Mercurial > repos > recetox > recetox_aplcms_merge_known_table

comparison recetox_aplcms_merge_known_table.xml @ 2:76d8d4c4ab35 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 14:47:45 +0000
parents 5403b36e7548
children 0e2ddbeb88eb
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1:2b3bcd28ba2f 2:76d8d4c4ab35
13 <configfiles> 13 <configfiles>
14 <configfile name="run_script"><![CDATA[ 14 <configfile name="run_script"><![CDATA[
15 metadata <- load_data_from_parquet_file('$metadata_file') 15 metadata <- load_data_from_parquet_file('$metadata_file')
16 rt_table <- load_data_from_parquet_file('$rt_file') 16 rt_table <- load_data_from_parquet_file('$rt_file')
17 intensity_table <- load_data_from_parquet_file('$intensity_file') 17 intensity_table <- load_data_from_parquet_file('$intensity_file')
18 tolerances <- load_data_from_parquet_file('$tolerances')
19 known_table <- read_known_table('$known_table') 18 known_table <- read_known_table('$known_table')
20 19
21 feature_tables <- join_tables_to_list(metadata, rt_table, intensity_table) 20 feature_tables <- join_tables_to_list(metadata, rt_table, intensity_table)
22 21
23 merged <- merge_features_and_known_table( 22 merged <- merge_features_and_known_table(
26 #if $match_tol_ppm: 25 #if $match_tol_ppm:
27 match_tol_ppm = $match_tol_ppm, 26 match_tol_ppm = $match_tol_ppm,
28 #else: 27 #else:
29 match_tol_ppm = NA, 28 match_tol_ppm = NA,
30 #end if 29 #end if
31 mz_tol_relative = get_mz_tol(tolerances), 30 mz_tol_relative = $mz_tol_relative_ppm * 1e-06,
32 rt_tol_relative = get_rt_tol(tolerances), 31 rt_tol_relative = $rt_tol,
33 #if $direction.selection == "TRUE": 32 #if $direction.selection == "TRUE":
34 new_feature_min_count = $direction.new_feature_min_count, 33 new_feature_min_count = $direction.new_feature_min_count,
35 #end if 34 #end if
36 from_features_to_known_table = $direction.selection 35 from_features_to_known_table = $direction.selection
37 ) 36 )
61 which the feature appeared), mz_min (minimum observed m/z value), mz_max (maximum observed m/z value), 60 which the feature appeared), mz_min (minimum observed m/z value), mz_max (maximum observed m/z value),
62 RT_mean (mean observed retention time), RT_sd (standard deviation of observed retention time), 61 RT_mean (mean observed retention time), RT_sd (standard deviation of observed retention time),
63 RT_min (minimum observed retention time), RT_max (maximum observed retention time), 62 RT_min (minimum observed retention time), RT_max (maximum observed retention time),
64 int_mean.log. (mean observed log intensity), int_sd.log. (standard deviation of observed log intensity), 63 int_mean.log. (mean observed log intensity), int_sd.log. (standard deviation of observed log intensity),
65 int_min.log. (minimum observed log intensity), int_max.log. (maximum observed log intensity)." /> 64 int_min.log. (minimum observed log intensity), int_max.log. (maximum observed log intensity)." />
66 <param label="Input tolerances values" name="tolerances" type="data" format="parquet" 65 <expand macro="tolerances"/>
67 help="Table containing tolerance values." />
68 66
69 <conditional name="direction"> 67 <conditional name="direction">
70 <param label="Tables merge direction" name="selection" type="select" 68 <param label="Tables merge direction" name="selection" type="select"
71 help="Choose between merging feature to known_table and known_table to features."> 69 help="Choose between merging feature to known_table and known_table to features.">
72 <option value="TRUE">Merge features to known table</option> 70 <option value="TRUE">Merge features to known table</option>