Mercurial > repos > recetox > recetox_aplcms_correct_time
view recetox_aplcms_correct_time.xml @ 8:1574b8a29e6f draft default tip
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit bc3445f7c41271b0062c7674108f57708d08dd28
author | recetox |
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date | Thu, 30 May 2024 14:52:30 +0000 |
parents | d69ec1171d71 |
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<tool id="recetox_aplcms_correct_time" name="recetox-aplcms - correct time" version="@TOOL_VERSION@+galaxy3" profile="21.09"> <description>correct retention time across samples for peak alignment</description> <macros> <import>macros.xml</import> <import>help.xml</import> </macros> <expand macro="annotation"/> <edam_operations> <edam_operation>operation_3628</edam_operation> </edam_operations> <expand macro="refs"/> <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[ features_table <- load_data_from_parquet_file('$features_table') sample_name <- load_sample_name(features_table) if(is.na(sample_name)) { message("The file does not contain sample name.") } template_features <- load_data_from_parquet_file('$template') corrected_table <- correct_time( this.feature = features_table, template_features = template_features, mz_tol_relative = $mz_tol_relative_ppm * 1e-06, rt_tol_relative = $rt_tol ) corrected_table <- save_sample_name(corrected_table, sample_name) save_data_as_parquet_file(corrected_table, '$output_file') ]]></configfile> </configfiles> <inputs> <param label="Input clustered features table" name="features_table" type="data" format="parquet" help="Mass spectrometry clustered features table." /> <param label="Input template features table" name="template" type="data" format="parquet" help="Template features table." /> <expand macro="tolerances"/> </inputs> <outputs> <data label="${($features_table.element_identifier).rsplit('.',1)[0]}.parquet" name="output_file" format="parquet" /> </outputs> <tests> <test expect_failure="true" /> </tests> <help> <![CDATA[ @CORRECT_TIME_HELP@ @GENERAL_HELP@ ]]> </help> <expand macro="citations"/> </tool>