| Previous changeset 1:cf62d2c0104e (2019-12-05) Next changeset 3:b800001c9f30 (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 combineAnnotations.xml 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 cf62d2c0104e -r d4376a743f7b combineAnnotations.R --- a/combineAnnotations.R Thu Dec 05 07:47:31 2019 -0500 +++ b/combineAnnotations.R Wed Apr 01 11:21:11 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$outdir, 'combined_annotations.tsv'), sep = '\t', row.names = FALSE) |
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| diff -r cf62d2c0104e -r d4376a743f7b combineAnnotations.xml --- a/combineAnnotations.xml Thu Dec 05 07:47:31 2019 -0500 +++ b/combineAnnotations.xml Wed Apr 01 11:21:11 2020 -0400 |
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| @@ -9,7 +9,11 @@ --sm_resultPth='$sm_resultPth' --metfrag_resultPth='$metfrag_resultPth' --sirius_csi_resultPth='$sirius_csi_resultPth' - --probmetab_resultPth='$probmetab_resultPth' + + #if $probmetabCond.probmetabChoice == 'probmetab' + --probmetab_resultPth='$probmetabCond.probmetab_resultPth' + #end if + --ms1_lookup_resultPth='$ms1_lookup_resultPth' #if $ms1_lookup_checkAdducts: @@ -25,8 +29,8 @@ --probmetab_weight=$probmetab_weight --ms1_lookup_weight=$ms1_lookup_weight --biosim_weight=$biosim_weight - - + + #if $create_new_database: --create_new_database #end if @@ -37,6 +41,10 @@ --compoundDbPth='$compoundDbTypeCond.compoundDbPth' #end if + #if $summaryOutput: + --summaryOutput + #end if + ]]></command> <inputs> @@ -48,8 +56,19 @@ help="The result of the MetFrag analysis (requires a column indicating the XCMS group ID)"/> <param argument="--sirius_csi_resultPth" type="data" label="Sirius CSI:FingerID result" format="tsv,tabular" optional="true" help="The result of the CSI:FingerID analysis (requires a column indicating the XCMS group ID)"/> - <param argument="--probmetab_resultPth" type="data" label="Probmetab result" format="tsv,tabular" optional="true" - help="The result of the Probmetab analysis (requires a column indicating the XCMS group ID)"/> + <conditional name="probmetabCond"> + <param name="probmetabChoice" type="select" label="Use probmetab data" help="The result of the Probmetab analysis" > + <option value="no_probmetab" selected="true" >Do not include probmetab results</option> + <option value="probmetab" >Include probmetab results</option> + </param> + <when value="probmetab"> + <param argument="--probmetab_resultPth" type="data" label="Probmetab result" format="tsv,tabular" optional="true" + help="The result of the Probmetab analysis (requires a column indicating the XCMS group ID). Alternatively any ms1 annotation tool can be used + instead of probmetab"/> + </when> + <when value="no_probmetab"> + </when> + </conditional> <param argument="--ms1_lookup_resultPth" type="data" label="MS1 Lookup result" format="tsv,tabular" optional="true" help="The result of the a generic MS1 lookup annotation software (e.g. BEAMS can be used)"/> <param argument="--ms1_lookup_keepAdducts" type="text" label="MS1 lookup adducts to keep" optional="true" @@ -67,6 +86,7 @@ <param argument="--probmetab_weight" type="float" min="0.0" max="1.0" value="0.0" label="Probmetab weight" help="all weights need to sum to 1" /> <param argument="--ms1_lookup_weight" type="float" min="0.0" max="1.0" value="0.05" label="MS1 Lookup weight" help="all weights need to sum to 1" /> <param argument="--biosim_weight" type="float" min="0.0" max="1.0" value="0.25" label="Biological similarity weight" help="all weights need to sum to 1" /> + <param argument="--summaryOutput" type="boolean" checked="true" label="Create summary output" help="Create tab separated file of all annotations and features"/> <param argument="--create_new_database" type="boolean" checked="true" label="Create a new database for the results?" help="A copy will be made of the input SQLite spectral matching database and the results will be added to this copy. When False, the input SQLite database will be updated the results. Use False @@ -93,8 +113,8 @@ <test> <param name="sm_resultPth" value="combinedAnnotation_input_spectralMatching.sqlite" /> <param name="metfrag_resultPth" value="combineAnnotations_input_metfrag.tsv" /> - <param name="sirius_csi_resultPth" value="combineAnnotations_input_sirus_csifingerid.tsv" /> - <param name="probmetab_resultPth" value="combineAnnotations_input_probmetab.tsv" /> + <param name="sirius_csi_resultPth" value="combineAnnotations_input_sirus_csifingerid.tsv" /> + <param name="compoundDbTypeCond|compoundDbPth" value="metab_compound_subset.sqlite" /> <param name="beams_resultPth" value="combineAnnotations_input_beams.tsv" /> <param name="compoundDbTypeCond|compoundDbPth" value="metab_compound_subset.sqlite" /> <output name="combined_annotations_tsv" file="combineAnnotations_combined_annotations.tsv" ftype="tsv" /> |
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| diff -r cf62d2c0104e -r d4376a743f7b createDatabase.R --- a/createDatabase.R Thu Dec 05 07:47:31 2019 -0500 +++ b/createDatabase.R Wed Apr 01 11:21:11 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 cf62d2c0104e -r d4376a743f7b macros.xml --- a/macros.xml Thu Dec 05 07:47:31 2019 -0500 +++ b/macros.xml Wed Apr 01 11:21:11 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 cf62d2c0104e -r d4376a743f7b test-data/averageFragSpectra_output_all.RData |
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| diff -r cf62d2c0104e -r d4376a743f7b test-data/averageFragSpectra_output_all_only.RData |
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| diff -r cf62d2c0104e -r d4376a743f7b test-data/averageFragSpectra_output_inter.RData |
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| diff -r cf62d2c0104e -r d4376a743f7b 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 cf62d2c0104e -r d4376a743f7b 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 cf62d2c0104e -r d4376a743f7b test-data/combineAnnotations_combined_annotations.tsv --- a/test-data/combineAnnotations_combined_annotations.tsv Thu Dec 05 07:47:31 2019 -0500 +++ b/test-data/combineAnnotations_combined_annotations.tsv Wed Apr 01 11:21:11 2020 -0400 |
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| b'@@ -1,107 +1,102 @@\n-"grpid"\t"grp_name"\t"mz"\t"rt"\t"inchikey"\t"inchi"\t"inchikey..7"\t"inchikey1"\t"inchikey2"\t"inchikey3"\t"name"\t"exact_mass"\t"molecular_formula"\t"pubchem_cids"\t"kegg_cids"\t"kegg_brite"\t"kegg_drugs"\t"hmdb_ids"\t"hmdb_bio_custom_flag"\t"hmdb_drug_flag"\t"biosim_max_count"\t"biosim_hmdb_ids"\t"fragmentation_acquistion_num"\t"mean_precursor_ion_purity"\t"accession"\t"sirius_score"\t"sirius_wscore"\t"metfrag_score"\t"metfrag_wscore"\t"sm_score"\t"sm_wscore"\t"probmetab_score"\t"probmetab_wscore"\t"ms1_lookup_score"\t"ms1_lookup_wscore"\t"biosim_max_score"\t"biosim_wscore"\t"wscore"\t"rank"\t"adduct_overall"\n-12\t"M116T48"\t116.070597631071\t47.7346706134597\t"ONIBWKKTOPOVIA-UHFFFAOYSA-N"\t"InChI=1S/C5H9NO2/c7-5(8)4-2-1-3-6-4/h4,6H,1-3H2,(H,7,8)"\t"ONIBWKKTOPOVIA-UHFFFAOYSA-N"\t"ONIBWKKTOPOVIA"\t"UHFFFAOYSA"\t"N"\t"DL-Proline"\t115.063328534\t"C5H9NO2"\t"614,25246272"\t"C16435"\t""\t""\t""\t""\t""\t33\t"HMDB0000162"\t"277,343,409,410"\t0.99\t"CCMSLIB00000577898"\t"1.0"\t0.2\t0.9\t0.18\t0.87867085623127\t0.263601256869381\t"0"\t0\t0\t0\t1\t0.25\t0.893601256869381\t1\t"[M+H]+,M+H"\n-12\t"M116T48"\t116.070597631071\t47.7346706134597\t"ONIBWKKTOPOVIA-AZXPZELESA-N"\t"InChI=1S/C5H9NO2/c7-5(8)4-2-1-3-6-4/h4,6H,1-3H2,(H,7,8)/i4+1"\t"ONIBWKKTOPOVIA-AZXPZELESA-N"\t"ONIBWKKTOPOVIA"\t"AZXPZELESA"\t"N"\t""\t116.066683369\t"C5H9NO2"\t"10290769"\t""\t""\t""\t""\t""\t""\t33\t"HMDB0000162"\t"277,343,409,410"\t0.99\tNA\t"1.0"\t0.2\t0\t0\t0\t0\t"0"\t0\t0\t0\t1\t0.25\t0.45\t2\t"[M+H]+"\n-12\t"M116T48"\t116.070597631071\t47.7346706134597\t"ONIBWKKTOPOVIA-BYPYZUCNSA-N"\t"InChI=1S/C5H9NO2/c7-5(8)4-2-1-3-6-4/h4,6H,1-3H2,(H,7,8)/t4-/m0/s1"\t"ONIBWKKTOPOVIA-BYPYZUCNSA-N"\t"ONIBWKKTOPOVIA"\t"BYPYZUCNSA"\t"N"\t"L-Pro"\t115.063328534\t"C5H9NO2"\t"145742,6971047"\t"C00148"\t"Compounds with biological roles [BR:br08001]"\t"D00035"\t"HMDB0000162"\t"True"\t"False"\t33\t"HMDB0000162"\t"277,343,409,410"\t0.99\tNA\t"1.0"\t0.2\t0\t0\t0\t0\t"0"\t0\t0\t0\t1\t0.25\t0.45\t2\t"[M+H]+"\n-12\t"M116T48"\t116.070597631071\t47.7346706134597\t"ONIBWKKTOPOVIA-GIZBTRSZSA-N"\t"InChI=1S/C5H9NO2/c7-5(8)4-2-1-3-6-4/h4,6H,1-3H2,(H,7,8)/t4-/m0/s1/i1+2,2+2,3+2,4+2,5+2"\t"ONIBWKKTOPOVIA-GIZBTRSZSA-N"\t"ONIBWKKTOPOVIA"\t"GIZBTRSZSA"\t"N"\t"L-PROLINE, [U-14C]"\t125.0795385\t"C5H9NO2"\t"12210869"\t""\t""\t""\t""\t""\t""\t33\t"HMDB0000162"\t"277,343,409,410"\t0.99\tNA\t"1.0"\t0.2\t0\t0\t0\t0\t"0"\t0\t0\t0\t1\t0.25\t0.45\t2\t"[M+H]+"\n-12\t"M116T48"\t116.070597631071\t47.7346706134597\t"ONIBWKKTOPOVIA-GTTLGWSSSA-N"\t"InChI=1S/C5H9NO2/c7-5(8)4-2-1-3-6-4/h4,6H,1-3H2,(H,7,8)/t4-/m0/s1/i1+1D,4+1,6+1/t1?,4-"\t"ONIBWKKTOPOVIA-GTTLGWSSSA-N"\t"ONIBWKKTOPOVIA"\t"GTTLGWSSSA"\t"N"\t"SCHEMBL16945363"\t119.07334984\t"C5H9NO2"\t"118264374"\t""\t""\t""\t""\t""\t""\t33\t"HMDB0000162"\t"277,343,409,410"\t0.99\tNA\t"1.0"\t0.2\t0\t0\t0\t0\t"0"\t0\t0\t0\t1\t0.25\t0.45\t2\t"[M+H]+"\n-12\t"M116T48"\t116.070597631071\t47.7346706134597\t"ONIBWKKTOPOVIA-HOSYLAQJSA-N"\t"InChI=1S/C5H9NO2/c7-5(8)4-2-1-3-6-4/h4,6H,1-3H2,(H,7,8)/i5+1"\t"ONIBWKKTOPOVIA-HOSYLAQJSA-N"\t"ONIBWKKTOPOVIA"\t"HOSYLAQJSA"\t"N"\t"DL-Proline-1-13C"\t116.066683369\t"C5H9NO2"\t"59340910"\t""\t""\t""\t""\t""\t""\t33\t"HMDB0000162"\t"277,343,409,410"\t0.99\tNA\t"1.0"\t0.2\t0\t0\t0\t0\t"0"\t0\t0\t0\t1\t0.25\t0.45\t2\t"[M+H]+"\n-12\t"M116T48"\t116.070597631071\t47.7346706134597\t"ONIBWKKTOPOVIA-IDEBNGHGSA-N"\t"InChI=1S/C5H9NO2/c7-5(8)4-2-1-3-6-4/h4,6H,1-3H2,(H,7,8)/i1+1,2+1,3+1,4+1,5+1,6+1"\t"ONIBWKKTOPOVIA-IDEBNGHGSA-N"\t"ONIBWKKTOPOVIA"\t"IDEBNGHGSA"\t"N"\t"SCHEMBL18875607"\t121.0771376\t"C5H9NO2"\t"129148531"\t""\t""\t""\t""\t""\t""\t33\t"HMDB0000162"\t"277,343,409,410"\t0.99\tNA\t"1.0"\t0.2\t0\t0\t0\t0\t"0"\t0\t0\t0\t1\t0.25\t0.45\t2\t"[M+H]+"\n-12\t"M116T48"\t116.070597631071\t47.7346706134597\t"ONIBWKKTOPOVIA-IXBOUXNVSA-N"\t"InChI=1S/C5H9NO2/c7-5(8)4-2-1-3-6-4/h4,6H,1-3H2,(H,7,8)/t4-/m0/s1/i4+1"\t"ONIBWKKTOPOVIA-IXBOUXNVSA-N"\t"ONIBWKKTOPOVIA"\t"IXBOUXNVSA"\t"N"\t""\t116.066683369\t"C5H9NO2"\t"100915807"\t""\t""\t""\t""\t""\t""\t33\t"HMDB0000162"\t"277,343,409,410"\t0.99\tNA\t"1.0"\t0.2\t0\t0\t0\t0\t"0"\t0\t0\t0\t1\t0.25\t0.45\t2\t"[M+H]+"\n-12\t"M116T48"\t116.070597631071\t47.7346706134597\t"ONIBWKKTOPOVIA-JGTYJTGKSA-N"\t"InChI=1S/C5H9NO2/c7-5(8)4-2-1-3-6-4/h4,6H,1-3H2,(H,7,8)/t4-/m0/s1/i6+1"\t"ONIBWKKTOPOVIA-JGTYJTGKSA-N"\t"ONIBWKKTOPOVIA"\t"JGTYJTGKSA"\t"N"\t"L-Proline-15N"\t116.'..b'/i3D2,4D2"\t"RWRDLPDLKQPQOW-KHORGVISSA-N"\t"RWRDLPDLKQPQOW"\t"KHORGVISSA"\t"N"\t"ACM42403258"\t75.098606278\t"C4H9N"\t"12196049"\t""\t""\t""\t""\t""\t""\t1\t"HMDB0031641"\t"277,343,409,410"\t0.99\tNA\t"0.0"\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.8696\t0.2174\t0.2174\t14\t"[M+H]+"\n+12\t"M116T48"\t116.070597631071\t47.7346706134597\t"RWRDLPDLKQPQOW-MNYXATJNSA-N"\t"InChI=1S/C4H9N/c1-2-4-5-3-1/h5H,1-4H2/i/hT"\t"RWRDLPDLKQPQOW-MNYXATJNSA-N"\t"RWRDLPDLKQPQOW"\t"MNYXATJNSA"\t"N"\t""\t73.081723544\t"C4H9N"\t"57750053"\t""\t""\t""\t""\t""\t""\t1\t"HMDB0031641"\t"277,343,409,410"\t0.99\tNA\t"0.0"\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.8696\t0.2174\t0.2174\t14\t"[M+H]+"\n+12\t"M116T48"\t116.070597631071\t47.7346706134597\t"RWRDLPDLKQPQOW-SMZGMGDZSA-N"\t"InChI=1S/C4H9N/c1-2-4-5-3-1/h5H,1-4H2/i3D2"\t"RWRDLPDLKQPQOW-SMZGMGDZSA-N"\t"RWRDLPDLKQPQOW"\t"SMZGMGDZSA"\t"N"\t""\t73.086052786\t"C4H9N"\t"57608710"\t""\t""\t""\t""\t""\t""\t1\t"HMDB0031641"\t"277,343,409,410"\t0.99\tNA\t"0.0"\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.8696\t0.2174\t0.2174\t14\t"[M+H]+"\n+12\t"M116T48"\t116.070597631071\t47.7346706134597\t"RWRDLPDLKQPQOW-LNLMKGTHSA-N"\t"InChI=1S/C4H9N/c1-2-4-5-3-1/h5H,1-4H2/i1D2,2D2"\t"RWRDLPDLKQPQOW-LNLMKGTHSA-N"\t"RWRDLPDLKQPQOW"\t"LNLMKGTHSA"\t"N"\t""\t75.098606278\t"C4H9N"\t"57608709"\t""\t""\t""\t""\t""\t""\t2\t"HMDB0031641"\t"277,343,409,410"\t0.99\tNA\t"0.0"\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.8333\t0.208325\t0.208325\t15\t"[M+H]+"\n+12\t"M116T48"\t116.070597631071\t47.7346706134597\t"RWRDLPDLKQPQOW-QAOQSSEZSA-N"\t"InChI=1S/C4H9N/c1-2-4-5-3-1/h5H,1-4H2/i1D,3D2"\t"RWRDLPDLKQPQOW-QAOQSSEZSA-N"\t"RWRDLPDLKQPQOW"\t"QAOQSSEZSA"\t"N"\t""\t74.092329532\t"C4H9N"\t"90927493"\t""\t""\t""\t""\t""\t""\t2\t"HMDB0031641"\t"277,343,409,410"\t0.99\tNA\t"0.0"\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.8\t0.2\t0.2\t16\t"[M+H]+"\n+12\t"M116T48"\t116.070597631071\t47.7346706134597\t"RWRDLPDLKQPQOW-SVYQBANQSA-N"\t"InChI=1S/C4H9N/c1-2-4-5-3-1/h5H,1-4H2/i1D2,2D2,3D2,4D2"\t"RWRDLPDLKQPQOW-SVYQBANQSA-N"\t"RWRDLPDLKQPQOW"\t"SVYQBANQSA"\t"N"\t"Pyrrolidine-2,2,3,3,4,4,5,5-d8"\t79.123713262\t"C4H9N"\t"12196044"\t""\t""\t""\t""\t""\t""\t2\t"HMDB0031641"\t"277,343,409,410"\t0.99\tNA\t"0.0"\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.8\t0.2\t0.2\t16\t"[M+H]+"\n+12\t"M116T48"\t116.070597631071\t47.7346706134597\t"RWRDLPDLKQPQOW-HJOWPTDZSA-N"\t"InChI=1S/C4H9N/c1-2-4-5-3-1/h5H,1-4H2/i1D2,2D2,3D,4D2/hD"\t"RWRDLPDLKQPQOW-HJOWPTDZSA-N"\t"RWRDLPDLKQPQOW"\t"HJOWPTDZSA"\t"N"\t"pyrrolidine-d8"\t79.123713262\t"C4H9N"\t"129715569"\t""\t""\t""\t""\t""\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"RWRDLPDLKQPQOW-KLRAWXKOSA-N"\t"InChI=1S/C4H9N/c1-2-4-5-3-1/h5H,1-4H2/i1D2,2D2,3D2,4D2/hD"\t"RWRDLPDLKQPQOW-KLRAWXKOSA-N"\t"RWRDLPDLKQPQOW"\t"KLRAWXKOSA"\t"N"\t""\t80.12999001\t"C4H9N"\t"60135501"\t""\t""\t""\t""\t""\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' |
| b |
| diff -r cf62d2c0104e -r d4376a743f7b test-data/createDatabase_output.sqlite |
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| Binary file test-data/createDatabase_output.sqlite has changed |
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| diff -r cf62d2c0104e -r d4376a743f7b test-data/createDatabase_output_eic.sqlite |
| b |
| Binary file test-data/createDatabase_output_eic.sqlite has changed |
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| diff -r cf62d2c0104e -r d4376a743f7b test-data/createMSP_output_av_all_metadata.msp --- a/test-data/createMSP_output_av_all_metadata.msp Thu Dec 05 07:47:31 2019 -0500 +++ b/test-data/createMSP_output_av_all_metadata.msp Wed Apr 01 11:21:11 2020 -0400 |
| b |
| @@ -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 |
| b |
| diff -r cf62d2c0104e -r d4376a743f7b test-data/filterFragSpectra_output.RData |
| b |
| Binary file test-data/filterFragSpectra_output.RData has changed |
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| diff -r cf62d2c0104e -r d4376a743f7b test-data/flagRemove_output.tsv --- a/test-data/flagRemove_output.tsv Thu Dec 05 07:47:31 2019 -0500 +++ b/test-data/flagRemove_output.tsv Wed Apr 01 11:21:11 2020 -0400 |
| b |
| @@ -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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