Mercurial > repos > recetox > recetox_aplcms_hybrid
changeset 2:acd25e4fda77 draft default tip
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
line wrap: on
line diff
--- a/macros.xml Thu May 26 16:46:40 2022 +0000 +++ b/macros.xml Fri Jun 10 10:15:14 2022 +0000 @@ -4,14 +4,23 @@ <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="0.9.4">r-recetox-aplcms</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> - <yield /> + <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" @@ -161,6 +170,15 @@ 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?" /> @@ -170,7 +188,6 @@ <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 ${on_string}" hidden="true" /> - <data name="updated_known_table" format="parquet" label="${tool.name} updated_known_table on ${on_string}"/> <yield /> </xml>
--- a/main.R Thu May 26 16:46:40 2022 +0000 +++ b/main.R Fri Jun 10 10:15:14 2022 +0000 @@ -79,11 +79,8 @@ res <- unsupervised(filenames = sample_files, ...) - save_all_extracted_features(res$extracted_features, sample_files) - save_all_corrected_features(res$corrected_features, sample_files) - - save_aligned_feature_table(res$aligned_feature_sample_table, aligned_file) - save_recovered_feature_table(res$recovered_feature_sample_table, recovered_file, out_format) + save_all_features(res, sample_files) + save_all_feature_tables(res$aligned_feature_sample_table, res$recovered_feature_sample_table, aligned_file, recovered_file, out_format) } hybrid_main <- function(sample_files, known_table_file, updated_known_table_file, pairing_file, aligned_file, recovered_file, out_format, ...) { @@ -95,11 +92,22 @@ save_known_table(res$updated_known_table, updated_known_table_file) save_pairing(res$features_known_table_pairing, pairing_file) - save_all_extracted_features(res$extracted_features, sample_files) - save_all_corrected_features(res$corrected_features, sample_files) + save_all_features(res, sample_files) + save_all_feature_tables(res$aligned_feature_sample_table, res$recovered_feature_sample_table, aligned_file, recovered_file, out_format) +} - save_aligned_feature_table(res$aligned_feature_sample_table, aligned_file) - save_recovered_feature_table(res$recovered_feature_sample_table, recovered_file, out_format) +save_all_features <- function(result, sample_files) { + save_all_extracted_features(result$extracted_features, sample_files) + save_all_corrected_features(result$corrected_features, sample_files) +} + +save_all_feature_tables <- function(aligned_feature_sample_table, + recovered_feature_sample_table, + aligned_file, + recovered_file, + out_format) { + save_aligned_feature_table(aligned_feature_sample_table, aligned_file) + save_recovered_feature_table(recovered_feature_sample_table, recovered_file, out_format) } two_step_hybrid_main <- function(sample_files, known_table_file, updated_known_table_file, recovered_file, aligned_file, out_format, metadata, ...) {
--- a/recetox_aplcms_hybrid.xml Thu May 26 16:46:40 2022 +0000 +++ b/recetox_aplcms_hybrid.xml Fri Jun 10 10:15:14 2022 +0000 @@ -78,6 +78,7 @@ <collection name="corrected_features" type="list" label="${tool.name} corrected_features on ${on_string}"> <discover_datasets pattern="__designation__" directory="corrected" format="parquet" /> </collection > + <data name="updated_known_table" format="parquet" label="${tool.name} updated_known_table on ${on_string}"/> </expand> <data name="feature_known_table_pairing" format="tabular" label="${tool.name} feature_known_table_pairing on ${on_string}" hidden="true"/>
Binary file test-data/unsupervised_output/unsupervised_aligned_feature_sample_table.parquet has changed