Mercurial > repos > recetox > recetox_aplcms_extract_features
changeset 0:d78dc8992e5a draft default tip
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Fri Jun 10 10:17:01 2022 +0000 @@ -0,0 +1,247 @@ +<macros> + <token name="@TOOL_VERSION@">0.9.4</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="4.1.0">r-base</requirement> + <requirement type="package" version="4.0.1">r-arrow</requirement> + <requirement type="package" version="@TOOL_VERSION@">r-recetox-aplcms</requirement> + <requirement type="package" version="1.0.7">r-dplyr</requirement> + </requirements> + </xml> + + <xml name="creator"> + <creator> + <person + givenName="Maksym" + familyName="Skoryk" + url="https://github.com/maximskorik" + identifier="0000-0003-2056-8018" /> + <person + givenName="Matej" + familyName="Troják" + url="https://github.com/xtrojak" + identifier="0000-0003-0841-2707" /> + <person + givenName="Martin" + familyName="Čech" + url="https://github.com/martenson" + identifier="0000-0002-9318-1781" /> + <person + givenName="Jiří" + familyName="Novotný" + url="https://github.com/xtracko" + identifier="0000-0001-5449-3523" /> + <organization + url="https://www.recetox.muni.cz/" + email="GalaxyToolsDevelopmentandDeployment@space.muni.cz" + name="RECETOX MUNI"/> + </creator> + </xml> + + <xml name="inputs"> + <inputs> + <param name="files" type="data" format="mzdata,mzml,mzxml,netcdf" multiple="true" min="3" label="data" + help="Mass spectrometry files for peak extraction." /> + <yield /> + </inputs> + </xml> + + <xml name="history_db"> + <param name="known_table" type="data" format="parquet" label="known_table" + help="A data table containing the known metabolite ions and previously found features. The table must contain these 18 columns: chemical_formula (optional), HMDB_ID (optional), KEGG_compound_ID (optional), neutral.mass (optional), ion.type (the ion form - optional), m.z (either theoretical or mean observed m/z value of previously found features), Number_profiles_processed (the total number of processed samples to build this database), Percent_found (the percentage of historically processed samples in which the feature appeared), mz_min (minimum observed m/z value), mz_max (maximum observed m/z value), RT_mean (mean observed retention time), RT_sd (standard deviation of observed retention time), RT_min (minimum observed retention time), RT_max (maximum observed retention time), int_mean.log. (mean observed log intensity), int_sd.log. (standard deviation of observed log intensity), int_min.log. (minimum observed log intensity), int_max.log. (maximum observed log intensity)." /> + <section name="history_db" title="Known-Table settings"> + <param name="match_tol_ppm" type="integer" optional="true" min="0" label="match_tol_ppm (optional)" + help="The ppm tolerance to match identified features to known metabolites/features." /> + <param name="new_feature_min_count" type="integer" value="2" min="1" label="new_feature_min_count" + help="The minimum number of occurrences of a historically unseen (unknown) feature to add this feature into the database of known features." /> + </section> + </xml> + + <xml name="noise_filtering"> + <section name="noise_filtering" title="Noise filtering and peak detection"> + <yield /> + <param name="min_pres" type="float" value="0.5" + label="min_pres" + help="The minimum proportion of presence in the time period for a series of signals grouped by m/z to be considered a peak." /> + <param name="min_run" type="float" value="12" + label="min_run" + help="The minimum length of elution time for a series of signals grouped by m/z to be considered a peak." /> + <param name="mz_tol" type="float" value="1e-05" + label="mz_tol" + help="The m/z tolerance level for the grouping of data points. This value is expressed as the fraction of the m/z value. This value, multiplied by the m/z value, becomes the cutoff level. The recommended value is the machine's nominal accuracy level. Divide the ppm value by 1e6. For FTMS, 1e-5 is recommended." /> + <param name="baseline_correct" type="float" value="0" label="baseline_correct" + help="After grouping the observations, the highest intensity in each group is found. If the highest is lower than this value, the entire group will be deleted. The default value is NA, in which case the program uses a percentile of the height of the noise groups. If given a value, the value will be used as the threshold, and baseline.correct.noise.percentile will be ignored." /> + <param name="baseline_correct_noise_percentile" type="float" value="0.05" + label="baseline_correct_noise_percentile" + help="The percentile of signal strength of those EIC that don't pass the run filter, to be used as the baseline threshold of signal strength." /> + <param name="intensity_weighted" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" + label="intensity_weighted" + help="Whether to weight the local density by signal intensities in initial peak detection." /> + </section> + </xml> + + <xml name="feature_detection"> + <section name="feature_detection" title="Feature detection"> + <param name="shape_model" type="select" display="radio" + label="shape_model" + help="The mathematical model for the shape of a peak. There are two choices - bi-Gaussian and Gaussian. When the peaks are asymmetric, the bi-Gaussian is better."> + <option value="Gaussian">Gaussian</option> + <option value="bi-Gaussian" selected="true">bi-Gaussian</option> + </param> + <param name="BIC_factor" type="float" value="2.0" + label="BIC_factor" + help="The factor that is multiplied on the number of parameters to modify the BIC criterion. If larger than 1, models with more peaks are penalized more." /> + <param name="peak_estim_method" type="select" display="radio" + label="peak_estim_method" + help="The estimation method for the bi-Gaussian peak model. Two possible values: moment and EM."> + <option value="moment" selected="true">Moment</option> + <option value="EM">EM</option> + </param> + <param name="min_bandwidth" type="float" optional="true" + label="min_bandwidth (optional)" + help="The minimum bandwidth to use in the kernel smoother." /> + <param name="max_bandwidth" type="float" optional="true" + label="max_bandwidth (optional)" + help="The maximum bandwidth to use in the kernel smoother." /> + <param name="sd_cut_min" type="float" value="0.01" + label="sd_cut_min" + help="The minimum standard deviation of a feature to be not eliminated." /> + <param name="sd_cut_max" type="float" value="500" + label="sd_cut_max" + help="The maximum standard deviation of a feature to be not eliminated." /> + <param name="sigma_ratio_lim_min" type="float" value="0.01" + label="sigma_ratio_lim_min" + help="The lower limit of the believed ratio range between the left-standard deviation and the right-standard deviation of the bi-Gaussian function used to fit the data." /> + <param name="sigma_ratio_lim_max" type="float" value="100" + label="sigma_ratio_lim_max" + help="The upper limit of the believed ratio range between the left-standard deviation and the right-standard deviation of the bi-Gaussian function used to fit the data." /> + <param name="component_eliminate" type="float" value="0.01" + label="component_eliminate" + help="In fitting mixture of bi-Gaussian (or Gaussian) model of an EIC, when a component accounts for a proportion of intensities less than this value, the component will be ignored." /> + <param name="moment_power" type="float" value="1" + label="moment_power" + help="The power parameter for data transformation when fitting the bi-Gaussian or Gaussian mixture model in an EIC." /> + </section> + </xml> + + <xml name="peak_alignment"> + <section name="peak_alignment" title="Peak Alignment"> + <param name="align_chr_tol" type="float" optional="true" + label="align_chr_tol (optional)" + help="The retention time tolerance level for peak alignment. The default is NA, which allows the program to search for the tolerance level based on the data." /> + <param name="align_mz_tol" type="float" optional="true" + label="align_mz_tol (optional)" + help="The m/z tolerance level for peak alignment. The default is NA, which allows the program to search for the tolerance level based on the data. The tolerance is given in absolute numbers, not scaled, i.e. for 10ppm tolerance enter '1e-05'. This value, multiplied by the m/z value, becomes the cutoff level." /> + <param name="max_align_mz_diff" type="float" value="0.01" + label="max_align_mz_diff" + help="As the m/z tolerance is expressed in relative terms (ppm), it may not be suitable when the m/z range is wide. This parameter limits the tolerance in absolute terms. It mostly influences feature matching in higher m/z range." /> + </section> + </xml> + + <xml name="weak_signal_recovery"> + <section name="weak_signal_recovery" title="Weak Signal Recovery"> + <param name="recover_mz_range" type="float" optional="true" + label="recover_mz_range (optional)" + help="The m/z around the feature m/z to search for observations. The default value is NA, in which case 1.5 times the m/z tolerance in the aligned object will be used." /> + <param name="recover_chr_range" type="float" optional="true" + label="recover_chr_range (optional)" + help="The retention time around the feature retention time to search for observations. The default value is NA, in which case 0.5 times the retention time tolerance in the aligned object will be used." /> + <param name="use_observed_range" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" + label="use_observed_range" + help="If the value is true, the actual range of the observed locations of the feature in all the spectra will be used." /> + <param name="recover_min_count" type="integer" value="3" + label="recover_min_count" + help="The minimum number of raw data points to be considered as a true feature." /> + </section> + </xml> + <xml name="multibatch_processing"> + <section name="multibatch_processing" title="Multibatch processing"> + <param name="min_within_batch_prop_detect" type="float" min="0" max="1" value="0.1" + label="minimum_batchwise_prop_detect" + help="The minimum detection frequency (relative) of a feature for it to be included in the final feature table." /> + <param name="min_batch_prop" type="float" min="0" max="1" value="0.5" + label="minimum_batch_prop" + help="The minimum proportion of batches that must have a given feature. The features that are less abundant than the value won't be reported." /> + <param name="batch_align_mz_tol" type="float" min="0" value="0.00001" + label="batch_align_mz_tol" + help="The m/z tolerance level for peak alignment within batch." /> + <param name="batch_align_chr_tol" type="float" min="0" value="50.0" + label="batch_align_chr_tol" + help="The retention time tolerance level for peak alignment within batch." /> + </section> + </xml> + + <xml name="mz_tol_macro"> + <param name="mz_tol" type="float" value="1e-05" label="mz_tol" + help="The m/z tolerance level for the grouping of data points. This value is expressed as the + fraction of the m/z value. This value, multiplied by the m/z value, becomes the cutoff level. + The recommended value is the machine's nominal accuracy level. Divide the ppm value by 1e6. + For FTMS, 1e-5 is recommended." /> + </xml> + + <xml name="output_format"> + <section name="output_format" title="Output Format"> + <param name="out_format" type="boolean" checked="false" truevalue="recetox" falsevalue="original" label="Use custom RECETOX output format?" /> + </section> + </xml> + + <xml name="unsupervised_outputs"> + <data name="recovered_feature_sample_table" format="parquet" label="${tool.name} recovered_feature_sample_table on ${on_string}" /> + <data name="aligned_feature_sample_table" format="parquet" label="${tool.name} aligned_feature_sample_table on ${on_string}" hidden="true" /> + <yield /> + </xml> + + <xml name="citations"> + <citations> + <citation type="doi">10.1093/bioinformatics/btp291</citation> + <citation type="doi">10.1186/1471-2105-11-559</citation> + <citation type="doi">10.1021/pr301053d</citation> + <citation type="doi">10.1093/bioinformatics/btu430</citation> + <yield /> + </citations> + </xml> + + <token name="@HELP_hybrid@"> + <![CDATA[ + This is the Hybrid version of apLCMS which is incorporating the knowledge of known metabolites and historically + detected features on the same machinery to help detect and quantify lower-intensity peaks. + + CAUTION: To use such knowledge, especially historical data, you must keep using (1) the same chromatography + system (otherwise the retention time will not match), and (2) the same type of samples with similar extraction + technique, such as human serum. + + @GENERAL_HELP@ + ]]> + </token> + + <token name="@HELP_unsupervised@"> + <![CDATA[ + This is the Unsupervised version of apLCMS which is not relying on any existing knowledge about metabolites or + any historically detected features. For such functionality please use the Hybrid version of apLCMS. + + @GENERAL_HELP@ + ]]> + </token> + + <token name="@HELP_two-step-hybrid@"> + <![CDATA[ + This is the **Two-Step Hybrid** version of **apLCMS**. This tool is improved upon the Hybrid version by accounting for the batch + effects in multi-batch experiments. As in the Hybrid version, this tool incorporates the knowledge of known metabolites and + historically detected features on the same machinery to help detect and quantify lower-intensity peaks. + + **CAUTION**: To use such knowledge, especially historical data, you must keep using (1) the same chromatography + system (otherwise the retention time will not match), and (2) the same type of samples with similar extraction + technique, such as human serum. + + @GENERAL_HELP@ + ]]> + </token> + + <token name="@GENERAL_HELP@"> + apLCMS is a software which generates a feature table from a batch of LC/MS spectra. The m/z and retention time + tolerance levels are estimated from the data. A run-filter is used to detect peaks and remove noise. + Non-parametric statistical methods are used to find-tune peak selection and grouping. After retention time + correction, a feature table is generated by aligning peaks across spectra. For further information on apLCMS + please refer to https://mypage.cuhk.edu.cn/academics/yutianwei/apLCMS/. + </token> +</macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros_split.xml Fri Jun 10 10:17:01 2022 +0000 @@ -0,0 +1,23 @@ +<macros> + <xml name="noise_filtering_split"> + <section name="noise_filtering" title="Noise filtering and peak detection"> + <param name="min_pres" type="float" value="0.5" + label="min_pres" + help="The minimum proportion of presence in the time period for a series of signals grouped by m/z to be considered a peak." /> + <param name="min_run" type="float" value="12" + label="min_run" + help="The minimum length of elution time for a series of signals grouped by m/z to be considered a peak." /> + <param name="mz_tol" type="float" value="1e-05" + label="mz_tol" + help="The m/z tolerance level for the grouping of data points. This value is expressed as the fraction of the m/z value. This value, multiplied by the m/z value, becomes the cutoff level. The recommended value is the machine's nominal accuracy level. Divide the ppm value by 1e6. For FTMS, 1e-5 is recommended." /> + <param name="baseline_correct" type="float" value="0" label="baseline_correct" + help="After grouping the observations, the highest intensity in each group is found. If the highest is lower than this value, the entire group will be deleted. The default value is NA, in which case the program uses a percentile of the height of the noise groups. If given a value, the value will be used as the threshold, and baseline.correct.noise.percentile will be ignored." /> + <param name="baseline_correct_noise_percentile" type="float" value="0.05" + label="baseline_correct_noise_percentile" + help="The percentile of signal strength of those EIC that don't pass the run filter, to be used as the baseline threshold of signal strength." /> + <param name="intensity_weighted" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" + label="intensity_weighted" + help="Whether to weight the local density by signal intensities in initial peak detection." /> + </section> + </xml> +</macros> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/recetox_aplcms_extract_features.xml Fri Jun 10 10:17:01 2022 +0000 @@ -0,0 +1,81 @@ +<tool id="recetox_aplcms_extract_features" name="RECETOX apLCMS - extract features" version="@TOOL_VERSION@+galaxy0"> + <description>extract features from LC/MS spectra</description> + <macros> + <import>macros.xml</import> + <import>macros_split.xml</import> + </macros> + <expand macro="creator"/> + + <expand macro="requirements"/> + <command detect_errors="aggressive"><![CDATA[ + Rscript -e 'source("${__tool_directory__}/utils.R")' -e 'source("${run_script}")' + ]]></command> + <configfiles> + <configfile name="run_script"><![CDATA[ + profile <- proc.cdf( + filename = "$file", + min.pres = $noise_filtering.min_pres, + min.run = $noise_filtering.min_run, + tol = $noise_filtering.mz_tol, + baseline.correct = $noise_filtering.baseline_correct, + baseline.correct.noise.percentile = $noise_filtering.baseline_correct_noise_percentile, + intensity.weighted = $noise_filtering.intensity_weighted, + do.plot = FALSE, + cache = FALSE + ) + + features <- prof.to.features( + a = profile, + min.bw = $feature_detection.min_bandwidth, + max.bw = $feature_detection.max_bandwidth, + sd.cut = c($feature_detection.sd_cut_min, $feature_detection.sd_cut_max), + sigma.ratio.lim = c($feature_detection.sigma_ratio_lim_min, $feature_detection.sigma_ratio_lim_max), + shape.model = '$feature_detection.shape_model', + estim.method = '$feature_detection.peak_estim_method', + component.eliminate = $feature_detection.component_eliminate, + power = $feature_detection.moment_power, + BIC.factor = $feature_detection.BIC_factor, + do.plot = FALSE + ) + + df <- as.data.frame(features) + arrow::write_parquet(df, "$feature_sample_table") + ]]></configfile> + </configfiles> + + <inputs> + <param name="file" type="data" format="mzdata,mzml,mzxml,netcdf" label="Input file" + help="Mass spectrometry file for peak extraction." /> + <expand macro="noise_filtering_split"/> + <expand macro="feature_detection"/> + </inputs> + + <outputs> + <data name="feature_sample_table" format="parquet" label="${tool.name} on ${on_string}" /> + </outputs> + + <tests> + <test> + <param name="file" value="mbr_test0.mzml" ftype="mzml"/> + <output name="feature_sample_table" file="extracted_expected/extracted_0.parquet" ftype="parquet"/> + </test> + <test> + <param name="file" value="mbr_test1.mzml" ftype="mzml"/> + <output name="feature_sample_table" file="extracted_expected/extracted_1.parquet" ftype="parquet"/> + </test> + <test> + <param name="file" value="mbr_test2.mzml" ftype="mzml"/> + <output name="feature_sample_table" file="extracted_expected/extracted_2.parquet" ftype="parquet"/> + </test> + </tests> + + <help> + <![CDATA[ + This is a tool which runs apLCMS features extraction. + + @GENERAL_HELP@ + ]]> + </help> + + <expand macro="citations"/> +</tool>
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/two_step_hybrid_info.csv Fri Jun 10 10:17:01 2022 +0000 @@ -0,0 +1,5 @@ +sample_name, batch +mbr_test0, 1 +mbr_test1, 1 +mbr_test2, 2 +mbr_test0_copy, 2
Binary file test-data/unsupervised_output/unsupervised_aligned_feature_sample_table.parquet has changed
Binary file test-data/unsupervised_output/unsupervised_recovered_feature_sample_table.parquet has changed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/utils.R Fri Jun 10 10:17:01 2022 +0000 @@ -0,0 +1,149 @@ +library(recetox.aplcms) + +align_features <- function(sample_names, ...) { + aligned <- feature.align(...) + feature_names <- seq_len(nrow(aligned$pk.times)) + + list( + mz_tolerance = as.numeric(aligned$mz.tol), + rt_tolerance = as.numeric(aligned$chr.tol), + rt_crosstab = as_feature_crosstab(feature_names, sample_names, aligned$pk.times), + int_crosstab = as_feature_crosstab(feature_names, sample_names, aligned$aligned.ftrs) + ) +} + +get_sample_name <- function(filename) { + tools::file_path_sans_ext(basename(filename)) +} + +as_feature_crosstab <- function(feature_names, sample_names, data) { + colnames(data) <- c("mz", "rt", "mz_min", "mz_max", sample_names) + rownames(data) <- feature_names + as.data.frame(data) +} + +as_feature_sample_table <- function(rt_crosstab, int_crosstab) { + feature_names <- rownames(rt_crosstab) + sample_names <- colnames(rt_crosstab)[- (1:4)] + + feature_table <- data.frame( + feature = feature_names, + mz = rt_crosstab[, 1], + rt = rt_crosstab[, 2] + ) + + # series of conversions to produce a table type from data.frame + rt_crosstab <- as.table(as.matrix(rt_crosstab[, - (1:4)])) + int_crosstab <- as.table(as.matrix(int_crosstab[, - (1:4)])) + + crosstab_axes <- list(feature = feature_names, sample = sample_names) + dimnames(rt_crosstab) <- dimnames(int_crosstab) <- crosstab_axes + + x <- as.data.frame(rt_crosstab, responseName = "sample_rt") + y <- as.data.frame(int_crosstab, responseName = "sample_intensity") + + data <- merge(x, y, by = c("feature", "sample")) + data <- merge(feature_table, data, by = "feature") + data +} + +load_features <- function(files) { + files_list <- sort_samples_by_acquisition_number(files) + features <- lapply(files_list, arrow::read_parquet) + features <- lapply(features, as.matrix) + return(features) +} + +save_data_as_parquet_files <- function(data, subdir) { + dir.create(subdir) + for (i in 0:(length(data) - 1)) { + filename <- file.path(subdir, paste0(subdir, "_features_", i, ".parquet")) + arrow::write_parquet(as.data.frame(data[i + 1]), filename) + } +} + +save_aligned_features <- function(aligned, rt_file, int_file, tol_file) { + arrow::write_parquet(as.data.frame(aligned$rt_crosstab), rt_file) + arrow::write_parquet(as.data.frame(aligned$int_crosstab), int_file) + + mz_tolerance <- c(aligned$mz_tolerance) + rt_tolerance <- c(aligned$rt_tolerance) + arrow::write_parquet(data.frame(mz_tolerance, rt_tolerance), tol_file) +} + +load_aligned_features <- function(rt_file, int_file, tol_file) { + rt_cross_table <- arrow::read_parquet(rt_file) + int_cross_table <- arrow::read_parquet(int_file) + tolerances_table <- arrow::read_parquet(tol_file) + + result <- list() + result$mz_tolerance <- tolerances_table$mz_tolerance + result$rt_tolerance <- tolerances_table$rt_tolerance + result$rt_crosstab <- rt_cross_table + result$int_crosstab <- int_cross_table + return(result) +} + +recover_signals <- function(cluster, + filenames, + extracted, + corrected, + aligned, + mz_tol = 1e-05, + mz_range = NA, + rt_range = NA, + use_observed_range = TRUE, + min_bandwidth = NA, + max_bandwidth = NA, + recover_min_count = 3) { + if (!is(cluster, "cluster")) { + cluster <- parallel::makeCluster(cluster) + on.exit(parallel::stopCluster(cluster)) + } + + clusterExport(cluster, c("extracted", "corrected", "aligned", "recover.weaker")) + clusterEvalQ(cluster, library("splines")) + + recovered <- parLapply(cluster, seq_along(filenames), function(i) { + recover.weaker( + loc = i, + filename = filenames[[i]], + this.f1 = extracted[[i]], + this.f2 = corrected[[i]], + pk.times = aligned$rt_crosstab, + aligned.ftrs = aligned$int_crosstab, + orig.tol = mz_tol, + align.mz.tol = aligned$mz_tolerance, + align.chr.tol = aligned$rt_tolerance, + mz.range = mz_range, + chr.range = rt_range, + use.observed.range = use_observed_range, + bandwidth = 0.5, + min.bw = min_bandwidth, + max.bw = max_bandwidth, + recover.min.count = recover_min_count + ) + }) + + feature_table <- aligned$rt_crosstab[, 1:4] + rt_crosstab <- cbind(feature_table, sapply(recovered, function(x) x$this.times)) + int_crosstab <- cbind(feature_table, sapply(recovered, function(x) x$this.ftrs)) + + feature_names <- rownames(feature_table) + sample_names <- colnames(aligned$rt_crosstab[, - (1:4)]) + + list( + extracted_features = lapply(recovered, function(x) x$this.f1), + corrected_features = lapply(recovered, function(x) x$this.f2), + rt_crosstab = as_feature_crosstab(feature_names, sample_names, rt_crosstab), + int_crosstab = as_feature_crosstab(feature_names, sample_names, int_crosstab) + ) +} + +create_feature_sample_table <- function(features) { + table <- as_feature_sample_table( + rt_crosstab = features$rt_crosstab, + int_crosstab = features$int_crosstab + ) + return(table) +}