Mercurial > repos > recetox > recetox_aplcms_recover_weaker_signals

comparison recetox_aplcms_recover_weaker_signals.xml @ 4:755ff0afaaff 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 14:50:25 +0000
parents c69a12bfc2fb
children fd66fc063ce8
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3:c69a12bfc2fb 4:755ff0afaaff
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>