Mercurial > repos > recetox > recetox_aplcms_correct_time
comparison recetox_aplcms_correct_time.xml @ 0:4d7db9cdd952 draft
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
author | recetox |
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date | Mon, 13 Feb 2023 10:28:51 +0000 |
parents | |
children | 7b0bf5d403ba |
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-1:000000000000 | 0:4d7db9cdd952 |
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1 <tool id="recetox_aplcms_correct_time" name="recetox-aplcms - correct time" version="@TOOL_VERSION@+galaxy0"> | |
2 <description>correct retention time across samples for peak alignment</description> | |
3 <macros> | |
4 <import>macros.xml</import> | |
5 <import>help.xml</import> | |
6 </macros> | |
7 <expand macro="creator"/> | |
8 <expand macro="requirements"/> | |
9 | |
10 <command detect_errors="aggressive"><![CDATA[ | |
11 Rscript -e 'source("${__tool_directory__}/utils.R")' -e 'source("${run_script}")' | |
12 ]]></command> | |
13 <configfiles> | |
14 <configfile name="run_script"><![CDATA[ | |
15 features_table <- load_data_from_parquet_file('$features_table') | |
16 sample_name <- load_sample_name(features_table) | |
17 | |
18 if(is.na(sample_name)) { | |
19 message("The file does not contain sample name.") | |
20 } | |
21 | |
22 template_features <- load_data_from_parquet_file('$template') | |
23 tolerances <- load_data_from_parquet_file('$tolerances') | |
24 | |
25 corrected_table <- correct_time( | |
26 this.feature = features_table, | |
27 template_features = template_features, | |
28 mz_tol_relative = get_mz_tol(tolerances), | |
29 rt_tol_relative = get_rt_tol(tolerances) | |
30 ) | |
31 | |
32 corrected_table <- save_sample_name(corrected_table, sample_name) | |
33 save_data_as_parquet_file(corrected_table, '$output_file') | |
34 ]]></configfile> | |
35 </configfiles> | |
36 | |
37 <inputs> | |
38 <param label="Input clustered features table" name="features_table" type="data" format="parquet" | |
39 help="Mass spectrometry clustered features table." /> | |
40 <param label="Input template features table" name="template" type="data" format="parquet" | |
41 help="Template features table." /> | |
42 <param label="Input tolerances values" name="tolerances" type="data" format="parquet" | |
43 help="Table containing tolerance values." /> | |
44 </inputs> | |
45 | |
46 <outputs> | |
47 <data label="${tool.name} on ${on_string}" name="output_file" format="parquet" /> | |
48 </outputs> | |
49 | |
50 <tests> | |
51 | |
52 </tests> | |
53 | |
54 <help> | |
55 <![CDATA[ | |
56 @CORRECT_TIME_HELP@ | |
57 | |
58 @GENERAL_HELP@ | |
59 | |
60 @EXAMPLE_OUTPUT@ | |
61 ]]> | |
62 </help> | |
63 | |
64 <expand macro="citations"/> | |
65 </tool> |