Mercurial > repos > recetox > test_recetox_aplcms_unsupervised

comparison recetox_aplcms_unsupervised.xml @ 0:be51059c2384 draft default tip

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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 65d42862f9265e8ba3783368ac0bddb154e3a427-dirty"
author recetox
date Fri, 18 Jun 2021 16:36:23 +0000
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-1:000000000000 0:be51059c2384
1 <tool id="_recetox_aplcms_unsupervised" name="apLCMS Unsupervised" version="@TOOL_VERSION@+galaxy0">
2 <description>generate a feature table from LC/MS spectra</description>
3 <macros>
4 <import>recetox_aplcms_macros.xml</import>
5 </macros>
6
7 <expand macro="requirements" />
8
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
14 <configfiles>
15 <configfile name="symlink_inputs">
16 #for $infile in $files
17 ln -s '${infile}' '${infile.element_identifier}'
18 #end for
19 </configfile>
20 <configfile name="run_script"><![CDATA[
21 #set filenames_str = str("', '").join([str($f.element_identifier) for $f in $files])
22
23 unsupervised_main(
24 sample_files = c('$filenames_str'),
25 aligned_file = '${aligned_feature_sample_table}',
26 recovered_file = '${recovered_feature_sample_table}',
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>
61
62 <outputs>
63 <expand macro="unsupervised_outputs" />
64 </outputs>
65
66 <tests>
67 <test>
68 <param name="files" value="mbr_test0.mzml,mbr_test1.mzml,mbr_test2.mzml" ftype="mzml" />
69 <output name="recovered_feature_sample_table" file="unsupervised_recovered_feature_sample_table.parquet" ftype="parquet" compare="sim_size" delta="1000" />
70 </test>
71 </tests>
72
73 <help>
74 This is the Unsupervised version of apLCMS which is not relying on any existing knowledge about metabolites or
75 any historically detected features. For such functionality please use the Hybrid version of apLCMS.
76
77 @GENERAL_HELP@
78 </help>
79
80 <expand macro="citations" />
81 </tool>