Mercurial > repos > recetox > recetox_aplcms_align_features

comparison recetox_aplcms_align_features.xml @ 5:c44c73efd6e5 draft

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 724ecb1b81ebd8a67488b8a9397177b2ff0357db
author recetox
date Wed, 24 May 2023 14:49:03 +0000
parents a85b9670051c
children 2d13fcae8b84
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4:a85b9670051c 5:c44c73efd6e5
20 20
21 ordering <- order(sample_names) 21 ordering <- order(sample_names)
22 feature_tables <- feature_tables[ordering] 22 feature_tables <- feature_tables[ordering]
23 sample_names <- sample_names[ordering] 23 sample_names <- sample_names[ordering]
24 24
25 tolerances <- load_data_from_parquet_file('$input_tolerances')
26
27 aligned_features <- create_aligned_feature_table( 25 aligned_features <- create_aligned_feature_table(
28 features_table = dplyr::bind_rows(feature_tables), 26 features_table = dplyr::bind_rows(feature_tables),
29 min_occurrence = $min_occurrence, 27 min_occurrence = $min_occurrence,
30 sample_names = sample_names, 28 sample_names = sample_names,
31 mz_tol_relative = get_mz_tol(tolerances), 29 mz_tol_relative = $mz_tol_relative_ppm * 1e-06,
32 rt_tol_relative = get_rt_tol(tolerances), 30 rt_tol_relative = $rt_tol,
33 cluster = cluster 31 cluster = cluster
34 ) 32 )
35 33
36 save_aligned_features(aligned_features, '$metadata_file', '$rt_file', '$intensity_file') 34 save_aligned_features(aligned_features, '$metadata_file', '$rt_file', '$intensity_file')
37 ]]></configfile> 35 ]]></configfile>
38 </configfiles> 36 </configfiles>
39 37
40 <inputs> 38 <inputs>
41 <param name="files" type="data_collection" collection_type="list" format="parquet" 39 <param name="files" type="data_collection" collection_type="list" format="parquet"
42 label="Clustered features" help="List of tables containing clustered features." /> 40 label="Clustered features" help="List of tables containing clustered features." />
43 <param label="Input tolerances values" name="input_tolerances" type="data" format="parquet" 41 <expand macro="tolerances"/>
44 help="Table containing tolerance values." />
45 <param name="min_occurrence" type="integer" min="2" value="2" label="Minimal occurrence in samples" 42 <param name="min_occurrence" type="integer" min="2" value="2" label="Minimal occurrence in samples"
46 help="A feature has to show up in at least this number of profiles to be included in the final result." /> 43 help="A feature has to show up in at least this number of profiles to be included in the final result." />
47 </inputs> 44 </inputs>
48 45
49 <outputs> 46 <outputs>