Mercurial > repos > recetox > recetox_aplcms_hybrid
comparison recetox_aplcms_hybrid.xml @ 0:1633a2a34255 draft
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
author | recetox |
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date | Tue, 22 Mar 2022 16:10:17 +0000 |
parents | |
children | 867c737a7f10 |
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-1:000000000000 | 0:1633a2a34255 |
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1 <tool id="recetox_aplcms_hybrid" name="RECETOX apLCMS Hybrid" version="@TOOL_VERSION@+galaxy3"> | |
2 <description>generate a feature table from LC/MS spectra</description> | |
3 <macros> | |
4 <import>macros.xml</import> | |
5 </macros> | |
6 <expand macro="creator"/> | |
7 | |
8 <expand macro="requirements"/> | |
9 <command detect_errors="aggressive"><![CDATA[ | |
10 sh ${symlink_inputs} && | |
11 Rscript -e 'source("${__tool_directory__}/main.R")' -e 'source("${run_script}")' | |
12 ]]></command> | |
13 <configfiles> | |
14 <configfile name="symlink_inputs"> | |
15 #for $infile in $files | |
16 ln -s '${infile}' '${infile.element_identifier}' | |
17 #end for | |
18 </configfile> | |
19 <configfile name="run_script"><![CDATA[ | |
20 #set filenames_str = str("', '").join([str($f.element_identifier) for $f in $files]) | |
21 | |
22 hybrid_main( | |
23 sample_files = c('$filenames_str'), | |
24 known_table_file = '${known_table}', | |
25 updated_known_table_file = '${updated_known_table}', | |
26 pairing_file = '${feature_known_table_pairing}', | |
27 aligned_file = '${aligned_feature_sample_table}', | |
28 recovered_file = '${recovered_feature_sample_table}', | |
29 out_format = '$output_format.out_format', | |
30 min_exp = $noise_filtering.min_exp, | |
31 min_pres = $noise_filtering.min_pres, | |
32 min_run = $noise_filtering.min_run, | |
33 mz_tol = $noise_filtering.mz_tol, | |
34 baseline_correct = $noise_filtering.baseline_correct, | |
35 baseline_correct_noise_percentile = $noise_filtering.baseline_correct_noise_percentile, | |
36 intensity_weighted = $noise_filtering.intensity_weighted, | |
37 shape_model = '$feature_detection.shape_model', | |
38 BIC_factor = $feature_detection.BIC_factor, | |
39 peak_estim_method = '$feature_detection.peak_estim_method', | |
40 min_bandwidth = $feature_detection.min_bandwidth, | |
41 max_bandwidth = $feature_detection.max_bandwidth, | |
42 sd_cut = c($feature_detection.sd_cut_min, $feature_detection.sd_cut_max), | |
43 sigma_ratio_lim = c($feature_detection.sigma_ratio_lim_min, $feature_detection.sigma_ratio_lim_max), | |
44 component_eliminate = $feature_detection.component_eliminate, | |
45 moment_power = $feature_detection.moment_power, | |
46 align_chr_tol = $peak_alignment.align_chr_tol, | |
47 align_mz_tol = $peak_alignment.align_mz_tol, | |
48 max_align_mz_diff = $peak_alignment.max_align_mz_diff, | |
49 match_tol_ppm = $history_db.match_tol_ppm, | |
50 new_feature_min_count = $history_db.new_feature_min_count, | |
51 recover_mz_range = $weak_signal_recovery.recover_mz_range, | |
52 recover_chr_range = $weak_signal_recovery.recover_chr_range, | |
53 use_observed_range = $weak_signal_recovery.use_observed_range, | |
54 recover_min_count = $weak_signal_recovery.recover_min_count, | |
55 cluster = as.integer(Sys.getenv('GALAXY_SLOTS', unset = 1)) | |
56 ) | |
57 ]]></configfile> | |
58 </configfiles> | |
59 | |
60 <expand macro="inputs"> | |
61 <expand macro="history_db"/> | |
62 <expand macro="noise_filtering"/> | |
63 <expand macro="feature_detection"/> | |
64 <expand macro="peak_alignment"/> | |
65 <expand macro="weak_signal_recovery"/> | |
66 <expand macro="output_format"/> | |
67 </expand> | |
68 | |
69 <outputs> | |
70 <expand macro="unsupervised_outputs"/> | |
71 <data name="updated_known_table" format="parquet" label="${tool.name} updated_known_table on ${on_string}"/> | |
72 <data name="feature_known_table_pairing" format="tabular" | |
73 label="${tool.name} feature_known_table_pairing on ${on_string}" hidden="true"/> | |
74 </outputs> | |
75 | |
76 <tests> | |
77 <test> | |
78 <param name="known_table" value="known_table.parquet" ftype="parquet"/> | |
79 <param name="files" value="mbr_test0.mzml,mbr_test1.mzml,mbr_test2.mzml" ftype="mzml"/> | |
80 <output name="recovered_feature_sample_table" file="hybrid_recovered_feature_sample_table.parquet" | |
81 ftype="parquet"/> | |
82 </test> | |
83 <test> | |
84 <param name="known_table" value="known_table.parquet" ftype="parquet"/> | |
85 <param name="files" value="mbr_test0.mzml,mbr_test1.mzml,mbr_test2.mzml" ftype="mzml"/> | |
86 <section name="output_format"> | |
87 <param name="out_format" value="recetox"/> | |
88 </section> | |
89 <output name="recovered_feature_sample_table" file="hybrid.recetox.parquet" ftype="parquet"/> | |
90 </test> | |
91 </tests> | |
92 | |
93 <help> | |
94 <![CDATA[ | |
95 @HELP_hybrid@ | |
96 ]]> | |
97 </help> | |
98 | |
99 <expand macro="citations"/> | |
100 </tool> |