Mercurial > repos > recetox > recetox_aplcms_correct_time
view recetox_aplcms_correct_time.xml @ 0:4d7db9cdd952 draft
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
author | recetox |
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date | Mon, 13 Feb 2023 10:28:51 +0000 |
parents | |
children | 7b0bf5d403ba |
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<tool id="recetox_aplcms_correct_time" name="recetox-aplcms - correct time" version="@TOOL_VERSION@+galaxy0"> <description>correct retention time across samples for peak alignment</description> <macros> <import>macros.xml</import> <import>help.xml</import> </macros> <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') tolerances <- load_data_from_parquet_file('$tolerances') corrected_table <- correct_time( this.feature = features_table, template_features = template_features, mz_tol_relative = get_mz_tol(tolerances), rt_tol_relative = get_rt_tol(tolerances) ) corrected_table <- save_sample_name(corrected_table, sample_name) save_data_as_parquet_file(corrected_table, '$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." /> <param label="Input tolerances values" name="tolerances" type="data" format="parquet" help="Table containing tolerance values." /> </inputs> <outputs> <data label="${tool.name} on ${on_string}" name="output_file" format="parquet" /> </outputs> <tests> </tests> <help> <![CDATA[ @CORRECT_TIME_HELP@ @GENERAL_HELP@ @EXAMPLE_OUTPUT@ ]]> </help> <expand macro="citations"/> </tool>