| Previous changeset 1:18f965163b4c (2023-04-03) Next changeset 3:92b45b7fcbca (2023-05-25) |
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Commit message:
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 724ecb1b81ebd8a67488b8a9397177b2ff0357db |
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modified:
help.xml macros.xml recetox_aplcms_merge_known_table.xml utils.R |
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added:
test-data/remove_noise_docker.parquet |
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| diff -r 18f965163b4c -r f2490df187db help.xml --- a/help.xml Mon Apr 03 14:57:46 2023 +0000 +++ b/help.xml Wed May 24 14:50:09 2023 +0000 |
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| @@ -110,7 +110,6 @@ ================================= Group features with `mz` and `rt` using tolerances within the tolerance into clusters, creating larger features from raw data points. -Custom tolerances for `mz` and `rt` are computed based on the given parameters. The tool takes a collection of all detected features and computes the clusters over a global feature table, adding the `sample_id` and `cluster` columns to the table. Example Output @@ -133,7 +132,7 @@ recetox-aplcms - correct time ============================= -Apply spline-based retention time correction to a feature table given the template table and the computed `mz` and `rt` tolerances. +Apply spline-based retention time correction to a feature table given the template table and the `mz` and `rt` tolerances. Example Output -------------- |
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| diff -r 18f965163b4c -r f2490df187db macros.xml --- a/macros.xml Mon Apr 03 14:57:46 2023 +0000 +++ b/macros.xml Wed May 24 14:50:09 2023 +0000 |
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| @@ -1,5 +1,5 @@ <macros> - <token name="@TOOL_VERSION@">0.10.3</token> + <token name="@TOOL_VERSION@">0.11.0</token> <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">r-recetox-aplcms</requirement> @@ -93,32 +93,11 @@ </section> </xml> - <xml name="compute_clusters_params"> - <conditional name="tolerances_input_method"> - <param name="input_method" type="select" display="radio" label="Tolerances input method" - help="Tolerances can be entered directly or loaded from a file."> - <option value="direct" selected="true">direct</option> - <option value="file">file</option> - </param> - <when value="direct"> - <param name="mz_tol_relative" type="float" optional="true" label="Relative m/z tolerance" - help="Relative m/z tolerance to use for grouping features. - If not provided, it is calculated from the data using kernel density estimation." /> - <param name="rt_tol_relative" type="float" optional="true" label="Relative rt tolerance [unit corresponds to the retention time]" - help="Relative retention time tolerance to use for grouping features. - If not provided, it is calculated from the data using kernel density estimation." /> - </when> - <when value="file"> - <param label="Input tolerances values" name="input_tolerances" type="data" format="parquet" - help="Table containing tolerance values." /> - </when> - </conditional> - <param name="mz_tol_absolute" type="float" label="Minimal absolute m/z tolerance [Da]" value="1e-05" - help="During the clustering, an m/z tolerance is computed based on the data and the specified relative tolerance. - This parameter allows the specification of a minimal value of this tolerance." /> - <param name="mz_max_diff" type="float" label="Maximal m/z difference [Da]" value="0.01" - help="Maximum allowed difference between feature m/z values to belong to the same cluster." /> - + <xml name="tolerances"> + <param name="mz_tol_relative_ppm" type="float" value="10" label="Relative m/z tolerance [ppm]" + help="Relative m/z tolerance to use for grouping features." /> + <param name="rt_tol" type="float" value="5" label="Retention time tolerance [unit corresponds to the retention time]" + help="Retention time tolerance to use for grouping features." /> </xml> <xml name="recover_weaker_params"> |
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| diff -r 18f965163b4c -r f2490df187db recetox_aplcms_merge_known_table.xml --- a/recetox_aplcms_merge_known_table.xml Mon Apr 03 14:57:46 2023 +0000 +++ b/recetox_aplcms_merge_known_table.xml Wed May 24 14:50:09 2023 +0000 |
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| @@ -15,7 +15,6 @@ metadata <- load_data_from_parquet_file('$metadata_file') rt_table <- load_data_from_parquet_file('$rt_file') intensity_table <- load_data_from_parquet_file('$intensity_file') - tolerances <- load_data_from_parquet_file('$tolerances') known_table <- read_known_table('$known_table') feature_tables <- join_tables_to_list(metadata, rt_table, intensity_table) @@ -28,8 +27,8 @@ #else: match_tol_ppm = NA, #end if - mz_tol_relative = get_mz_tol(tolerances), - rt_tol_relative = get_rt_tol(tolerances), + mz_tol_relative = $mz_tol_relative_ppm * 1e-06, + rt_tol_relative = $rt_tol, #if $direction.selection == "TRUE": new_feature_min_count = $direction.new_feature_min_count, #end if @@ -63,8 +62,7 @@ RT_min (minimum observed retention time), RT_max (maximum observed retention time), int_mean.log. (mean observed log intensity), int_sd.log. (standard deviation of observed log intensity), int_min.log. (minimum observed log intensity), int_max.log. (maximum observed log intensity)." /> - <param label="Input tolerances values" name="tolerances" type="data" format="parquet" - help="Table containing tolerance values." /> + <expand macro="tolerances"/> <conditional name="direction"> <param label="Tables merge direction" name="selection" type="select" |
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| diff -r 18f965163b4c -r f2490df187db test-data/remove_noise_docker.parquet |
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| Binary file test-data/remove_noise_docker.parquet has changed |
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| diff -r 18f965163b4c -r f2490df187db utils.R --- a/utils.R Mon Apr 03 14:57:46 2023 +0000 +++ b/utils.R Wed May 24 14:50:09 2023 +0000 |
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| @@ -39,11 +39,11 @@ return(features) } -save_parquet_collection <- function(table, sample_names, subdir) { +save_parquet_collection <- function(feature_tables, sample_names, subdir) { dir.create(subdir) - for (i in seq_len(length(table$feature_tables))) { + for (i in seq_len(length(feature_tables))) { filename <- file.path(subdir, paste0(subdir, "_", sample_names[i], ".parquet")) - feature_table <- as.data.frame(table$feature_tables[[i]]) + feature_table <- as.data.frame(feature_tables[[i]]) feature_table <- save_sample_name(feature_table, sample_names[i]) arrow::write_parquet(feature_table, filename) } @@ -59,14 +59,6 @@ arrow::write_parquet(data.frame(mz_tolerance, rt_tolerance), tol_file) } -get_mz_tol <- function(tolerances) { - return(tolerances$mz_tolerance) -} - -get_rt_tol <- function(tolerances) { - return(tolerances$rt_tolerance) -} - save_aligned_features <- function(aligned_features, metadata_file, rt_file, intensity_file) { save_data_as_parquet_file(aligned_features$metadata, metadata_file) save_data_as_parquet_file(aligned_features$rt, rt_file) |