024" "2793.436" "2803.044" "3" "0" "3" NA NA NA "1507943.06947222" "1533767.074875" "1354004.93486208" NA "1507943.06947222" NA "6.63321894286696" "0" "1" NA "0.19255594131829" "0.19255594131829" "1" "0" "1" "1" "205" "205" "2767.512" "2816.3" "M205T2794" +"2" "2" "231" "231" "231" "2519.839" "2504.508" "2535.473" "6" "1" "3" NA NA "30766.3350000011" "45103.2999999989" "104989.362833335" "49776.3899999999" "30766.3350000011" "49776.3899999999" NA "49.9951594827002" "0.333333333333333" "1" NA "0.360049078987311" "0.432545161192324" "2" "0" "1" "1" "231" "231" "2507.963" "2514.738" "M231T2520" +"3" "3" "402.200012207031" "402.200012207031" "402.200012207031" "3598.551" "3592.212" "3610.036" "4" "1" "3" NA NA "14554.4999999997" "37458.7453333329" "91785.7281052629" "142007.379692308" "14554.4999999997" "91785.7281052629" NA "57.8293736085665" "0.333333333333333" "1" NA "0.251337522585405" "0.206331444617903" "3" "0" "1" "1" "402.200012207031" "402.200012207031" "3563.503" "3597.137" "M402T3599" +"4" "4" "449.100006103516" "449.100006103516" "449.100006103516" "2667.26" "2664.638" "2676.652" "3" "0" "3" NA NA NA "6663.76999999991" "11221.0499999998" "6830.35200000006" NA "6830.35200000006" NA "31.3702198972974" "0" "1" NA "0.236631537850627" "0.236631537850627" "4" "0" "1" "1" "449.100006103516" "449.100006103516" "2659.233" "2670.393" "M449T2667" +"5" "5" "564.200012207031" "564.200012207031" "564.200012207031" "3498.002" "3491.993" "3507.349" "4" "0" "3" NA NA NA "149980.21" "87237.7950000002" "160589.344999999" NA "149980.21" NA "29.896461605479" "0" "1" NA "0.135256683436928" "0.135256683436928" "5" "0" "1" "1" "564.200012207031" "564.200012207031" "3473.214" "3501.034" "M564T3498" +"6" "6" "586.299987792969" "586.299987792969" "586.299987792969" "3308.894" "3308.249" "3310.396" "3" "0" "3" NA NA NA "10504.2799999998" "7491.65500000026" "12363.4999999997" NA "10504.2799999998" NA "24.294650028749" "0" "1" NA "0.0332903660058522" "0.0332903660058522" "6" "0" "1" "1" "586.299987792969" "586.299987792969" "3304.199" "3312.024" "M586T3309" |
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