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view recetox_aplcms_align_features.xml @ 14:ec196e27a61a draft default tip
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 5da5b5e8b95d93a24424155e5aebfbd337d2c4b6
author | recetox |
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date | Thu, 31 Oct 2024 11:23:30 +0000 |
parents | 79ad928a0dae |
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<tool id="recetox_aplcms_align_features" name="recetox-aplcms - align features" version="@TOOL_VERSION@+galaxy0" profile="21.09"> <description>align peaks across samples</description> <macros> <import>macros.xml</import> <import>help.xml</import> </macros> <expand macro="annotation"/> <edam_operations> <edam_operation>operation_2928</edam_operation> </edam_operations> <expand macro="refs"/> <expand macro="creator"/> <expand macro="requirements"/> <command detect_errors="aggressive"><![CDATA[ Rscript -e "cluster <- \${GALAXY_SLOTS:-1}" -e 'source("${__tool_directory__}/utils.R")' -e 'source("${run_script}")' ]]></command> <configfiles> <configfile name="run_script"><![CDATA[ #set filenames = str("', '").join([str($f) for $f in $files]) feature_tables <- load_parquet_collection(c('$filenames')) sample_names <- unlist(lapply(feature_tables, load_sample_name)) validate_sample_names(sample_names) ordering <- order(sample_names) feature_tables <- feature_tables[ordering] sample_names <- sample_names[ordering] aligned_features <- create_aligned_feature_table( features_table = dplyr::bind_rows(feature_tables), min_occurrence = $min_occurrence, sample_names = sample_names, mz_tol_relative = $mz_tol_relative_ppm * 1e-06, rt_tol_relative = $rt_tol, cluster = cluster ) save_aligned_features(aligned_features, '$metadata_file', '$rt_file', '$intensity_file') ]]></configfile> </configfiles> <inputs> <param name="files" type="data_collection" collection_type="list" format="parquet" label="Clustered features" help="List of tables containing clustered features." /> <expand macro="tolerances"/> <param name="min_occurrence" type="integer" min="2" value="2" label="Minimal occurrence in samples" help="A feature has to show up in at least this number of profiles to be included in the final result." /> </inputs> <outputs> <data name="metadata_file" format="parquet" label="${tool.name} on ${on_string} (metadata table)"/> <data name="rt_file" format="parquet" label="${tool.name} on ${on_string} (rt table)"/> <data name="intensity_file" format="parquet" label="${tool.name} on ${on_string} (intensity table)"/> </outputs> <tests> <test expect_failure="true" /> </tests> <help> <![CDATA[ @ALIGN_FEATURES_HELP@ @GENERAL_HELP@ ]]> </help> <expand macro="citations"/> </tool>