Mercurial > repos > recetox > recetox_aplcms_merge_known_table
diff recetox_aplcms_merge_known_table.xml @ 2:76d8d4c4ab35 draft
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 724ecb1b81ebd8a67488b8a9397177b2ff0357db
| author | recetox |
|---|---|
| date | Wed, 24 May 2023 14:47:45 +0000 |
| parents | 5403b36e7548 |
| children | 0e2ddbeb88eb |
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--- a/recetox_aplcms_merge_known_table.xml Mon Apr 03 14:55:16 2023 +0000 +++ b/recetox_aplcms_merge_known_table.xml Wed May 24 14:47:45 2023 +0000 @@ -15,7 +15,6 @@ metadata <- load_data_from_parquet_file('$metadata_file') rt_table <- load_data_from_parquet_file('$rt_file') intensity_table <- load_data_from_parquet_file('$intensity_file') - tolerances <- load_data_from_parquet_file('$tolerances') known_table <- read_known_table('$known_table') feature_tables <- join_tables_to_list(metadata, rt_table, intensity_table) @@ -28,8 +27,8 @@ #else: match_tol_ppm = NA, #end if - mz_tol_relative = get_mz_tol(tolerances), - rt_tol_relative = get_rt_tol(tolerances), + mz_tol_relative = $mz_tol_relative_ppm * 1e-06, + rt_tol_relative = $rt_tol, #if $direction.selection == "TRUE": new_feature_min_count = $direction.new_feature_min_count, #end if @@ -63,8 +62,7 @@ RT_min (minimum observed retention time), RT_max (maximum observed retention time), int_mean.log. (mean observed log intensity), int_sd.log. (standard deviation of observed log intensity), int_min.log. (minimum observed log intensity), int_max.log. (maximum observed log intensity)." /> - <param label="Input tolerances values" name="tolerances" type="data" format="parquet" - help="Table containing tolerance values." /> + <expand macro="tolerances"/> <conditional name="direction"> <param label="Tables merge direction" name="selection" type="select"