Mercurial > repos > recetox > recetox_aplcms_recover_weaker_signals
comparison recetox_aplcms_recover_weaker_signals.xml @ 0:067a308223e3 draft
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
author | recetox |
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date | Fri, 10 Jun 2022 10:18:24 +0000 |
parents | |
children | f9fb9d8fb710 |
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1 <tool id="recetox_aplcms_recover_weaker_signals" name="RECETOX apLCMS - recover weaker signals" version="@TOOL_VERSION@+galaxy0"> | |
2 <description>recover weaker signals from LC/MS spectra</description> | |
3 <macros> | |
4 <import>macros.xml</import> | |
5 <import>macros_split.xml</import> | |
6 </macros> | |
7 <expand macro="creator"/> | |
8 | |
9 <expand macro="requirements"/> | |
10 <command detect_errors="aggressive"><![CDATA[ | |
11 sh ${symlink_inputs} && | |
12 Rscript -e 'source("${__tool_directory__}/utils.R")' -e 'source("${__tool_directory__}/main.R")' -e 'source("${run_script}")' | |
13 ]]></command> | |
14 <configfiles> | |
15 <configfile name="symlink_inputs"> | |
16 #for $infile in $ms_files | |
17 ln -s '${infile}' '${infile.element_identifier}' | |
18 #end for | |
19 #for $infile in $extracted_files | |
20 ln -s '${infile}' '${infile.element_identifier}' | |
21 #end for | |
22 #for $infile in $corrected_files | |
23 ln -s '${infile}' '${infile.element_identifier}' | |
24 #end for | |
25 </configfile> | |
26 <configfile name="run_script"><![CDATA[ | |
27 #set filenames = str("', '").join([str($f.element_identifier) for $f in $ms_files]) | |
28 filenames <- sort_samples_by_acquisition_number(c('$filenames')) | |
29 | |
30 #set extracted_files = str("', '").join([str($f.element_identifier) for $f in $extracted_files]) | |
31 extracted <- load_features(c('$extracted_files')) | |
32 | |
33 #set corrected_files = str("', '").join([str($f.element_identifier) for $f in $corrected_files]) | |
34 corrected <- load_features(c('$corrected_files')) | |
35 | |
36 aligned <- load_aligned_features('$rt_cross_table_file', '$int_cross_table_file', '$tolerances_file') | |
37 | |
38 cluster <- as.integer(Sys.getenv('GALAXY_SLOTS', unset = 1)) | |
39 | |
40 recovered <- recover_signals(cluster, | |
41 filenames, | |
42 extracted, | |
43 corrected, | |
44 aligned, | |
45 $mz_tol, | |
46 $weak_signal_recovery.recover_mz_range, | |
47 $weak_signal_recovery.recover_chr_range, | |
48 $weak_signal_recovery.use_observed_range, | |
49 $min_bandwidth, | |
50 $max_bandwidth, | |
51 $weak_signal_recovery.recover_min_count | |
52 ) | |
53 | |
54 aligned_feature_sample_table <- create_feature_sample_table(aligned) | |
55 recovered_feature_sample_table <- create_feature_sample_table(recovered) | |
56 | |
57 save_all_features(recovered, filenames) | |
58 save_all_feature_tables(aligned_feature_sample_table, recovered_feature_sample_table, | |
59 '${aligned_feature_sample_table}', '${recovered_feature_sample_table}', | |
60 '$output_format.out_format') | |
61 ]]></configfile> | |
62 </configfiles> | |
63 | |
64 <inputs> | |
65 <param name="ms_files" type="data" format="mzdata,mzml,mzxml,netcdf" multiple="true" min="2" label="Input data" | |
66 help="Mass spectrometry file for peak extraction." /> | |
67 <param name="extracted_files" type="data" format="parquet" multiple="true" min="2" label="Input extracted feature samples" | |
68 help="Mass spectrometry files containing feature samples." /> | |
69 <param name="corrected_files" type="data" format="parquet" multiple="true" min="2" label="Input corrected feature samples" | |
70 help="Mass spectrometry file containing corrected feature samples." /> | |
71 <param name="tolerances_file" type="data" format="parquet" label="Input tolerances" help="TBD"/> | |
72 <param name="rt_cross_table_file" type="data" format="parquet" label="Input rt cross table" help="TBD"/> | |
73 <param name="int_cross_table_file" type="data" format="parquet" label="Input int cross table" help="TBD"/> | |
74 <expand macro="mz_tol_macro"/> | |
75 <param name="min_bandwidth" type="float" optional="true" label="min_bandwidth (optional)" | |
76 help="The minimum bandwidth to use in the kernel smoother." /> | |
77 <param name="max_bandwidth" type="float" optional="true" label="max_bandwidth (optional)" | |
78 help="The maximum bandwidth to use in the kernel smoother." /> | |
79 <expand macro="weak_signal_recovery"/> | |
80 <expand macro="output_format"/> | |
81 </inputs> | |
82 | |
83 <outputs> | |
84 <expand macro="unsupervised_outputs"> | |
85 <collection name="extracted_features" type="list" label="${tool.name} extracted_features on ${on_string}"> | |
86 <discover_datasets pattern="__designation__" directory="extracted" format="parquet" /> | |
87 </collection > | |
88 <collection name="corrected_features" type="list" label="${tool.name} corrected_features on ${on_string}"> | |
89 <discover_datasets pattern="__designation__" directory="corrected" format="parquet" /> | |
90 </collection > | |
91 </expand> | |
92 </outputs> | |
93 | |
94 <tests> | |
95 <test> | |
96 <param name="ms_files" value="mbr_test2.mzml,mbr_test1.mzml,mbr_test0.mzml" ftype="mzml"/> | |
97 <param name="extracted_files" ftype="parquet" | |
98 value="extracted_expected/extracted_0.parquet,extracted_expected/extracted_1.parquet,extracted_expected/extracted_2.parquet"/> | |
99 <param name="corrected_files" ftype="parquet" | |
100 value="corrected_expected/corrected_0.parquet,corrected_expected/corrected_1.parquet,corrected_expected/corrected_2.parquet"/> | |
101 <param name="tolerances_file" value="tolerances.parquet" ftype="parquet"/> | |
102 <param name="rt_cross_table_file" value="rt_cross_table.parquet" ftype="parquet"/> | |
103 <param name="int_cross_table_file" value="int_cross_table.parquet" ftype="parquet"/> | |
104 | |
105 <output name="recovered_feature_sample_table" ftype="parquet" | |
106 file="unsupervised_output/unsupervised_recovered_feature_sample_table.parquet"/> | |
107 <output name="aligned_feature_sample_table" ftype="parquet" | |
108 file="unsupervised_output/unsupervised_aligned_feature_sample_table.parquet"/> | |
109 <output_collection name="corrected_features" type="list"> | |
110 <element name="mbr_test0.parquet" file="unsupervised_output/corrected_features_0.parquet" ftype="parquet"/> | |
111 <element name="mbr_test1.parquet" file="unsupervised_output/corrected_features_1.parquet" ftype="parquet"/> | |
112 <element name="mbr_test2.parquet" file="unsupervised_output/corrected_features_2.parquet" ftype="parquet"/> | |
113 </output_collection> | |
114 <output_collection name="extracted_features" type="list"> | |
115 <element name="mbr_test0.parquet" file="unsupervised_output/extracted_features_0.parquet" ftype="parquet"/> | |
116 <element name="mbr_test1.parquet" file="unsupervised_output/extracted_features_1.parquet" ftype="parquet"/> | |
117 <element name="mbr_test2.parquet" file="unsupervised_output/extracted_features_2.parquet" ftype="parquet"/> | |
118 </output_collection> | |
119 </test> | |
120 </tests> | |
121 | |
122 <help> | |
123 <![CDATA[ | |
124 This is a tool which runs apLCMS recovery of weaker signals. | |
125 | |
126 @GENERAL_HELP@ | |
127 ]]> | |
128 </help> | |
129 | |
130 <expand macro="citations"/> | |
131 </tool> |