| Next changeset 1:9a0d83c1b4b3 (2022-04-22) |
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Commit message:
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122" |
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added:
macros.xml ramclustr.xml ramclustr_wrapper.R test-data/gc-ramclustr-define-experiment.csv test-data/lc-ramclustr-define-experiment.csv test-data/test1_fill_xcms_1.msp test-data/test1_spec_abundance_xcms_1.csv test-data/test1_xcmsObj_1.rdata.xcms.fillpeaks test-data/test2_fill_xcms_2.msp test-data/test2_sample_metadata_xcms_2.csv test-data/test2_spec_abundance_xcms_2.csv test-data/test2_xcmsObj_2.rdata.xcms.fillpeaks test-data/test3_csv_test-input_1_2.csv test-data/test3_spec_abundance_csv_1.csv test-data/test3_spectra_csv_1.msp test-data/test4_sample_metadata_csv_2.csv test-data/test4_spec_abundance_csv_2.csv test-data/test4_spectra_csv_2.msp |
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| diff -r 000000000000 -r 36104baf75da macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Tue Mar 22 16:09:16 2022 +0000 |
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| b'@@ -0,0 +1,306 @@\n+<macros>\n+ <token name="@TOOL_VERSION@">1.2.2</token>\n+\n+ <xml name="creator">\n+ <creator>\n+ <person\n+ givenName="Helge"\n+ familyName="Hecht"\n+ url="https://github.com/hechth"\n+ identifier="0000-0001-6744-996X" />\n+ <person\n+ givenName="Maksym"\n+ familyName="Skoryk"\n+ url="https://github.com/maximskorik"\n+ identifier="0000-0003-2056-8018" />\n+ <person\n+ givenName="Matej"\n+ familyName="Troj\xc3\xa1k"\n+ url="https://github.com/xtrojak"\n+ identifier="0000-0003-0841-2707" />\n+ <person\n+ givenName="Martin"\n+ familyName="\xc4\x8cech"\n+ url="https://github.com/martenson"\n+ identifier="0000-0002-9318-1781" />\n+ <organization\n+ url="https://www.recetox.muni.cz/"\n+ email="GalaxyToolsDevelopmentandDeployment@space.muni.cz"\n+ name="RECETOX MUNI"/>\n+ </creator>\n+ </xml>\n+\n+ <xml name="parameters_csv">\n+ <section name="ms_csv" title="Input MS Data as CSV" expanded="true">\n+ <param label="Input CSV" name="ms" type="data" format="csv"\n+ help="Features as columns, rows as samples. Column header in format mz_rt."/>\n+ <param label="idMSMS" name="idmsms" type="data" format="csv" optional="true"\n+ help="Optional idMSMS / MSe csv data. Same dimension and names as in input CSV are required."/>\n+ </section>\n+ </xml>\n+\n+ <xml name="parameters_xcms">\n+ <section name="xcms" title="Input MS Data as XCMS" expanded="true">\n+ <param name="input_xcms" label="Input XCMS" type="data" format="rdata.xcms.fillpeaks"\n+ help="Grouped feature data for clustering." />\n+ <param label="Preserve phenotype" name="usePheno" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true"\n+ help="Transfer phenotype data from XCMS object to Spec abundance file."/>\n+ </section>\n+ </xml>\n+\n+ <xml name="parameters_required">\n+ <param label="Sigma r" name="sr" type="float" value="0.5" help="Correlational similarity between features."/>\n+ <param label="Correlation method" name="cor_method" type="select" display="radio"\n+ help="Choose correlational method to be used - see [1] for details.">\n+ <option value="pearson" selected="true">pearson</option>\n+ <option value="everything">everything</option>\n+ <option value="spearman">spearman</option>\n+ <option value="kendall">kendall</option>\n+ </param>\n+ <param label="Maximum RT difference" name="maxt" value="60" type="float"\n+ help="Maximum difference to calculate RT similarity - values beyond this are assigned zero similarity."/>\n+ </xml>\n+\n+ <xml name="main_parameters">\n+ <section name="clustering" title="Clustering" expanded="true">\n+ <param label="Clustering linkage method" name="linkage" type="select" display="radio"\n+ help="Choose hierarchical clustering linkage method - see [2] for details.">\n+ <option value="average" selected="true">average</option>\n+ <option value="ward.D">ward.D</option>\n+ <option value="ward.D2">ward.D2</option>\n+ <option value="single">single</option>\n+ <option value="complete">complete</option>\n+ <option value="mcquitty">mcquitty</option>\n+ <option value="median">median</option>\n+ <option value="centroid">centroid</option>\n+ </param>\n+ <param label="Minimal cluster size" name="minModuleSize" type="integer" value="2"\n+ help="Minimal size (number of features) of a cluster."/>\n+ <par'..b' of the elemental composition of the analyte. In EI, fragmentation is a byproduct of ionization, and has\n+ driven the generation of large mass spectral libraries. In ESI, in-source fragmentation frequently\n+ occurs, the magnitude of which is compound dependent, with more labile compounds being more prone to\n+ in-source fragmentation. ESI can also product multiple adduct forms (protonated, potassiated, sodiated,\n+ ammoniated...), and can produce multimers (i.e. [2M+H]+, [3M+K]+, etc) and multiple charged species\n+ ([M+2H]++). This can become further complicated by considering combinations of these phenomena. For\n+ example [2M+3H]+++ (triply charged dimer) or an in-source fragment of a dimer.\n+\n+ RAMClustR approach\n+ RAMClustR was designed to group features designed from the same compound using an approach which is\n+ **1.** unsupervised, **2.** platform agnostic, and **3.** devoid of curated rules, as the depth of\n+ understanding of these processes is insufficient to enable accurate curation/prediction of all phenomenon\n+ that may occur. We achieve this by making two assumptions. The first is that two features derived\n+ from the same compound with have (approximately) the same retention time. The second is that two\n+ features derived from the same compound will have (approximately) the same quantitative trend across\n+ all samples in the xcms sample set. From these assumptions, we can calculate a retention time\n+ similarity score and a correlational similarity score for each feature pair. A high similarity score\n+ for both retention time and correlation indicates a strong probability that two features derive from\n+ the same compound. Since both conditions must be met, the product of the two similarity scores provides\n+ the best approximation of the total similarity score - i.e. a feature pair with retention time similarity\n+ of 1 and correlational similarity of 0 is unlikely to derive from one compound - 1 x 0 = 0, the final\n+ similarity score is zero, indicating the two features represent two different compounds. Similarly, a\n+ feature pair with retention time similarity of 0 and correlational similarity of 1 is unlikely to derive\n+ from one compound - 0 x 1 = 0. Alternatively - a feature pair with retention time similarity of 1 and\n+ correlational similarity of 1 is likely to derive from one compound - 1 x 1 = 1.\n+\n+ The RAMClustR algorithm is built on creating similarity scores for all pairs of features, submitting\n+ this score matrix for hierarchical clustering, and then cutting the resulting dendrogram into neat\n+ chunks using the dynamicTreeCut package - where each \'chunk\' of the dendrogram results in a group of\n+ features likely to be derived from a single compound. Importantly, this is achieved without looking for\n+ specific phenomenon (i.e. sodiation), meaning that grouping can be performed on any dataset, whether it\n+ is positive or negative ionization mode, EI or ESI, LC-MS GC-MS or CE-MS, in-source fragment or complex\n+ adduction event, and predictable or unpredictable signals.\n+ </token>\n+\n+ <token name="@HELP_experiment@">\n+ <![CDATA[\n+ Create an Experimental Design specification for RAMClustR experiment.\n+\n+ Downstream Tools\n+ +-----------+-----------------------+--------+\n+ | Name | Output File | Format |\n+ +===========+=======================+========+\n+ | RAMClustR | Experiment definition | csv |\n+ +-----------+-----------------------+--------+\n+\n+ ]]>\n+ </token>\n+</macros>\n' |
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| diff -r 000000000000 -r 36104baf75da ramclustr.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ramclustr.xml Tue Mar 22 16:09:16 2022 +0000 |
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| b'@@ -0,0 +1,175 @@\n+<tool id="ramclustr" name="RAMClustR" version="@TOOL_VERSION@+galaxy2">\n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n+ <expand macro="creator"/>\n+\n+ <requirements>\n+ <requirement type="package" version="@TOOL_VERSION@">r-ramclustr</requirement>\n+ <requirement type="package" version="3.14.0">bioconductor-xcms</requirement>\n+ </requirements>\n+\n+ <command detect_errors="aggressive"><![CDATA[\n+ Rscript\n+ -e \'source("${__tool_directory__}/ramclustr_wrapper.R")\'\n+ -e \'source("${ramclustr_method}")\'\n+ ]]>\n+ </command>\n+ <configfiles>\n+ <configfile name="ramclustr_method">\n+ store_output(\n+ #if $filetype.type_choice == "xcms":\n+ ramclustr_xcms(\n+ input_xcms = "$filetype.xcms.input_xcms",\n+ use_pheno = $filetype.xcms.usePheno,\n+ #else:\n+ ramclustr_csv(\n+ ms = "$filetype.ms_csv.ms",\n+ idmsms = "$filetype.ms_csv.idmsms",\n+ #end if\n+ sr = $filetype.required.sr,\n+ #if $filetype.type_choice == "xcms":\n+ #if $filetype.required.st\n+ st = $filetype.required.st,\n+ #end if\n+ #else:\n+ st = $filetype.required.st,\n+ #end if\n+ cor_method = "$filetype.required.cor_method",\n+ maxt = $filetype.required.maxt,\n+ linkage = "$clustering.linkage",\n+ min_module_size = $clustering.minModuleSize,\n+ hmax = $clustering.hmax,\n+ deep_split = "$clustering.deepSplit",\n+ normalize = "$normalisation.normalisation_method.normalize",\n+ #if "$normalisation.normalisation_method.normalize" == "batch.qc":\n+ metadata_file = "$normalisation.normalisation_method.batch_order_qc",\n+ qc_inj_range = $normalisation.normalisation_method.qc_inj_range,\n+ #end if\n+ block_size = $performance.blocksize,\n+ mult = $performance.mult,\n+ mzdec = $msp_output_details.mzdec,\n+ rt_only_low_n = $extras.rt_only_low_n,\n+ replace_zeros = $extras.replace_zeros,\n+ #if $extras.ExpDes:\n+ exp_design = "${$extras.ExpDes}"\n+ #end if\n+ ),\n+ $msp_output_details.merge_msp,\n+ "$spec_abundance",\n+ #if $msp_output_details.merge_msp:\n+ "$mass_spectra_merged"\n+ #else:\n+ NULL\n+ #end if\n+ )\n+ </configfile>\n+ </configfiles>\n+ <inputs>\n+ <conditional name="filetype">\n+ <param name="type_choice" type="select" label="Choose input format:">\n+ <option value="xcms" selected="true">XCMS</option>\n+ <option value="csv">CSV</option>\n+ </param>\n+ <when value="xcms">\n+ <expand macro="parameters_xcms" />\n+ <section name="required" title="General parameters" expanded="true">\n+ <param label="Sigma t" name="st" type="float" optional="true" help="Retention time similarity (optional).\n+ A recommended starting point is half the value of your average chromatographic peak width at half max (seconds))."/>\n+ <expand macro="parameters_required" />\n+ </section>\n+ </when>\n+ <when value="csv">\n+ <expand macro="parameters_csv" />\n+ <section name="required" title="General parameters" expanded="true">\n+ <param label="Sigma t" name="st" type="float" value="1" help="R'..b' />\n+ </inputs>\n+\n+ <outputs>\n+ <data label="Spec Abundance of ${on_string}" name="spec_abundance" format="csv" />\n+ <expand macro="output_msp"/>\n+ </outputs>\n+\n+ <tests>\n+ <test><!-- TEST 1 -->\n+ <section name="filetype">\n+ <param name="type_choice" value="xcms"/>\n+ <section name="xcms">\n+ <param name="input_xcms" value="test1_xcmsObj_1.rdata.xcms.fillpeaks" ftype="rdata.xcms.fillpeaks"/>\n+ </section>\n+ <section name="required">\n+ <param name="maxt" value="259.8"/>\n+ </section>\n+ </section>\n+ <section name="extras">\n+ <param name="ExpDes" value="lc-ramclustr-define-experiment.csv" ftype="csv"/>\n+ </section>\n+ <output name="mass_spectra_merged" file="test1_fill_xcms_1.msp" ftype="msp"/>\n+ <output name="spec_abundance" file="test1_spec_abundance_xcms_1.csv" ftype="csv" compare="sim_size" delta="100"/>\n+ </test>\n+ <test><!-- TEST 2 -->\n+ <section name="filetype">\n+ <param name="type_choice" value="xcms"/>\n+ <section name="xcms">\n+ <param name="input_xcms" value="test2_xcmsObj_2.rdata.xcms.fillpeaks" ftype="rdata.xcms.fillpeaks"/>\n+ </section>\n+ <section name="required">\n+ <param name="maxt" value="78.4"/>\n+ </section>\n+ </section>\n+ <section name="normalisation">\n+ <section name="normalisation_method">\n+ <param name="batch_order_qc" value="test2_sample_metadata_xcms_2.csv" ftype="csv" />\n+ </section>\n+ </section>\n+ <output name="mass_spectra_merged" file="test2_fill_xcms_2.msp" ftype="msp" compare="diff" lines_diff="10"/>\n+ <output name="spec_abundance" file="test2_spec_abundance_xcms_2.csv" ftype="csv" compare="sim_size" delta="100"/>\n+ </test>\n+ <test><!-- TEST 3 -->\n+ <section name="filetype">\n+ <param name="type_choice" value="csv"/>\n+ <section name="ms_csv">\n+ <param name="ms" value="test3_csv_test-input_1_2.csv" ftype="csv"/>\n+ </section>\n+ <section name="required">\n+ <param name="st" value="5.0"/>\n+ <param name="maxt" value="1"/>\n+ </section>\n+ </section>\n+ <section name="performance">\n+ <param name="blocksize" value="1000"/>\n+ <param name="mult" value="1"/>\n+ </section>\n+ <output name="mass_spectra_merged" file="test3_spectra_csv_1.msp" ftype="msp"/>\n+ <output name="spec_abundance" file="test3_spec_abundance_csv_1.csv" ftype="csv"/>\n+ </test>\n+ <test><!-- TEST 4 -->\n+ <section name="filetype">\n+ <param name="type_choice" value="csv"/>\n+ <section name="ms_csv">\n+ <param name="ms" value="test3_csv_test-input_1_2.csv" ftype="csv"/>\n+ </section>\n+ </section>\n+ <output name="mass_spectra_merged" file="test4_spectra_csv_2.msp" ftype="msp" lines_diff="10"/>\n+ </test>\n+ </tests>\n+\n+ <help>\n+ <![CDATA[\n+ @HELP@\n+\n+ .. rubric:: **Footnotes**\n+ .. [1] Correlation, Variance and Covariance - `stats::cor <https://www.rdocumentation.org/packages/stats/versions/3.6.2/topics/cor>`_\n+ .. [2] Hierarchical Clustering - `stats::hclust <https://www.rdocumentation.org/packages/stats/versions/3.6.2/topics/hclust>`_\n+ .. [3] Dynamic Dendrogram Pruning Based on Dendrogram Only - `dynamicTreeCut::cutreeDynamicTree <https://www.rdocumentation.org/packages/dynamicTreeCut/versions/1.63-1/topics/cutreeDynamicTree>`_\n+ ]]>\n+ </help>\n+\n+ <expand macro="citations" />\n+</tool>\n' |
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| diff -r 000000000000 -r 36104baf75da ramclustr_wrapper.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ramclustr_wrapper.R Tue Mar 22 16:09:16 2022 +0000 |
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| @@ -0,0 +1,174 @@ +store_output <- function( + ramclustr_obj, + output_merge_msp, + output_spec_abundance, + msp_file) { + RAMClustR::write.msp(ramclustr_obj, one.file = output_merge_msp) + write.csv(ramclustr_obj$SpecAbund, file = output_spec_abundance, row.names = TRUE) + + if (!is.null(msp_file)) { + exp.name <- ramclustr_obj$ExpDes[[1]][which(row.names(ramclustr_obj$ExpDes[[1]]) == "Experiment"), 1] + filename <- paste("spectra/", exp.name, ".msp", sep = "") + file.copy(from = filename, to = msp_file, overwrite = TRUE) + } +} + +load_experiment_definition <- function(filename) { + experiment <- RAMClustR::defineExperiment(csv = filename) + return(experiment) +} + +read_metadata <- function(filename) { + data <- read.csv(filename, header = TRUE, stringsAsFactors = FALSE) + + if (!"qc" %in% colnames(data)) { + if ("sampleType" %in% colnames(data)) { + data$qc <- ifelse(data$sampleType == "qc", TRUE, FALSE) + } + } + + if (!"order" %in% colnames(data)) { + if ("injectionOrder" %in% colnames(data)) { + names(data)[names(data) == "injectionOrder"] <- "order" + } + } + + return(data) +} + +ramclustr_xcms <- function( + input_xcms, + use_pheno, + sr, + st = NULL, + cor_method, + maxt, + linkage, + min_module_size, + hmax, + deep_split, + normalize, + metadata_file = NULL, + qc_inj_range, + block_size, + mult, + mzdec, + rt_only_low_n, + replace_zeros, + exp_design = NULL +) { + obj <- load(input_xcms) + + batch <- NULL + order <- NULL + qc <- NULL + + if (!is.null(metadata_file)) { + metadata <- read_metadata(metadata_file) + batch <- metadata$batch + order <- metadata$order + qc <- metadata$qc + } + + experiment <- NULL + + if (!is.null(exp_design)) { + experiment <- load_experiment_definition(exp_design) + } + + x <- RAMClustR::ramclustR( + xcmsObj = xdata, + st = st, + maxt = maxt, + sr = sr, + deepSplit = deep_split, + blocksize = block_size, + mult = mult, + hmax = hmax, + usePheno = use_pheno, + mspout = FALSE, + qc.inj.range = qc_inj_range, + normalize = normalize, + minModuleSize = min_module_size, + linkage = linkage, + mzdec = mzdec, + cor.method = cor_method, + rt.only.low.n = rt_only_low_n, + fftempdir = NULL, + replace.zeros = replace_zeros, + batch = batch, + order = order, + qc = qc, + ExpDes = experiment + ) + return(x) +} + +ramclustr_csv <- function( + ms, + idmsms, + sr, + st, + cor_method, + maxt, + linkage, + min_module_size, + hmax, + deep_split, + normalize, + metadata_file = NULL, + qc_inj_range, + block_size, + mult, + mzdec, + rt_only_low_n, + replace_zeros, + exp_design = NULL +) { + if (!file.exists(idmsms)) + idmsms <- NULL + + batch <- NULL + order <- NULL + qc <- NULL + + if (!is.null(metadata_file)) { + metadata <- read_metadata(metadata_file) + batch <- metadata$batch + order <- metadata$order + qc <- metadata$qc + } + + experiment <- NULL + + if (!is.null(exp_design)) { + experiment <- load_experiment_definition(exp_design) + } + + x <- RAMClustR::ramclustR( + ms = ms, + idmsms = idmsms, + st = st, + maxt = maxt, + sr = sr, + deepSplit = deep_split, + blocksize = block_size, + mult = mult, + hmax = hmax, + mspout = FALSE, + qc.inj.range = qc_inj_range, + normalize = normalize, + minModuleSize = min_module_size, + linkage = linkage, + mzdec = mzdec, + cor.method = cor_method, + rt.only.low.n = rt_only_low_n, + fftempdir = NULL, + replace.zeros = replace_zeros, + batch = batch, + order = order, + qc = qc, + ExpDes = experiment + ) + return(x) +} |
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| diff -r 000000000000 -r 36104baf75da test-data/gc-ramclustr-define-experiment.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gc-ramclustr-define-experiment.csv Tue Mar 22 16:09:16 2022 +0000 |
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| @@ -0,0 +1,38 @@ +parameter,Value,Description +,, +Experimental Design,, +Experiment,experiment_gc,"Experiment name, no spaces." +Species,mus musculus,Genus species from which samples are derived. +Sample,serum,"Type of sample (e.g., serum, leaf)." +Contributer,recetox,Your or your PI's name. +platform,GC-MS,Either GC-MS or LC-MS. +,, +GC-MS,, +chrominst,ISQ 7000,Model of LC/GC instrument. +msinst,ISQ7K-VPI,Model of MS instrument. +column,These columns enable analysis of ppm levels of amines without column priming,Column description. +InletTemp,33,Temperature of inlet. +TransferTemp,23,Temperature of GC to MS transfer line. +mstype,QTOF,"Type of mass spectrometer (one of QQQ, TOF, QTOF, Orbi, Q)." +msmode,positive,Positive or negative ion mode. +ionization,AP,"Ionization (EI, AP, or CI)." +msscanrange,100,Scan range used for acquisition. +scantime,0.2,Time for each full scan spectrum (e.g. 0.2 seconds). +deriv,TMS,"Derivitization (TMS, TBDMS, or None)." +MSlevs,1.0,Number of levels of energy acquired - 1 typically. +,, +LC-MS,, +chrominst,fill,Model of LC/GC instrument. +msinst,fill,Model of MS instrument. +column,fill,Column description. +solvA,fill,Solvent A composition. +solvB,fill,Solvent B composition. +CE1,fill,Collision energy of acquisition of MS data. +CE2,fill,Collision energy of acquisition for MSe/idMSMS data (when applicable). +mstype,fill,"Type of mass spectrometer (one of QQQ, TOF, QTOF, Orbi, Q)." +msmode,fill,Positive or negative ion mode. +ionization,fill,"Ionization (EI, AP, or CI)." +colgas,fill,Gas used for collisional dissociation. +msscanrange,fill,Scan range used for acquisition. +conevol,fill,Cone voltage used for acquisition. +MSlevs,fill,Number of levels of energy acquired - 1 typically. |
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| diff -r 000000000000 -r 36104baf75da test-data/lc-ramclustr-define-experiment.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/lc-ramclustr-define-experiment.csv Tue Mar 22 16:09:16 2022 +0000 |
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| @@ -0,0 +1,38 @@ +parameter,Value,Description +,, +Experimental Design,, +Experiment,experiment_lc,"Experiment name, no spaces." +Species,mus musculus,Genus species from which samples are derived. +Sample,serum,"Type of sample (e.g., serum, leaf)." +Contributer,recetox,Your or your PI's name. +platform,LC-MS,Either GC-MS or LC-MS. +,, +GC-MS,, +chrominst,fill,Model of LC/GC instrument. +msinst,fill,Model of MS instrument. +column,fill,Column description. +InletTemp,fill,Temperature of inlet. +TransferTemp,fill,Temperature of GC to MS transfer line. +mstype,fill,"Type of mass spectrometer (one of QQQ, TOF, QTOF, Orbi, Q)." +msmode,fill,Positive or negative ion mode. +ionization,fill,"Ionization (EI, AP, or CI)." +msscanrange,fill,Scan range used for acquisition. +scantime,fill,Time for each full scan spectrum (e.g. 0.2 seconds). +deriv,fill,"Derivitization (TMS, TBDMS, or None)." +MSlevs,fill,Number of levels of energy acquired - 1 typically. +,, +LC-MS,, +chrominst,UltiMateX 3000 BioRS System,Model of LC/GC instrument. +msinst,FSN04-10000,Model of MS instrument. +column,These columns enable analysis of ppm levels of amines without column priming,Column description. +solvA,H20,Solvent A composition. +solvB,CO2,Solvent B composition. +CE1,50,Collision energy of acquisition of MS data. +CE2,100,Collision energy of acquisition for MSe/idMSMS data (when applicable). +mstype,Q,"Type of mass spectrometer (one of QQQ, TOF, QTOF, Orbi, Q)." +msmode,negative,Positive or negative ion mode. +ionization,ESI,"Ionization (EI, AP, or CI)." +colgas,He,Gas used for collisional dissociation. +msscanrange,1000,Scan range used for acquisition. +conevol,12,Cone voltage used for acquisition. +MSlevs,1.0,Number of levels of energy acquired - 1 typically. |
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| diff -r 000000000000 -r 36104baf75da test-data/test1_fill_xcms_1.msp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test1_fill_xcms_1.msp Tue Mar 22 16:09:16 2022 +0000 |
| b |
| b'@@ -0,0 +1,1991 @@\n+NAME:C001\n+IONMODE:Negative\n+SPECTRUMTYPE:Centroid\n+RETENTIONTIME:38.74\n+Num Peaks:57\n+216.9205 32607700\n+256.8215 31377637\n+175.0641 26780143\n+206.9034 26130980\n+254.8252 23747536\n+198.8647 21688594\n+196.8658 21390430\n+372.7383 19374863\n+258.8237 15532799\n+382.8218 12815572\n+488.6825 12267966\n+392.7685 10913351\n+316.7777 10734168\n+440.7322 10603010\n+138.9121 10186226\n+312.7841 10051801\n+434.7287 9943329\n+266.8652 9805546\n+370.7418 9765463\n+450.7016 8762673\n+324.9549 8619910\n+428.7834 8554675\n+384.8177 8311500\n+442.7401 8271752\n+200.8848 7742528\n+492.744 7662344\n+494.8953 7188793\n+546.6093 7177067\n+498.8794 6811405\n+500.8484 6520691\n+322.8157 6317648\n+350.9875 6150799\n+550.6949 6104789\n+426.7772 5431633\n+566.5977 5171811\n+510.763 4989757\n+486.7743 4886062\n+460.7076 4528973\n+484.7242 4273989\n+518.7415 4243468\n+334.849 4178412\n+413.2664 3965867\n+436.8161 3705247\n+502.7832 3567833\n+342.8093 3285552\n+366.8281 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57647644\n+994.6801 53549573\n+770.964 49250157\n+483.3283 36245876\n+275.6336 28001849\n+771.9675 22666873\n+1020.6591 12469103\n+783.9721 9839299\n+949.6233 8009033\n+124.1405 6517662\n+950.6274 3674694\n+784.9749 3622908\n+170.2437 1237313\n+\n+NAME:C005\n+IONMODE:Negative\n+SPECTRUMTYPE:Centroid\n+RETENTIONTIME:41.72\n+Num Peaks:20\n+337.0623 88672453\n+359.0443 48435582\n+353.0361 37061354\n+375.018 29159485\n+218.1386 14009249\n+417.0027 13822994\n+381.0261 13522755\n+438.9851 11307111\n+396.9999 10317665\n+454.9592 9820452\n+432.9764 9779399\n+338.0654 8770055\n+360.0459 5025128\n+418.9966 4386311\n+512.8989 4072570\n+456.9603 3774845\n+470.9263 3632486\n+572.871 3485486\n+440.9796 3364168\n+376.0216 2740193\n+\n+NAME:C006\n+IONMODE:Negative\n+SPECTRUMTYPE:Centroid\n+RETENTIONTIME:452.08\n+Num Peaks:19\n+494.3249 803829845\n+495.3278 207959661\n+542.3239 193323900\n+543.3276 55501736\n+1087.6715 34676828\n+516.3076 24092471\n+274.6257 21694276\n+1088.6773 21466528\n+1001.658 11852076\n+1089.682 9948820\n+290.6256 9704443\n+1061.6562 9417442\n+987.6411 7453650\n+1037.6578 7076912\n+1062.6592 5657208\n+484.3311 5283943\n+265.6196 4371245\n+988.6455 3739523\n+471.1945 2160605\n+\n+NAME:C007\n+IONMODE:Negative\n+SPECTRUMTYPE:Centroid\n+RET'..b'143\n+IONMODE:Negative\n+SPECTRUMTYPE:Centroid\n+RETENTIONTIME:548.78\n+Num Peaks:2\n+387.1432 12915848\n+407.6598 4564346\n+\n+NAME:C144\n+IONMODE:Negative\n+SPECTRUMTYPE:Centroid\n+RETENTIONTIME:553.62\n+Num Peaks:2\n+359.1781 45383099\n+360.185 9704481\n+\n+NAME:C145\n+IONMODE:Negative\n+SPECTRUMTYPE:Centroid\n+RETENTIONTIME:545.31\n+Num Peaks:2\n+443.3331 1151694\n+394.3559 432819\n+\n+NAME:C146\n+IONMODE:Negative\n+SPECTRUMTYPE:Centroid\n+RETENTIONTIME:551.39\n+Num Peaks:2\n+350.1838 4199726\n+365.2288 1932289\n+\n+NAME:C147\n+IONMODE:Negative\n+SPECTRUMTYPE:Centroid\n+RETENTIONTIME:563.22\n+Num Peaks:2\n+282.2792 241362345\n+256.2615 19433189\n+\n+NAME:C148\n+IONMODE:Negative\n+SPECTRUMTYPE:Centroid\n+RETENTIONTIME:548.47\n+Num Peaks:2\n+305.2468 9633582\n+329.249 5814756\n+\n+NAME:C149\n+IONMODE:Negative\n+SPECTRUMTYPE:Centroid\n+RETENTIONTIME:350.93\n+Num Peaks:2\n+130.0643 7419216\n+190.0865 4433780\n+\n+NAME:C150\n+IONMODE:Negative\n+SPECTRUMTYPE:Centroid\n+RETENTIONTIME:365.37\n+Num Peaks:2\n+490.2083 5275418\n+465.1226 1763287\n+\n+NAME:C151\n+IONMODE:Negative\n+SPECTRUMTYPE:Centroid\n+RETENTIONTIME:394.87\n+Num Peaks:2\n+328.2481 11119434\n+329.2519 2068394\n+\n+NAME:C152\n+IONMODE:Negative\n+SPECTRUMTYPE:Centroid\n+RETENTIONTIME:385.78\n+Num Peaks:2\n+427.1607 2275086\n+409.1497 1369551\n+\n+NAME:C153\n+IONMODE:Negative\n+SPECTRUMTYPE:Centroid\n+RETENTIONTIME:401.39\n+Num Peaks:2\n+107.0557 2271180\n+197.1612 1286942\n+\n+NAME:C154\n+IONMODE:Negative\n+SPECTRUMTYPE:Centroid\n+RETENTIONTIME:388.72\n+Num Peaks:2\n+239.1276 1743749\n+286.9585 1645545\n+\n+NAME:C155\n+IONMODE:Negative\n+SPECTRUMTYPE:Centroid\n+RETENTIONTIME:373.67\n+Num Peaks:2\n+507.1617 6285930\n+508.1657 1535734\n+\n+NAME:C156\n+IONMODE:Negative\n+SPECTRUMTYPE:Centroid\n+RETENTIONTIME:378.37\n+Num Peaks:2\n+777.6928 4522421\n+257.2254 3302868\n+\n+NAME:C157\n+IONMODE:Negative\n+SPECTRUMTYPE:Centroid\n+RETENTIONTIME:473.08\n+Num Peaks:2\n+534.2949 13399261\n+267.6425 11780168\n+\n+NAME:C158\n+IONMODE:Negative\n+SPECTRUMTYPE:Centroid\n+RETENTIONTIME:508.15\n+Num Peaks:2\n+380.2992 5790633\n+423.2518 1386850\n+\n+NAME:C159\n+IONMODE:Negative\n+SPECTRUMTYPE:Centroid\n+RETENTIONTIME:471.89\n+Num Peaks:2\n+304.2357 21716257\n+306.1523 8327492\n+\n+NAME:C160\n+IONMODE:Negative\n+SPECTRUMTYPE:Centroid\n+RETENTIONTIME:465.45\n+Num Peaks:2\n+295.1974 20379534\n+193.1239 1274413\n+\n+NAME:C161\n+IONMODE:Negative\n+SPECTRUMTYPE:Centroid\n+RETENTIONTIME:488.7\n+Num Peaks:2\n+667.4214 3075774\n+1189.7766 2040172\n+\n+NAME:C162\n+IONMODE:Negative\n+SPECTRUMTYPE:Centroid\n+RETENTIONTIME:471.97\n+Num Peaks:2\n+393.2201 8389493\n+316.6601 7221684\n+\n+NAME:C163\n+IONMODE:Negative\n+SPECTRUMTYPE:Centroid\n+RETENTIONTIME:465.16\n+Num Peaks:2\n+431.3157 12163271\n+422.3267 4962906\n+\n+NAME:C164\n+IONMODE:Negative\n+SPECTRUMTYPE:Centroid\n+RETENTIONTIME:474.29\n+Num Peaks:2\n+398.3268 11918127\n+239.1779 8236995\n+\n+NAME:C165\n+IONMODE:Negative\n+SPECTRUMTYPE:Centroid\n+RETENTIONTIME:477.74\n+Num Peaks:2\n+307.15 1941191\n+249.1858 1576729\n+\n+NAME:C166\n+IONMODE:Negative\n+SPECTRUMTYPE:Centroid\n+RETENTIONTIME:494.51\n+Num Peaks:2\n+355.2846 54372680\n+373.2951 6108864\n+\n+NAME:C167\n+IONMODE:Negative\n+SPECTRUMTYPE:Centroid\n+RETENTIONTIME:497.67\n+Num Peaks:2\n+474.3486 2732000\n+649.4483 2434649\n+\n+NAME:C168\n+IONMODE:Negative\n+SPECTRUMTYPE:Centroid\n+RETENTIONTIME:498.02\n+Num Peaks:2\n+539.4163 5285541\n+459.2569 3550909\n+\n+NAME:C169\n+IONMODE:Negative\n+SPECTRUMTYPE:Centroid\n+RETENTIONTIME:492.45\n+Num Peaks:2\n+732.5452 4526953\n+733.5465 1043642\n+\n+NAME:C170\n+IONMODE:Negative\n+SPECTRUMTYPE:Centroid\n+RETENTIONTIME:497.3\n+Num Peaks:2\n+451.3631 6446370\n+450.3586 4210116\n+\n+NAME:C171\n+IONMODE:Negative\n+SPECTRUMTYPE:Centroid\n+RETENTIONTIME:467.81\n+Num Peaks:2\n+185.0776 5067455\n+200.203 1398415\n+\n+NAME:C172\n+IONMODE:Negative\n+SPECTRUMTYPE:Centroid\n+RETENTIONTIME:457.02\n+Num Peaks:2\n+263.2347 3933284\n+615.2633 1132491\n+\n+NAME:C173\n+IONMODE:Negative\n+SPECTRUMTYPE:Centroid\n+RETENTIONTIME:443.89\n+Num Peaks:2\n+370.2956 41596161\n+371.304 9966707\n+\n+NAME:C174\n+IONMODE:Negative\n+SPECTRUMTYPE:Centroid\n+RETENTIONTIME:438.81\n+Num Peaks:2\n+579.2938 6044865\n+330.2563 5274387\n+\n' |
| b |
| diff -r 000000000000 -r 36104baf75da test-data/test1_spec_abundance_xcms_1.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test1_spec_abundance_xcms_1.csv Tue Mar 22 16:09:16 2022 +0000 |
| b |
| b'@@ -0,0 +1,21 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449,8109156.36459577,5038951.1941462\n+"VT_160120_040",9934799.25263992,375836247.174509,2884373047.77547,7905301044.22145,35573132.2266095,560387015.661853,63984244.9827572,698385769.976211,4317099037.59284,151604425.143095,196659379.588214,42475863.9975798,63672587.4872164,11672577.2394498,957650455.061172,38277672.0418209,14663135.0807262,193764912.185701,21847421.2370331,1776491710.18456,219384517.34675,8134547.31426432,67031405.4295678,86128351.9530911,169094486.796142,11927291.612244,17099735.0114863,56987972.8270169,184617430.189418,6380565.92562305,49799157.9983667,39339741.7221688,67730803.6121619,158088964.700247,77784470.41518,7261968.14694198,19366117.0357642,575967487.14093,31228350.4237222,28749021.6606678,114152953.620449,32837476.001478,32313689.6082591,49037900.4597961,47923935.0904822,11920541.5503579,45302490.2670043,8009917.67162212,25676037.4957024,10215928.2063743,19784232.0977507,30225996.4107507,20393856.5020287,13619724.8886577,4799552.82620209,296424678.235081,7062029.55375609,48848209.3559762,101323813.923856,4439500.12796503,2220358.88866602,35246869.4741919,49710713.0864728,121727321,46950407.9311092,27150702.1783594,19474544.8078591,132245080.214264,36280741.4248055,5285185.41341366,600016.989319636,1418448.33573977,159474509.725069,13110398.8393007,4999824.64133883,26139820.5030213,26213265.2529846,8124057.89988214,21897039.2704881,24453471.1284649,4261685.53357104,2198442.4682436,25298771.4410718,8204391.11995749,38359981.2263799,14381181.0834863,12470759.0110495,4513799.42038729,8276453.11275374,342507775.798005,31433715.2319776,7575385.88884809,2902017.66296793,123409718.476101,7465071.31714924,6297211.26647415,706892.229336319,4789495.94318605,1230699.88256605,123461259.759045,1622745.51087538,3927917.76946473,2123307.99652869,3828533.09446011,11846880.990395,13168395.4970154,8780619.83074943,63635250.2252369,5330271.72591704,91258286.9807226,9656198.56632925,46162652.2583335,4149817.72577566,8854465.37429845,1931534.82177527,3401749.74453956,3095370.84783698,9644818.34360461,1368678.67459345,17234636.0601444,2785373.04929555,9881934.42695221,12568959.7693456,21100358.1920544,5867219.29185353,236932876.729115,2904846.50728148,8719937.07549249,4228207.86925475,3624635.7453292,77719840.4794496,2466026.78548825,220712642.88383,778968494.028449,18211869.4106139,3552955.67831798,3090117.07708974,7305928.87017414,4469944.59281558,7921992.1109694,1586368.23328241,4885515.40764741,9866157.50261439,41987649.9280603,859018.580344819,855402.855651353,1958863.68711785,981476.935521276,9086609.86176663,3588768.7633977,6136277.45781362,1526970.58621673,2072417.0660832,1923374.88726624,1526197.52507684,4304648.56079495,13003904.0929066,4329421.11585443,5397418.05431216,18454516.2047903,2666788.32880361,7374046.62878731,11122827.1903071,5168033.64186004,1765658.4883592,49322159.1546131,2392087.59185383,4399240.41858028,3498005.25636277,5396857.46348111,3048506.72264773,4414135.34455428,8167061.84351309,5138026.01743978\n' |
| b |
| diff -r 000000000000 -r 36104baf75da test-data/test1_xcmsObj_1.rdata.xcms.fillpeaks |
| b |
| Binary file test-data/test1_xcmsObj_1.rdata.xcms.fillpeaks has changed |
| b |
| diff -r 000000000000 -r 36104baf75da test-data/test2_fill_xcms_2.msp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test2_fill_xcms_2.msp Tue Mar 22 16:09:16 2022 +0000 |
| b |
| b'@@ -0,0 +1,11378 @@\n+NAME:C001\n+IONMODE:Negative\n+SPECTRUMTYPE:Centroid\n+RETENTIONTIME:36.79\n+Num Peaks:96\n+216.9231 23812075\n+264.853 15633213\n+90.9768 9937629\n+332.8403 6700746\n+334.8374 6244676\n+390.799 5989314\n+458.7867 5380038\n+578.698 4329004\n+520.7398 4155104\n+752.572 3475955\n+586.7298 3473848\n+462.7808 3325264\n+742.5445 3292214\n+518.7427 3078744\n+149.9931 3023780\n+694.6141 2816970\n+574.7039 2812261\n+684.5851 2804751\n+628.6241 2771595\n+792.4708 2747070\n+744.5417 2723035\n+790.4735 2559104\n+750.5749 2551725\n+754.5691 2517690\n+692.6169 2308865\n+682.5881 2302495\n+516.7004 2288712\n+740.5475 2194363\n+584.7325 2155658\n+686.5823 2152071\n+704.6429 2046793\n+812.5286 2031345\n+410.8565 2028964\n+632.662 1690731\n+580.695 1665145\n+696.6111 1635271\n+672.5604 1613164\n+584.6431 1578515\n+572.6171 1481717\n+868.4898 1415037\n+746.5386 1380123\n+818.5633 1328616\n+822.5576 1305232\n+870.4868 1286702\n+858.4605 1188870\n+860.4575 1149101\n+612.6039 1118509\n+630.5753 1020003\n+730.5184 1018850\n+756.566 1011846\n+918.4172 1006595\n+928.4461 1002603\n+576.6112 1002293\n+926.4493 966734\n+642.6013 959842\n+632.5722 941075\n+678.5502 910659\n+688.6199 859498\n+736.5096 843054\n+866.4923 825066\n+938.4754 824955\n+986.4041 813458\n+876.5214 756349\n+680.5909 752164\n+758.5169 723754\n+862.4542 649096\n+920.4142 647500\n+796.5987 629428\n+808.4447 615895\n+760.5144 595038\n+908.388 594520\n+547.8013 585412\n+806.4706 573832\n+698.608 572969\n+826.5055 539012\n+644.5984 527246\n+856.6163 527245\n+864.6488 497980\n+1036.3322 450227\n+766.5492 434850\n+824.5546 433320\n+924.452 422642\n+974.378 422061\n+738.7031 413993\n+910.3853 409230\n+850.4283 396836\n+626.8091 394850\n+798.658 388593\n+1052.3964 374849\n+934.481 359173\n+810.442 352271\n+433.8803 317792\n+906.3909 291445\n+750.4853 267660\n+812.7097 238323\n+1032.338 203600\n+\n+NAME:C002\n+IONMODE:Negative\n+SPECTRUMTYPE:Centroid\n+RETENTIONTIME:466.7\n+Num Peaks:71\n+167.0342 192495571\n+121.0286 119397402\n+150.0269 106175070\n+280.2355 53172038\n+184.0736 28613720\n+611.2297 17050507\n+302.1447 13015985\n+190.0502 11272231\n+889.3815 10408263\n+553.7864 9304105\n+122.0319 8899166\n+151.0278 7462020\n+579.2934 7459443\n+612.2331 6527969\n+890.3849 5983244\n+554.2867 5677698\n+217.9902 5556243\n+828.4108 5551911\n+261.9801 4715799\n+302.3058 4575165\n+151.0303 3762442\n+303.0065 3458540\n+152.007 2798727\n+601.2757 2712582\n+829.4139 2666373\n+891.3854 2537054\n+545.8001 2440233\n+426.7093 2412441\n+580.2967 2382531\n+163.515 2236547\n+554.7881 2115421\n+415.7124 2081224\n+219.9906 1917349\n+447.3474 1857827\n+879.4262 1631029\n+818.4551 1469116\n+499.1057 1333390\n+798.4789 1255220\n+332.1158 1160058\n+613.2346 1146563\n+169.0384 1139653\n+373.1422 994095\n+553.2882 965085\n+654.2573 944823\n+342.1678 902406\n+654.3889 813341\n+259.0169 796005\n+371.1303 791956\n+323.1233 786527\n+602.279 713112\n+880.4289 710492\n+892.3867 693024\n+828.9124 689362\n+921.0322 680433\n+569.2412 651203\n+261.0831 641763\n+652.2336 624935\n+873.4089 595710\n+331.1188 590719\n+221.986 585108\n+189.9953 549589\n+246.0078 493212\n+887.386 475283\n+673.3656 473402\n+303.148 463817\n+888.3867 456652\n+662.3758 408625\n+135.0636 408505\n+152.0311 366061\n+334.1113 306436\n+416.1353 303481\n+\n+NAME:C003\n+IONMODE:Negative\n+SPECTRUMTYPE:Centroid\n+RETENTIONTIME:40.37\n+Num Peaks:57\n+86.0966 39898045\n+118.0653 20097234\n+150.9771 16674266\n+163.1098 15306868\n+409.1839 13252151\n+365.1575 11918350\n+146.0603 9993830\n+144.0811 9711210\n+481.2626 9052124\n+388.7124 8370798\n+150.0587 7263844\n+212.8394 6186731\n+194.0226 5775623\n+148.1101 5397479\n+165.0549 5120564\n+174.1856 5078184\n+525.2893 4681728\n+121.0843 4321800\n+217.105 4260545\n+348.9904 4187255\n+462.6453 4125319\n+206.1009 3834475\n+166.9511 3210588\n+117.0575 2977341\n+180.9901 2802727\n+136.0065 2726754\n+87.1 2350394\n+350.1359 2252754\n+258.1308 2244142\n+480.6163 2017624\n+285.1004 1956381\n+454.2136 1887161\n+393.1201 1844775\n+482.266 1785595\n+123.0442 1779221\n+569.3147 1751821\n+560.7189 1672197\n+102.0551 1540732\n+640.5146 1517440\n+379.0453 1432795\n+90.0551 1421488\n+812.3927 987883\n+249.9989 814727\n+526.2926 756951'..b' Peaks:2\n+494.8125 1624052\n+285.2581 408043\n+\n+NAME:C918\n+IONMODE:Negative\n+SPECTRUMTYPE:Centroid\n+RETENTIONTIME:375.07\n+Num Peaks:2\n+282.9108 1509467\n+403.321 175994\n+\n+NAME:C919\n+IONMODE:Negative\n+SPECTRUMTYPE:Centroid\n+RETENTIONTIME:372.64\n+Num Peaks:2\n+253.0976 2752671\n+535.1935 558326\n+\n+NAME:C920\n+IONMODE:Negative\n+SPECTRUMTYPE:Centroid\n+RETENTIONTIME:378.15\n+Num Peaks:2\n+376.187 80026\n+457.2916 44959\n+\n+NAME:C921\n+IONMODE:Negative\n+SPECTRUMTYPE:Centroid\n+RETENTIONTIME:384.97\n+Num Peaks:2\n+351.2377 84299\n+382.2592 63782\n+\n+NAME:C922\n+IONMODE:Negative\n+SPECTRUMTYPE:Centroid\n+RETENTIONTIME:382.01\n+Num Peaks:2\n+255.2112 2623406\n+342.1737 51293\n+\n+NAME:C923\n+IONMODE:Negative\n+SPECTRUMTYPE:Centroid\n+RETENTIONTIME:380.77\n+Num Peaks:2\n+247.1333 782460\n+360.0898 83304\n+\n+NAME:C924\n+IONMODE:Negative\n+SPECTRUMTYPE:Centroid\n+RETENTIONTIME:391.37\n+Num Peaks:2\n+275.8893 1374393\n+231.1595 45385\n+\n+NAME:C925\n+IONMODE:Negative\n+SPECTRUMTYPE:Centroid\n+RETENTIONTIME:388.83\n+Num Peaks:2\n+494.8126 1378128\n+281.2268 251187\n+\n+NAME:C926\n+IONMODE:Negative\n+SPECTRUMTYPE:Centroid\n+RETENTIONTIME:403.88\n+Num Peaks:2\n+240.2326 912540\n+270.2432 59873\n+\n+NAME:C927\n+IONMODE:Negative\n+SPECTRUMTYPE:Centroid\n+RETENTIONTIME:405.16\n+Num Peaks:2\n+236.2377 335918\n+365.1705 94732\n+\n+NAME:C928\n+IONMODE:Negative\n+SPECTRUMTYPE:Centroid\n+RETENTIONTIME:405.59\n+Num Peaks:2\n+158.1543 14432294\n+254.2483 240394\n+\n+NAME:C929\n+IONMODE:Negative\n+SPECTRUMTYPE:Centroid\n+RETENTIONTIME:405.12\n+Num Peaks:2\n+273.1349 246131\n+369.2041 66038\n+\n+NAME:C930\n+IONMODE:Negative\n+SPECTRUMTYPE:Centroid\n+RETENTIONTIME:420.81\n+Num Peaks:2\n+366.2641 338849\n+229.1803 53773\n+\n+NAME:C931\n+IONMODE:Negative\n+SPECTRUMTYPE:Centroid\n+RETENTIONTIME:420.04\n+Num Peaks:2\n+414.3331 124761\n+455.2291 74434\n+\n+NAME:C932\n+IONMODE:Negative\n+SPECTRUMTYPE:Centroid\n+RETENTIONTIME:415.45\n+Num Peaks:2\n+526.2658 111387\n+407.3008 97465\n+\n+NAME:C933\n+IONMODE:Negative\n+SPECTRUMTYPE:Centroid\n+RETENTIONTIME:389.56\n+Num Peaks:2\n+262.1136 902163\n+279.2048 174974\n+\n+NAME:C934\n+IONMODE:Negative\n+SPECTRUMTYPE:Centroid\n+RETENTIONTIME:397.27\n+Num Peaks:2\n+139.9882 14598109\n+451.3636 130810\n+\n+NAME:C935\n+IONMODE:Negative\n+SPECTRUMTYPE:Centroid\n+RETENTIONTIME:306.2\n+Num Peaks:2\n+303.8841 9644530\n+490.818 144394\n+\n+NAME:C936\n+IONMODE:Negative\n+SPECTRUMTYPE:Centroid\n+RETENTIONTIME:291.88\n+Num Peaks:2\n+303.8841 4770525\n+149.9563 2871279\n+\n+NAME:C937\n+IONMODE:Negative\n+SPECTRUMTYPE:Centroid\n+RETENTIONTIME:273.59\n+Num Peaks:2\n+303.8841 9507576\n+275.8892 2233507\n+\n+NAME:C938\n+IONMODE:Negative\n+SPECTRUMTYPE:Centroid\n+RETENTIONTIME:264.11\n+Num Peaks:2\n+293.0983 29627006\n+490.818 831879\n+\n+NAME:C939\n+IONMODE:Negative\n+SPECTRUMTYPE:Centroid\n+RETENTIONTIME:261.76\n+Num Peaks:2\n+186.9566 11812445\n+149.9563 4049777\n+\n+NAME:C940\n+IONMODE:Negative\n+SPECTRUMTYPE:Centroid\n+RETENTIONTIME:242.51\n+Num Peaks:2\n+148.9773 5819004\n+303.8841 4733851\n+\n+NAME:C941\n+IONMODE:Negative\n+SPECTRUMTYPE:Centroid\n+RETENTIONTIME:246.1\n+Num Peaks:2\n+241.8843 2476354\n+354.1273 898357\n+\n+NAME:C942\n+IONMODE:Negative\n+SPECTRUMTYPE:Centroid\n+RETENTIONTIME:243.17\n+Num Peaks:2\n+158.9616 47753531\n+372.1588 496137\n+\n+NAME:C943\n+IONMODE:Negative\n+SPECTRUMTYPE:Centroid\n+RETENTIONTIME:227.01\n+Num Peaks:2\n+354.1273 577096\n+372.1588 506473\n+\n+NAME:C944\n+IONMODE:Negative\n+SPECTRUMTYPE:Centroid\n+RETENTIONTIME:231.49\n+Num Peaks:2\n+171.9932 10387198\n+176.9722 7012941\n+\n+NAME:C945\n+IONMODE:Negative\n+SPECTRUMTYPE:Centroid\n+RETENTIONTIME:233.11\n+Num Peaks:2\n+149.9563 6680326\n+156.9663 4658486\n+\n+NAME:C946\n+IONMODE:Negative\n+SPECTRUMTYPE:Centroid\n+RETENTIONTIME:197.8\n+Num Peaks:2\n+149.9563 6365632\n+199.9882 3301364\n+\n+NAME:C947\n+IONMODE:Negative\n+SPECTRUMTYPE:Centroid\n+RETENTIONTIME:190.19\n+Num Peaks:2\n+303.884 6200176\n+171.9932 5842204\n+\n+NAME:C948\n+IONMODE:Negative\n+SPECTRUMTYPE:Centroid\n+RETENTIONTIME:201.67\n+Num Peaks:2\n+293.0983 68432527\n+186.9566 7116605\n+\n+NAME:C949\n+IONMODE:Negative\n+SPECTRUMTYPE:Centroid\n+RETENTIONTIME:209.56\n+Num Peaks:2\n+199.9883 2497500\n+156.9663 1804531\n+\n' |
| b |
| diff -r 000000000000 -r 36104baf75da test-data/test2_sample_metadata_xcms_2.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test2_sample_metadata_xcms_2.csv Tue Mar 22 16:09:16 2022 +0000 |
| b |
| @@ -0,0 +1,6 @@ +sample_name,class,sampleType,injectionOrder,batch +VT_160120_002,sample,sample,1,1 +VT_160120_004,sample,sample,2,1 +VT_160120_006,sample,sample,3,1 +VT_160120_008,sample,sample,4,1 +VT_160120_010,sample,sample,5,1 |
| b |
| diff -r 000000000000 -r 36104baf75da test-data/test2_spec_abundance_xcms_2.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test2_spec_abundance_xcms_2.csv Tue Mar 22 16:09:16 2022 +0000 |
| b |
| b'@@ -0,0 +1,6 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|
| b |
| diff -r 000000000000 -r 36104baf75da test-data/test2_xcmsObj_2.rdata.xcms.fillpeaks |
| b |
| Binary file test-data/test2_xcmsObj_2.rdata.xcms.fillpeaks has changed |
| b |
| diff -r 000000000000 -r 36104baf75da test-data/test3_csv_test-input_1_2.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test3_csv_test-input_1_2.csv Tue Mar 22 16:09:16 2022 +0000 |
| b |
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|
| b |
| diff -r 000000000000 -r 36104baf75da test-data/test3_spec_abundance_csv_1.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test3_spec_abundance_csv_1.csv Tue Mar 22 16:09:16 2022 +0000 |
| b |
| @@ -0,0 +1,4 @@ +"","C01","C02","C03","C04","C05","C06","C07","C08","C09","C10","C11","C12","C13","C14","C15","C16","C17","C18","C19","C20","C21","C22" +"dataset_10908",1143359.6024874,14232152.476587,50449.9418344623,705676.707142857,37132.3539979397,29822.3430533531,48305.5183116056,16320.5463588464,233029.800680246,47298.0528173405,34827.0153828901,24530.3375165206,64864.9659048501,92746.0557178936,398852.491270866,20462.4444316982,315657.07173388,18224.8801651832,119901.384914687,112084.028638642,461198.718995128,10125.6569474277 +"dataset_10909",1143359.6024874,14232152.476587,50449.9418344623,705676.707142857,37132.3539979397,29822.3430533531,48305.5183116056,16320.5463588464,233029.800680246,47298.0528173405,34827.0153828901,24530.3375165206,64864.9659048501,92746.0557178936,398852.491270866,20462.4444316982,315657.07173388,18224.8801651832,119901.384914687,112084.028638642,461198.718995128,10125.6569474277 +"dataset_10910",1143359.6024874,14232152.476587,50449.9418344623,705676.707142857,37132.3539979397,29822.3430533531,48305.5183116056,16320.5463588464,233029.800680246,47298.0528173405,34827.0153828901,24530.3375165206,64864.9659048501,92746.0557178936,398852.491270866,20462.4444316982,315657.07173388,18224.8801651832,119901.384914687,112084.028638642,461198.718995128,10125.6569474277 |
| b |
| diff -r 000000000000 -r 36104baf75da test-data/test3_spectra_csv_1.msp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test3_spectra_csv_1.msp Tue Mar 22 16:09:16 2022 +0000 |
| b |
| @@ -0,0 +1,335 @@ +NAME:C01 +IONMODE:Negative +SPECTRUMTYPE:Centroid +RETENTIONTIME:90.26 +Num Peaks:24 +478.194549560547 2314271 +834.349975585938 606824 +537.164489746094 393358 +447.174102783203 283147 +833.342163085938 238978 +519.137573242188 215160 +684.278930664062 197800 +443.162109375 156187 +505.162445068359 143553 +516.154113769531 135057 +511.189483642578 112230 +758.220520019531 97526 +431.084686279297 88381 +486.089019775391 65106 +675.038391113281 50436 +832.335144042969 48360 +613.180694580078 47315 +594.09521484375 45866 +448.116226196289 45744 +415.051574707031 43641 +434.881164550781 36371 +512.104309082031 32526 +293.024536132812 24937 +989.4306640625 13240 + +NAME:C02 +IONMODE:Negative +SPECTRUMTYPE:Centroid +RETENTIONTIME:88.55 +Num Peaks:19 +477.197784423828 18001838 +530.115020751953 1384864 +536.1640625 804471 +531.120971679688 693764 +528.099395751953 489327 +499.1416015625 316608 +610.183410644531 288468 +532.111907958984 226354 +538.161437988281 198517 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| b |
| diff -r 000000000000 -r 36104baf75da test-data/test4_sample_metadata_csv_2.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test4_sample_metadata_csv_2.csv Tue Mar 22 16:09:16 2022 +0000 |
| b |
| @@ -0,0 +1,4 @@ +sample_name,class,sampleType,injectionOrder,batch +dataset_10908,sample,sample,1,1 +dataset_10909,sample,sample,2,1 +dataset_10910,sample,sample,3,1 |
| b |
| diff -r 000000000000 -r 36104baf75da test-data/test4_spec_abundance_csv_2.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test4_spec_abundance_csv_2.csv Tue Mar 22 16:09:16 2022 +0000 |
| b |
| @@ -0,0 +1,4 @@ +"","C01","C02","C03","C04","C05","C06","C07","C08","C09","C10","C11","C12","C13","C14","C15","C16","C17","C18","C19","C20","C21","C22","C23","C24","C25","C26","C27","C28","C29","C30","C31","C32","C33","C34","C35","C36","C37","C38" +"dataset_10908",15486747.5366514,705676.707142857,29822.3430533531,224421.528087479,240472.056093119,83802.7176826829,53891.3450571771,46940.0774103402,22283.2365363616,398852.491270866,16487.928248967,1983470.1118411,11998.5253787137,55783.8355817233,185478.847522515,315657.07173388,39349.4112699936,21728.8824232737,32441.4747147792,119901.384914687,461198.718995128,19834.4473795901,43602.3586534436,31889.6464337142,68360.3997127846,21854.49991187,1073398.26666055,156861.055191184,493341.849474475,16176.4044227296,10125.6569474277,37890.4782477985,29454.7192721113,66717.3172710142,4822.46628554095,24485.0599767888,21288.8896720112,103775.906887161 +"dataset_10909",15486747.5366514,705676.707142857,29822.3430533531,224421.528087479,240472.056093119,83802.7176826829,53891.3450571771,46940.0774103402,22283.2365363616,398852.491270866,16487.928248967,1983470.1118411,11998.5253787137,55783.8355817233,185478.847522515,315657.07173388,39349.4112699936,21728.8824232737,32441.4747147792,119901.384914687,461198.718995128,19834.4473795901,43602.3586534436,31889.6464337142,68360.3997127846,21854.49991187,1073398.26666055,156861.055191184,493341.849474475,16176.4044227296,10125.6569474277,37890.4782477985,29454.7192721113,66717.3172710142,4822.46628554095,24485.0599767888,21288.8896720112,103775.906887161 +"dataset_10910",15486747.5366514,705676.707142857,29822.3430533531,224421.528087479,240472.056093119,83802.7176826829,53891.3450571771,46940.0774103402,22283.2365363616,398852.491270866,16487.928248967,1983470.1118411,11998.5253787137,55783.8355817233,185478.847522515,315657.07173388,39349.4112699936,21728.8824232737,32441.4747147792,119901.384914687,461198.718995128,19834.4473795901,43602.3586534436,31889.6464337142,68360.3997127846,21854.49991187,1073398.26666055,156861.055191184,493341.849474475,16176.4044227296,10125.6569474277,37890.4782477985,29454.7192721113,66717.3172710142,4822.46628554095,24485.0599767888,21288.8896720112,103775.906887161 |
| b |
| diff -r 000000000000 -r 36104baf75da test-data/test4_spectra_csv_2.msp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test4_spectra_csv_2.msp Tue Mar 22 16:09:16 2022 +0000 |
| b |
| b'@@ -0,0 +1,430 @@\n+NAME:C01\n+IONMODE:Negative\n+SPECTRUMTYPE:Centroid\n+RETENTIONTIME:88.6\n+Num Peaks:14\n+477.197784423828 18001838\n+536.1640625 804471\n+531.120971679688 693764\n+528.099395751953 489327\n+610.183410644531 288468\n+538.161437988281 198517\n+612.181274414062 105204\n+500.104736328125 99498\n+429.088195800781 94304\n+520.137969970703 70949\n+539.161560058594 55029\n+408.10986328125 54777\n+698.25390625 35262\n+504.106689453125 33017\n+\n+NAME:C02\n+IONMODE:Negative\n+SPECTRUMTYPE:Centroid\n+RETENTIONTIME:91.9\n+Num Peaks:13\n+445.118927001953 1316181\n+521.134979248047 404791\n+446.119018554688 358676\n+623.21337890625 312967\n+239.105407714844 171842\n+685.273254394531 115852\n+699.272094726562 114712\n+522.197998046875 92722\n+503.178649902344 62452\n+413.361190795898 61792\n+668.175964355469 55513\n+614.219604492188 29983\n+403.584045410156 19485\n+\n+NAME:C03\n+IONMODE:Negative\n+SPECTRUMTYPE:Centroid\n+RETENTIONTIME:85.48\n+Num Peaks:11\n+551.216796875 45171\n+425.929626464844 42426\n+550.216369628906 30942\n+492.120056152344 30281\n+540.15869140625 28244\n+614.177856445312 20117\n+772.270812988281 19172\n+552.213073730469 18758\n+505.085510253906 18347\n+662.440002441406 13176\n+832.23828125 9696\n+\n+NAME:C04\n+IONMODE:Negative\n+SPECTRUMTYPE:Centroid\n+RETENTIONTIME:89.59\n+Num Peaks:10\n+760.359802246094 373922\n+491.182922363281 283047\n+761.362854003906 165128\n+616.898010253906 162997\n+740.749694824219 70004\n+420.318115234375 69759\n+439.828140258789 64799\n+700.2734375 40831\n+587.022033691406 36848\n+449.113311767578 33160\n+\n+NAME:C05\n+IONMODE:Negative\n+SPECTRUMTYPE:Centroid\n+RETENTIONTIME:90.71\n+Num Peaks:10\n+537.164489746094 393358\n+447.174102783203 283147\n+431.084686279297 88381\n+486.089019775391 65106\n+675.038391113281 50436\n+832.335144042969 48360\n+594.09521484375 45866\n+434.881164550781 36371\n+512.104309082031 32526\n+293.024536132812 24937\n+\n+NAME:C06\n+IONMODE:Negative\n+SPECTRUMTYPE:Centroid\n+RETENTIONTIME:87.25\n+Num Peaks:9\n+463.145568847656 162038\n+593.156372070312 58861\n+430.887084960938 49274\n+453.965087890625 36928\n+430.087738037109 36101\n+625.235046386719 34998\n+436.341064453125 31148\n+595.154052734375 28289\n+417.375946044922 17005\n+\n+NAME:C07\n+IONMODE:Negative\n+SPECTRUMTYPE:Centroid\n+RETENTIONTIME:81.16\n+Num Peaks:8\n+227.950347900391 97459\n+759.220153808594 36500\n+612.164733886719 33669\n+761.218078613281 31370\n+459.171142578125 26823\n+467.861480712891 21247\n+407.919708251953 9997\n+587.341857910156 7956\n+\n+NAME:C08\n+IONMODE:Negative\n+SPECTRUMTYPE:Centroid\n+RETENTIONTIME:76.47\n+Num Peaks:7\n+667.174713134766 76576\n+781.87451171875 38252\n+416.372436523438 28313\n+505.085510253906 24583\n+760.217834472656 21499\n+587.369018554688 5230\n+741.193237304688 2118\n+\n+NAME:C09\n+IONMODE:Negative\n+SPECTRUMTYPE:Centroid\n+RETENTIONTIME:74.76\n+Num Peaks:7\n+675.246398925781 28976\n+402.194549560547 27974\n+1092.14379882812 22803\n+566.138488769531 21976\n+832.238098144531 14210\n+417.786468505859 12908\n+687.198364257812 9851\n+\n+NAME:C10\n+IONMODE:Negative\n+SPECTRUMTYPE:Centroid\n+RETENTIONTIME:84.07\n+Num Peaks:7\n+120.587036132812 613913\n+136.655395507812 421655\n+145.905563354492 277238\n+156.139678955078 223228\n+167.501968383789 177538\n+742.193054199219 42273\n+432.884124755859 40010\n+\n+NAME:C11\n+IONMODE:Negative\n+SPECTRUMTYPE:Centroid\n+RETENTIONTIME:66.18\n+Num Peaks:7\n+403.304351806641 24861\n+429.087951660156 17764\n+685.202392578125 16309\n+675.249084472656 10824\n+698.253234863281 6015\n+595.154296875 4898\n+593.15576171875 3648\n+\n+NAME:C12\n+IONMODE:Negative\n+SPECTRUMTYPE:Centroid\n+RETENTIONTIME:89.56\n+Num Peaks:6\n+478.194549560547 2314271\n+684.278930664062 197800\n+511.189483642578 112230\n+613.180694580078 47315\n+415.051574707031 43641\n+989.4306640625 13240\n+\n+NAME:C13\n+IONMODE:Negative\n+SPECTRUMTYPE:Centroid\n+RETENTIONTIME:67.75\n+Num Peaks:6\n+462.145599365234 14910\n+700.250854492188 14781\n+917.771545410156 5270\n+414.850494384766 4156\n+503.106567382812 1483\n+447.116027832031 74\n+\n+NAME:C14\n+IONMODE:Negative\n+SPECTRUMTYPE:Centroid\n+RETENTIONTIME:93.71\n+Num Peaks:5\n+173.45786285400'..b'UMTYPE:Centroid\n+RETENTIONTIME:90.22\n+Num Peaks:5\n+833.342163085938 238978\n+519.137573242188 215160\n+443.162109375 156187\n+505.162445068359 143553\n+758.220520019531 97526\n+\n+NAME:C16\n+IONMODE:Negative\n+SPECTRUMTYPE:Centroid\n+RETENTIONTIME:82.92\n+Num Peaks:5\n+128.228332519531 430253\n+180.131500244141 193476\n+248.229713439941 63115\n+511.470672607422 18502\n+516.242248535156 14020\n+\n+NAME:C17\n+IONMODE:Negative\n+SPECTRUMTYPE:Centroid\n+RETENTIONTIME:55.41\n+Num Peaks:5\n+436.340972900391 61681\n+699.252685546875 23925\n+1092.04553222656 14864\n+490.176452636719 14317\n+407.878967285156 9625\n+\n+NAME:C18\n+IONMODE:Negative\n+SPECTRUMTYPE:Centroid\n+RETENTIONTIME:58.73\n+Num Peaks:5\n+420.317749023438 34434\n+587.398254394531 15861\n+675.74951171875 11400\n+833.238525390625 10189\n+917.472229003906 7875\n+\n+NAME:C19\n+IONMODE:Negative\n+SPECTRUMTYPE:Centroid\n+RETENTIONTIME:62.38\n+Num Peaks:5\n+833.238525390625 48408\n+516.263549804688 22053\n+540.158386230469 20249\n+772.271392822266 15168\n+551.216766357422 1115\n+\n+NAME:C20\n+IONMODE:Negative\n+SPECTRUMTYPE:Centroid\n+RETENTIONTIME:87.24\n+Num Peaks:4\n+464.142517089844 150272\n+626.232360839844 33874\n+759.220581054688 9214\n+566.138305664062 5506\n+\n+NAME:C21\n+IONMODE:Negative\n+SPECTRUMTYPE:Centroid\n+RETENTIONTIME:90.44\n+Num Peaks:4\n+462.145843505859 529069\n+433.177734375 509139\n+759.291687011719 131728\n+661.706604003906 40178\n+\n+NAME:C22\n+IONMODE:Negative\n+SPECTRUMTYPE:Centroid\n+RETENTIONTIME:56.75\n+Num Peaks:4\n+625.236511230469 26556\n+663.369201660156 19207\n+687.198425292969 15104\n+761.218200683594 8084\n+\n+NAME:C23\n+IONMODE:Negative\n+SPECTRUMTYPE:Centroid\n+RETENTIONTIME:54.55\n+Num Peaks:4\n+465.142272949219 63482\n+430.08708190918 34413\n+564.195281982422 23456\n+417.375671386719 20361\n+\n+NAME:C24\n+IONMODE:Negative\n+SPECTRUMTYPE:Centroid\n+RETENTIONTIME:69.19\n+Num Peaks:4\n+834.235961914062 43046\n+684.201171875 32028\n+490.177062988281 18688\n+612.180358886719 11909\n+\n+NAME:C25\n+IONMODE:Negative\n+SPECTRUMTYPE:Centroid\n+RETENTIONTIME:73.5\n+Num Peaks:3\n+476.197448730469 80876\n+742.190856933594 11128\n+540.158752441406 6021\n+\n+NAME:C26\n+IONMODE:Negative\n+SPECTRUMTYPE:Centroid\n+RETENTIONTIME:93.72\n+Num Peaks:3\n+194.399047851562 28933\n+328.256500244141 16755\n+297.833831787109 10742\n+\n+NAME:C27\n+IONMODE:Negative\n+SPECTRUMTYPE:Centroid\n+RETENTIONTIME:88.75\n+Num Peaks:3\n+530.115020751953 1384864\n+499.1416015625 316608\n+532.111907958984 226354\n+\n+NAME:C28\n+IONMODE:Negative\n+SPECTRUMTYPE:Centroid\n+RETENTIONTIME:91.72\n+Num Peaks:3\n+611.183166503906 203950\n+687.272521972656 46205\n+444.403594970703 37684\n+\n+NAME:C29\n+IONMODE:Negative\n+SPECTRUMTYPE:Centroid\n+RETENTIONTIME:90.22\n+Num Peaks:3\n+834.349975585938 606824\n+516.154113769531 135057\n+448.116226196289 45744\n+\n+NAME:C30\n+IONMODE:Negative\n+SPECTRUMTYPE:Centroid\n+RETENTIONTIME:78.53\n+Num Peaks:3\n+485.896362304688 20365\n+442.819763183594 13059\n+564.195129394531 12651\n+\n+NAME:C31\n+IONMODE:Negative\n+SPECTRUMTYPE:Centroid\n+RETENTIONTIME:79.66\n+Num Peaks:3\n+209.655685424805 13679\n+564.2421875 5038\n+402.435363769531 3435\n+\n+NAME:C32\n+IONMODE:Negative\n+SPECTRUMTYPE:Centroid\n+RETENTIONTIME:63.63\n+Num Peaks:3\n+686.199340820312 50825\n+989.671630859375 21036\n+674.156646728516 11456\n+\n+NAME:C33\n+IONMODE:Negative\n+SPECTRUMTYPE:Centroid\n+RETENTIONTIME:71.4\n+Num Peaks:3\n+594.22265625 33704\n+457.247741699219 27928\n+587.15966796875 3943\n+\n+NAME:C34\n+IONMODE:Negative\n+SPECTRUMTYPE:Centroid\n+RETENTIONTIME:77.39\n+Num Peaks:2\n+420.330932617188 73324\n+918.001159667969 8291\n+\n+NAME:C35\n+IONMODE:Negative\n+SPECTRUMTYPE:Centroid\n+RETENTIONTIME:74.73\n+Num Peaks:2\n+625.235534667969 5676\n+430.086853027344 3396\n+\n+NAME:C36\n+IONMODE:Negative\n+SPECTRUMTYPE:Centroid\n+RETENTIONTIME:65.19\n+Num Peaks:2\n+610.182739257812 25206\n+624.235229492188 23719\n+\n+NAME:C37\n+IONMODE:Negative\n+SPECTRUMTYPE:Centroid\n+RETENTIONTIME:67.85\n+Num Peaks:2\n+522.2021484375 25695\n+758.219665527344 10937\n+\n+NAME:C38\n+IONMODE:Negative\n+SPECTRUMTYPE:Centroid\n+RETENTIONTIME:70.12\n+Num Peaks:2\n+419.314514160156 115416\n+550.216186523438 15160\n+\n' |