Mercurial > repos > recetox > recetox_aplcms_correct_time
comparison recetox_aplcms_correct_time.xml @ 9:9064aecc78a7 draft default tip
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b88eaca14b030fc0023989f3c83479e4975d172a
author | recetox |
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date | Thu, 01 Aug 2024 10:58:09 +0000 |
parents | d69ec1171d71 |
children |
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8:1574b8a29e6f | 9:9064aecc78a7 |
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1 <tool id="recetox_aplcms_correct_time" name="recetox-aplcms - correct time" version="@TOOL_VERSION@+galaxy3" profile="21.09"> | 1 <tool id="recetox_aplcms_correct_time" name="recetox-aplcms - correct time" version="@TOOL_VERSION@+galaxy0" profile="21.09"> |
2 <description>correct retention time across samples for peak alignment</description> | 2 <description>correct retention time across samples for peak alignment</description> |
3 <macros> | 3 <macros> |
4 <import>macros.xml</import> | 4 <import>macros.xml</import> |
5 <import>help.xml</import> | 5 <import>help.xml</import> |
6 </macros> | 6 </macros> |
26 | 26 |
27 template_features <- load_data_from_parquet_file('$template') | 27 template_features <- load_data_from_parquet_file('$template') |
28 | 28 |
29 corrected_table <- correct_time( | 29 corrected_table <- correct_time( |
30 this.feature = features_table, | 30 this.feature = features_table, |
31 template_features = template_features, | 31 template_features = template_features |
32 mz_tol_relative = $mz_tol_relative_ppm * 1e-06, | |
33 rt_tol_relative = $rt_tol | |
34 ) | 32 ) |
35 | 33 |
36 corrected_table <- save_sample_name(corrected_table, sample_name) | 34 corrected_table <- save_sample_name(corrected_table, sample_name) |
37 save_data_as_parquet_file(corrected_table, '$output_file') | 35 save_data_as_parquet_file(corrected_table, '$output_file') |
38 ]]></configfile> | 36 ]]></configfile> |
41 <inputs> | 39 <inputs> |
42 <param label="Input clustered features table" name="features_table" type="data" format="parquet" | 40 <param label="Input clustered features table" name="features_table" type="data" format="parquet" |
43 help="Mass spectrometry clustered features table." /> | 41 help="Mass spectrometry clustered features table." /> |
44 <param label="Input template features table" name="template" type="data" format="parquet" | 42 <param label="Input template features table" name="template" type="data" format="parquet" |
45 help="Template features table." /> | 43 help="Template features table." /> |
46 <expand macro="tolerances"/> | |
47 </inputs> | 44 </inputs> |
48 | 45 |
49 <outputs> | 46 <outputs> |
50 <data label="${($features_table.element_identifier).rsplit('.',1)[0]}.parquet" name="output_file" format="parquet" /> | 47 <data label="${($features_table.element_identifier).rsplit('.',1)[0]}.parquet" name="output_file" format="parquet" /> |
51 </outputs> | 48 </outputs> |