Mercurial > repos > recetox > recetox_aplcms_unsupervised

comparison recetox_aplcms_unsupervised.xml @ 0:d740352d272a draft

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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
author recetox
date Tue, 22 Mar 2022 16:09:47 +0000
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children 4e6281945270
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-1:000000000000 0:d740352d272a
1 <tool id="recetox_aplcms_unsupervised" name="RECETOX apLCMS Unsupervised" 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 $files])
21
22 unsupervised_main(
23 sample_files = c('$filenames_str'),
24 aligned_file = '${aligned_feature_sample_table}',
25 recovered_file = '${recovered_feature_sample_table}',
26 out_format = '$output_format.out_format',
27 min_exp = $noise_filtering.min_exp,
28 min_pres = $noise_filtering.min_pres,
29 min_run = $noise_filtering.min_run,
30 mz_tol = $noise_filtering.mz_tol,
31 baseline_correct = $noise_filtering.baseline_correct,
32 baseline_correct_noise_percentile = $noise_filtering.baseline_correct_noise_percentile,
33 intensity_weighted = $noise_filtering.intensity_weighted,
34 shape_model = '$feature_detection.shape_model',
35 BIC_factor = $feature_detection.BIC_factor,
36 peak_estim_method = '$feature_detection.peak_estim_method',
37 min_bandwidth = $feature_detection.min_bandwidth,
38 max_bandwidth = $feature_detection.max_bandwidth,
39 sd_cut = c($feature_detection.sd_cut_min, $feature_detection.sd_cut_max),
40 sigma_ratio_lim = c($feature_detection.sigma_ratio_lim_min, $feature_detection.sigma_ratio_lim_max),
41 component_eliminate = $feature_detection.component_eliminate,
42 moment_power = $feature_detection.moment_power,
43 align_chr_tol = $peak_alignment.align_chr_tol,
44 align_mz_tol = $peak_alignment.align_mz_tol,
45 max_align_mz_diff = $peak_alignment.max_align_mz_diff,
46 recover_mz_range = $weak_signal_recovery.recover_mz_range,
47 recover_chr_range = $weak_signal_recovery.recover_chr_range,
48 use_observed_range = $weak_signal_recovery.use_observed_range,
49 recover_min_count = $weak_signal_recovery.recover_min_count,
50 cluster = as.integer(Sys.getenv('GALAXY_SLOTS', unset = 1))
51 )
52 ]]></configfile>
53 </configfiles>
54
55 <expand macro="inputs">
56 <expand macro="noise_filtering"/>
57 <expand macro="feature_detection"/>
58 <expand macro="peak_alignment"/>
59 <expand macro="weak_signal_recovery"/>
60 <expand macro="output_format"/>
61 </expand>
62
63 <outputs>
64 <expand macro="unsupervised_outputs"/>
65 </outputs>
66
67 <tests>
68 <test>
69 <param name="files" value="mbr_test0.mzml,mbr_test1.mzml,mbr_test2.mzml" ftype="mzml"/>
70 <output name="recovered_feature_sample_table" file="unsupervised_recovered_feature_sample_table.parquet"
71 ftype="parquet"/>
72 </test>
73 <test>
74 <param name="files" value="mbr_test0.mzml,mbr_test1.mzml,mbr_test2.mzml" ftype="mzml"/>
75 <section name="output_format">
76 <param name="out_format" value="recetox"/>
77 </section>
78 <output name="recovered_feature_sample_table" file="unsupervised.recetox.parquet" ftype="parquet"/>
79 </test>
80 </tests>
81
82 <help>
83 <![CDATA[
84 @HELP_unsupervised@
85 ]]>
86 </help>
87
88 <expand macro="citations"/>
89 </tool>