Mercurial > repos > recetox > recetox_aplcms_compute_clusters
view recetox_aplcms_compute_clusters.xml @ 10:18ec7635bac6 draft
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit f5e491b0f3f4005e3d8f75954f2d469297b300bf
author | recetox |
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date | Mon, 16 Sep 2024 15:17:27 +0000 |
parents | f3a18e020cdd |
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<tool id="recetox_aplcms_compute_clusters" name="recetox-aplcms - compute clusters" version="@TOOL_VERSION@+galaxy0" profile="21.09"> <description>compute clusters of mz and rt across samples and assign cluster IDs to individual features</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 '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] clusters <- compute_clusters_simple( feature_tables = feature_tables, sample_names = sample_names, mz_tol_ppm = $mz_tol_relative_ppm, rt_tol = $rt_tol ) sample_names <- unlist(lapply(clusters, restore_sample_name)) save_parquet_collection(clusters, sample_names, "clustered") ]]></configfile> </configfiles> <inputs> <param name="files" type="data_collection" collection_type="list" format="parquet" label="Input data" help="List of tables containing features." /> <expand macro="tolerances"/> </inputs> <outputs> <collection name="clustered_feature_tables" type="list" label="${tool.name} feature_tables on ${on_string}"> <discover_datasets pattern="__designation__" directory="clustered" format="parquet" /> </collection> </outputs> <tests> <test expect_failure="true" /> </tests> <help> <![CDATA[ @COMPUTE_CLUSTERS_HELP@ @GENERAL_HELP@ ]]> </help> <expand macro="citations"/> </tool>