Mercurial > repos > recetox > recetox_aplcms_recover_weaker_signals
view recetox_aplcms_recover_weaker_signals.xml @ 11:d7f5878a98c3 draft default tip
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b88eaca14b030fc0023989f3c83479e4975d172a
author | recetox |
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date | Thu, 01 Aug 2024 10:57:41 +0000 |
parents | a9bb2ccc53de |
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<tool id="recetox_aplcms_recover_weaker_signals" name="recetox-aplcms - recover weaker signals" version="@TOOL_VERSION@+galaxy0" profile="21.09"> <description>recover weaker signals from raw data using an aligned feature table</description> <macros> <import>macros.xml</import> <import>help.xml</import> </macros> <expand macro="annotation"/> <edam_operations> <edam_operation>operation_3215</edam_operation> <edam_operation>operation_3799</edam_operation> </edam_operations> <expand macro="refs"/> <expand macro="creator"/> <expand macro="requirements"/> <command detect_errors="aggressive"><![CDATA[ python '${__tool_directory__}/mzml_id_getter.py' '$input_file'; Rscript -e 'source("${__tool_directory__}/utils.R")' -e 'source("${run_script}")' ]]></command> <configfiles> <configfile name="run_script"><![CDATA[ sample_name <- readChar('sample_name.txt', file.info('sample_name.txt')\$size) if(is.na(sample_name)) { stop("The mzML file does not contain run ID.") } #set extracted_filenames = str("', '").join([str($f) for $f in $extracted_files]) extracted_feature_tables <- load_parquet_collection(c('$extracted_filenames')) sample_names <- unlist(lapply(extracted_feature_tables, load_sample_name)) validate_sample_names(sample_names) extracted_features <- select_table_with_sample_name(extracted_feature_tables, sample_name) #set corrected_filenames = str("', '").join([str($f) for $f in $corrected_files]) corrected_feature_tables <- load_parquet_collection(c('$corrected_filenames')) sample_names <- unlist(lapply(corrected_feature_tables, load_sample_name)) validate_sample_names(sample_names) corrected_features <- select_table_with_sample_name(corrected_feature_tables, sample_name) metadata <- load_data_from_parquet_file('$metadata_file') rt_table <- load_data_from_parquet_file('$rt_file') intensity_table <- load_data_from_parquet_file('$intensity_file') recovered <- recover.weaker( filename = '$input_file', sample_name = sample_name, extracted_features = extracted_features, adjusted_features = corrected_features, metadata_table = metadata, rt_table = rt_table, intensity_table = intensity_table, mz_tol = $mz_tol/1e6, mz_tol_relative = $mz_tol_relative_ppm * 1e-06, rt_tol_relative = $rt_tol, #if $recover_mz_range: recover_mz_range = $recover_mz_range/1e6, #else: recover_mz_range = NA, #end if #if $recover_rt_range: recover_rt_range = $recover_rt_range, #else: recover_rt_range = NA, #end if use_observed_range = $use_observed_range, bandwidth = $bandwidth, #if $min_bandwidth: min_bandwidth = $min_bandwidth, #else: min_bandwidth = NA, #end if #if $max_bandwidth: max_bandwidth = $max_bandwidth, #else: max_bandwidth = NA, #end if recover_min_count = $recover_min_count, intensity_weighted = $intensity_weighted ) recovered <- select_adjusted(recovered) recovered <- save_sample_name(recovered, sample_name) save_data_as_parquet_file(recovered, '$output_file') ]]></configfile> </configfiles> <inputs> <param name="input_file" type="data" format="mzml" label="Input spectra data" help="Mass spectrometry sample-wise features table." /> <param name="extracted_files" type="data_collection" collection_type="list" format="parquet" label="Input extracted feature samples collection" help="Mass spectrometry files containing feature samples." /> <param name="corrected_files" type="data_collection" collection_type="list" format="parquet" label="Input corrected feature samples collection" help="Mass spectrometry file containing corrected feature samples." /> <param name="metadata_file" type="data" format="parquet" label="Metadata table" help="Peak metadata table from the align features step." /> <param name="rt_file" type="data" format="parquet" label="RT table" help="Table with retention times for features (rows) across samples (columns)." /> <param name="intensity_file" type="data" format="parquet" label="Intensity table" help="Table with intensities for features (rows) across samples (columns)." /> <expand macro="tolerances"/> <expand macro="recover_weaker_params"/> <expand macro="bandwidth_params"/> </inputs> <outputs> <data label="${($input_file.element_identifier).rsplit('.',1)[0]}.parquet" name="output_file" format="parquet" /> </outputs> <tests> <test expect_failure="true" /> </tests> <help> <![CDATA[ @RECOVER_WEAKER_SIGNALS_HELP@ @GENERAL_HELP@ ]]> </help> <expand macro="citations"/> </tool>