Mercurial > repos > recetox > recetox_aplcms_compute_clusters
comparison recetox_aplcms_compute_clusters.xml @ 2:ce00e1d03c31 draft
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 724ecb1b81ebd8a67488b8a9397177b2ff0357db
| author | recetox |
|---|---|
| date | Wed, 24 May 2023 14:48:47 +0000 |
| parents | 092bbb03a217 |
| children | 15aae2bfa67d |
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| 1:092bbb03a217 | 2:ce00e1d03c31 |
|---|---|
| 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 #if $tolerances_input_method.input_method == "file" | 25 clusters <- compute_clusters_simple( |
| 26 tolerances <- load_data_from_parquet_file('$input_tolerances') | |
| 27 #end if | |
| 28 | |
| 29 clusters <- compute_clusters( | |
| 30 feature_tables = feature_tables, | 26 feature_tables = feature_tables, |
| 31 #if $tolerances_input_method.input_method == "file" | |
| 32 mz_tol_relative = get_mz_tol(tolerances), | |
| 33 rt_tol_relative = get_rt_tol(tolerances), | |
| 34 #else | |
| 35 #if $tolerances_input_method.mz_tol_relative: | |
| 36 mz_tol_relative = $tolerances_input_method.mz_tol_relative, | |
| 37 #else: | |
| 38 mz_tol_relative = NA, | |
| 39 #end if | |
| 40 #if $tolerances_input_method.rt_tol_relative: | |
| 41 rt_tol_relative = $tolerances_input_method.rt_tol_relative, | |
| 42 #else: | |
| 43 rt_tol_relative = NA, | |
| 44 #end if | |
| 45 #end if | |
| 46 mz_max_diff = 10 * $mz_max_diff, | |
| 47 mz_tol_absolute = $mz_tol_absolute, | |
| 48 sample_names = sample_names, | 27 sample_names = sample_names, |
| 49 do.plot = FALSE | 28 mz_tol_ppm = $mz_tol_relative_ppm, |
| 29 rt_tol = $rt_tol | |
| 50 ) | 30 ) |
| 51 | 31 |
| 52 save_parquet_collection(clusters, sample_names, "clustered") | 32 save_parquet_collection(clusters, sample_names, "clustered") |
| 53 save_tolerances(clusters, '$tolerances') | |
| 54 ]]></configfile> | 33 ]]></configfile> |
| 55 </configfiles> | 34 </configfiles> |
| 56 | 35 |
| 57 <inputs> | 36 <inputs> |
| 58 <param name="files" type="data_collection" collection_type="list" format="parquet" label="Input data" | 37 <param name="files" type="data_collection" collection_type="list" format="parquet" label="Input data" |
| 59 help="List of tables containing features." /> | 38 help="List of tables containing features." /> |
| 60 <expand macro="compute_clusters_params"/> | 39 <expand macro="tolerances"/> |
| 61 </inputs> | 40 </inputs> |
| 62 | 41 |
| 63 <outputs> | 42 <outputs> |
| 64 <collection name="clustered_feature_tables" type="list" | 43 <collection name="clustered_feature_tables" type="list" |
| 65 label="${tool.name} feature_tables on ${on_string}"> | 44 label="${tool.name} feature_tables on ${on_string}"> |
| 66 <discover_datasets pattern="__designation__" directory="clustered" format="parquet" /> | 45 <discover_datasets pattern="__designation__" directory="clustered" format="parquet" /> |
| 67 </collection> | 46 </collection> |
| 68 <data name="tolerances" format="parquet" label="${tool.name} on ${on_string} (updated tolerances)" /> | |
| 69 </outputs> | 47 </outputs> |
| 70 | 48 |
| 71 <tests> | 49 <tests> |
| 72 | 50 |
| 73 </tests> | 51 </tests> |