Mercurial > repos > recetox > recetox_aplcms_correct_time
comparison recetox_aplcms_correct_time.xml @ 2:353b9d58d360 draft
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 724ecb1b81ebd8a67488b8a9397177b2ff0357db
| author | recetox |
|---|---|
| date | Wed, 24 May 2023 14:49:35 +0000 |
| parents | 7b0bf5d403ba |
| children | 5f667da3804a |
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| 1:7b0bf5d403ba | 2:353b9d58d360 |
|---|---|
| 18 if(is.na(sample_name)) { | 18 if(is.na(sample_name)) { |
| 19 message("The file does not contain sample name.") | 19 message("The file does not contain sample name.") |
| 20 } | 20 } |
| 21 | 21 |
| 22 template_features <- load_data_from_parquet_file('$template') | 22 template_features <- load_data_from_parquet_file('$template') |
| 23 tolerances <- load_data_from_parquet_file('$tolerances') | |
| 24 | 23 |
| 25 corrected_table <- correct_time( | 24 corrected_table <- correct_time( |
| 26 this.feature = features_table, | 25 this.feature = features_table, |
| 27 template_features = template_features, | 26 template_features = template_features, |
| 28 mz_tol_relative = get_mz_tol(tolerances), | 27 mz_tol_relative = $mz_tol_relative_ppm * 1e-06, |
| 29 rt_tol_relative = get_rt_tol(tolerances) | 28 rt_tol_relative = $rt_tol |
| 30 ) | 29 ) |
| 31 | 30 |
| 32 corrected_table <- save_sample_name(corrected_table, sample_name) | 31 corrected_table <- save_sample_name(corrected_table, sample_name) |
| 33 save_data_as_parquet_file(corrected_table, '$output_file') | 32 save_data_as_parquet_file(corrected_table, '$output_file') |
| 34 ]]></configfile> | 33 ]]></configfile> |
| 37 <inputs> | 36 <inputs> |
| 38 <param label="Input clustered features table" name="features_table" type="data" format="parquet" | 37 <param label="Input clustered features table" name="features_table" type="data" format="parquet" |
| 39 help="Mass spectrometry clustered features table." /> | 38 help="Mass spectrometry clustered features table." /> |
| 40 <param label="Input template features table" name="template" type="data" format="parquet" | 39 <param label="Input template features table" name="template" type="data" format="parquet" |
| 41 help="Template features table." /> | 40 help="Template features table." /> |
| 42 <param label="Input tolerances values" name="tolerances" type="data" format="parquet" | 41 <expand macro="tolerances"/> |
| 43 help="Table containing tolerance values." /> | |
| 44 </inputs> | 42 </inputs> |
| 45 | 43 |
| 46 <outputs> | 44 <outputs> |
| 47 <data label="${tool.name} on ${on_string}" name="output_file" format="parquet" /> | 45 <data label="${tool.name} on ${on_string}" name="output_file" format="parquet" /> |
| 48 </outputs> | 46 </outputs> |