Mercurial > repos > recetox > recetox_aplcms_unsupervised
changeset 1:4e6281945270 draft
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
| author | recetox |
|---|---|
| date | Thu, 26 May 2022 16:46:13 +0000 |
| parents | d740352d272a |
| children | 10093dea9b3f |
| files | macros.xml main.R recetox_aplcms_unsupervised.xml test-data/hybrid_recovered_feature_sample_table.parquet test-data/mbr_test0_copy.mzml test-data/two_step_hybrid.recetox.parquet test-data/two_step_hybrid_info.csv test-data/unsupervised.recetox.parquet test-data/unsupervised_recovered_feature_sample_table.parquet |
| diffstat | 9 files changed, 26976 insertions(+), 14 deletions(-) [+] |
line wrap: on
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--- a/macros.xml Tue Mar 22 16:09:47 2022 +0000 +++ b/macros.xml Thu May 26 16:46:13 2022 +0000 @@ -1,16 +1,17 @@ <macros> - <token name="@TOOL_VERSION@">0.9.3</token> + <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="0.9.3">r-recetox-aplcms</requirement> + <requirement type="package" version="0.9.4">r-recetox-aplcms</requirement> <requirement type="package" version="1.0.7">r-dplyr</requirement> </requirements> </xml> <xml name="creator"> <creator> + <yield /> <person givenName="Martin" familyName="Čech" @@ -49,9 +50,7 @@ <xml name="noise_filtering"> <section name="noise_filtering" title="Noise filtering and peak detection"> - <param name="min_exp" type="integer" min="1" value="2" - label="min_exp" - help="If a feature is to be included in the final feature table, it must be present in at least this number of spectra." /> + <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." /> @@ -146,6 +145,22 @@ 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="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?" /> @@ -155,12 +170,8 @@ <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 ${on_string}" hidden="true" /> - <collection name="corrected_features" type="list" label="${tool.name} corrected_features on ${on_string}"> - <discover_datasets pattern="__designation__" directory="corrected" format="parquet" /> - </collection > - <collection name="extracted_features" type="list" label="${tool.name} extracted_features on ${on_string}"> - <discover_datasets pattern="__designation__" directory="extracted" format="parquet" /> - </collection > + <data name="updated_known_table" format="parquet" label="${tool.name} updated_known_table on ${on_string}"/> + <yield /> </xml> <xml name="citations"> @@ -169,6 +180,7 @@ <citation type="doi">10.1186/1471-2105-11-559</citation> <citation type="doi">10.1021/pr301053d</citation> <citation type="doi">10.1093/bioinformatics/btu430</citation> + <yield /> </citations> </xml> @@ -194,6 +206,20 @@ ]]> </token> + <token name="@HELP_two-step-hybrid@"> + <![CDATA[ + This is the **Two-Step Hybrid** version of **apLCMS**. This tool is improved upon the Hybrid version by accounting for the batch + effects in multi-batch experiments. As in the Hybrid version, this tool incorporates the knowledge of known metabolites and + historically detected features on the same machinery to help detect and quantify lower-intensity peaks. + + **CAUTION**: To use such knowledge, especially historical data, you must keep using (1) the same chromatography + system (otherwise the retention time will not match), and (2) the same type of samples with similar extraction + technique, such as human serum. + + @GENERAL_HELP@ + ]]> + </token> + <token name="@GENERAL_HELP@"> apLCMS is a software which generates a feature table from a batch of LC/MS spectra. The m/z and retention time tolerance levels are estimated from the data. A run-filter is used to detect peaks and remove noise.
--- a/main.R Tue Mar 22 16:09:47 2022 +0000 +++ b/main.R Thu May 26 16:46:13 2022 +0000 @@ -27,7 +27,7 @@ col_base <- c("feature", "mz", "rt") output_table <- peak_table %>% distinct(across(any_of(col_base))) - for (level in levels(peak_table$sample)) { + for (level in levels(factor(peak_table$sample))) { subdata <- peak_table %>% filter(sample == level) %>% select(any_of(c(col_base, "sample_intensity"))) %>% @@ -101,3 +101,15 @@ save_aligned_feature_table(res$aligned_feature_sample_table, aligned_file) save_recovered_feature_table(res$recovered_feature_sample_table, recovered_file, out_format) } + +two_step_hybrid_main <- function(sample_files, known_table_file, updated_known_table_file, recovered_file, aligned_file, out_format, metadata, ...) { + sample_files <- sort_samples_by_acquisition_number(sample_files) + metadata <- read.table(metadata, sep = ",", header = TRUE) + + known_table <- read_known_table(known_table_file) + res <- two.step.hybrid(filenames = sample_files, known.table = known_table, work_dir = getwd(), metadata = metadata, ...) + + save_known_table(res$known_table, updated_known_table_file) + save_aligned_feature_table(res$aligned_features, aligned_file) + save_recovered_feature_table(res$final_features, recovered_file, out_format) +}
--- a/recetox_aplcms_unsupervised.xml Tue Mar 22 16:09:47 2022 +0000 +++ b/recetox_aplcms_unsupervised.xml Thu May 26 16:46:13 2022 +0000 @@ -53,7 +53,11 @@ </configfiles> <expand macro="inputs"> - <expand macro="noise_filtering"/> + <expand macro="noise_filtering"> + <param name="min_exp" type="integer" min="1" value="2" + label="min_exp" + help="If a feature is to be included in the final feature table, it must be present in at least this number of samples." /> + </expand> <expand macro="feature_detection"/> <expand macro="peak_alignment"/> <expand macro="weak_signal_recovery"/> @@ -61,7 +65,14 @@ </expand> <outputs> - <expand macro="unsupervised_outputs"/> + <expand macro="unsupervised_outputs"> + <collection name="extracted_features" type="list" label="${tool.name} extracted_features on ${on_string}"> + <discover_datasets pattern="__designation__" directory="extracted" format="parquet" /> + </collection > + <collection name="corrected_features" type="list" label="${tool.name} corrected_features on ${on_string}"> + <discover_datasets pattern="__designation__" directory="corrected" format="parquet" /> + </collection > + </expand> </outputs> <tests>
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