Mercurial > repos > recetox > recetox_aplcms_recover_weaker_signals
comparison recetox_aplcms_recover_weaker_signals.xml @ 4:755ff0afaaff draft
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 724ecb1b81ebd8a67488b8a9397177b2ff0357db
author | recetox |
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date | Wed, 24 May 2023 14:50:25 +0000 |
parents | c69a12bfc2fb |
children | fd66fc063ce8 |
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3:c69a12bfc2fb | 4:755ff0afaaff |
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33 | 33 |
34 metadata <- load_data_from_parquet_file('$metadata_file') | 34 metadata <- load_data_from_parquet_file('$metadata_file') |
35 rt_table <- load_data_from_parquet_file('$rt_file') | 35 rt_table <- load_data_from_parquet_file('$rt_file') |
36 intensity_table <- load_data_from_parquet_file('$intensity_file') | 36 intensity_table <- load_data_from_parquet_file('$intensity_file') |
37 | 37 |
38 tolerances <- load_data_from_parquet_file('$tolerances') | |
39 | |
40 recovered <- recover.weaker( | 38 recovered <- recover.weaker( |
41 filename = '$input_file', | 39 filename = '$input_file', |
42 sample_name = sample_name, | 40 sample_name = sample_name, |
43 extracted_features = extracted_features, | 41 extracted_features = extracted_features, |
44 adjusted_features = corrected_features, | 42 adjusted_features = corrected_features, |
45 metadata_table = metadata, | 43 metadata_table = metadata, |
46 rt_table = rt_table, | 44 rt_table = rt_table, |
47 intensity_table = intensity_table, | 45 intensity_table = intensity_table, |
48 mz_tol = $mz_tol/1e6, | 46 mz_tol = $mz_tol/1e6, |
49 mz_tol_relative = get_mz_tol(tolerances), | 47 mz_tol_relative = $mz_tol_relative_ppm * 1e-06, |
50 rt_tol_relative = get_rt_tol(tolerances), | 48 rt_tol_relative = $rt_tol, |
51 #if $recover_mz_range: | 49 #if $recover_mz_range: |
52 recover_mz_range = $recover_mz_range/1e6, | 50 recover_mz_range = $recover_mz_range/1e6, |
53 #else: | 51 #else: |
54 recover_mz_range = NA, | 52 recover_mz_range = NA, |
55 #end if | 53 #end if |
92 help="Peak metadata table from the align features step." /> | 90 help="Peak metadata table from the align features step." /> |
93 <param name="rt_file" type="data" format="parquet" label="RT table" | 91 <param name="rt_file" type="data" format="parquet" label="RT table" |
94 help="Table with retention times for features (rows) across samples (columns)." /> | 92 help="Table with retention times for features (rows) across samples (columns)." /> |
95 <param name="intensity_file" type="data" format="parquet" label="Intensity table" | 93 <param name="intensity_file" type="data" format="parquet" label="Intensity table" |
96 help="Table with intensities for features (rows) across samples (columns)." /> | 94 help="Table with intensities for features (rows) across samples (columns)." /> |
97 <param label="Input tolerances values" name="tolerances" type="data" format="parquet" | 95 <expand macro="tolerances"/> |
98 help="Table containing tolerance values." /> | |
99 <expand macro="recover_weaker_params"/> | 96 <expand macro="recover_weaker_params"/> |
100 <expand macro="bandwidth_params"/> | 97 <expand macro="bandwidth_params"/> |
101 </inputs> | 98 </inputs> |
102 | 99 |
103 <outputs> | 100 <outputs> |