Mercurial > repos > recetox > aplcms_unsupervised

comparison aplcms_unsupervised.xml @ 2:8c6dbef97001 draft

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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ef35fcaaee8f8ae4aa72f3bc0f47dc20e0e70116"
author recetox
date Mon, 19 Apr 2021 12:26:57 +0000
parents bcc9f27fea2b
children
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1:bcc9f27fea2b 2:8c6dbef97001
1 <tool id="aplcms_unsupervised" name="apLCMS - Unsupervised" version="@TOOL_VERSION@+galaxy2"> 1 <tool id="aplcms_unsupervised" name="apLCMS - Unsupervised" version="@TOOL_VERSION@+galaxy3">
2 <macros> 2 <macros>
3 <import>aplcms_macros.xml</import> 3 <import>aplcms_macros.xml</import>
4 </macros> 4 </macros>
5 5
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
7 7
8 <command detect_errors="aggressive"><![CDATA[ 8 <command detect_errors="aggressive"><![CDATA[
9 #set file_str = str("', '").join([str($f) for $f in $files]) 9 Rscript ${run_script}
10 ]]></command>
10 11
11 Rscript 12 <configfiles>
12 -e "x <- apLCMS::unsupervised( 13 <configfile name="run_script"><![CDATA[
13 files = c('$file_str'), 14 #set file_str = str("', '").join([str($f) for $f in $files])
14 min_exp = $noise_filtering.min_exp, 15
15 min_pres = $noise_filtering.min_pres, 16 x <- apLCMS::unsupervised(
16 min_run = $noise_filtering.min_run, 17 files = c('$file_str'),
17 mz_tol = $noise_filtering.mz_tol, 18 min_exp = $noise_filtering.min_exp,
18 baseline_correct = $noise_filtering.baseline_correct, 19 min_pres = $noise_filtering.min_pres,
19 baseline_correct_noise_percentile = $noise_filtering.baseline_correct_noise_percentile, 20 min_run = $noise_filtering.min_run,
20 intensity_weighted = $noise_filtering.intensity_weighted, 21 mz_tol = $noise_filtering.mz_tol,
21 shape_model = '$feature_detection.shape_model', 22 baseline_correct = $noise_filtering.baseline_correct,
22 BIC_factor = $feature_detection.BIC_factor, 23 baseline_correct_noise_percentile = $noise_filtering.baseline_correct_noise_percentile,
23 peak_estim_method = '$feature_detection.peak_estim_method', 24 intensity_weighted = $noise_filtering.intensity_weighted,
24 min_bandwidth = $feature_detection.min_bandwidth, 25 shape_model = '$feature_detection.shape_model',
25 max_bandwidth = $feature_detection.max_bandwidth, 26 BIC_factor = $feature_detection.BIC_factor,
26 sd_cut = c($feature_detection.sd_cut_min, $feature_detection.sd_cut_max), 27 peak_estim_method = '$feature_detection.peak_estim_method',
27 sigma_ratio_lim = c($feature_detection.sigma_ratio_lim_min, $feature_detection.sigma_ratio_lim_max), 28 min_bandwidth = $feature_detection.min_bandwidth,
28 component_eliminate = $feature_detection.component_eliminate, 29 max_bandwidth = $feature_detection.max_bandwidth,
29 moment_power = $feature_detection.moment_power, 30 sd_cut = c($feature_detection.sd_cut_min, $feature_detection.sd_cut_max),
30 align_chr_tol = $peak_alignment.align_chr_tol, 31 sigma_ratio_lim = c($feature_detection.sigma_ratio_lim_min, $feature_detection.sigma_ratio_lim_max),
31 align_mz_tol = $peak_alignment.align_mz_tol, 32 component_eliminate = $feature_detection.component_eliminate,
32 max_align_mz_diff = $peak_alignment.max_align_mz_diff, 33 moment_power = $feature_detection.moment_power,
33 recover_mz_range = $weak_signal_recovery.recover_mz_range, 34 align_chr_tol = $peak_alignment.align_chr_tol,
34 recover_chr_range = $weak_signal_recovery.recover_chr_range, 35 align_mz_tol = $peak_alignment.align_mz_tol,
35 use_observed_range = $weak_signal_recovery.use_observed_range, 36 max_align_mz_diff = $peak_alignment.max_align_mz_diff,
36 recover_min_count = $weak_signal_recovery.recover_min_count, 37 recover_mz_range = $weak_signal_recovery.recover_mz_range,
37 cluster = as.integer(\${GALAXY_SLOTS:-1}) 38 recover_chr_range = $weak_signal_recovery.recover_chr_range,
38 )" 39 use_observed_range = $weak_signal_recovery.use_observed_range,
39 -e "apLCMS::save_peaks_to_hdf('$peaks', x)" 40 recover_min_count = $weak_signal_recovery.recover_min_count,
40 ]]></command> 41 cluster = as.integer(Sys.getenv('GALAXY_SLOTS', unset = 1))
42 )
43
44 apLCMS::save_peaks_to_hdf('$peaks', x)
45 ]]></configfile>
46 </configfiles>
41 47
42 <expand macro="inputs"> 48 <expand macro="inputs">
43 <expand macro="noise_filtering" /> 49 <expand macro="noise_filtering" />
44 <expand macro="feature_detection" /> 50 <expand macro="feature_detection" />
45 <expand macro="peak_alignment" /> 51 <expand macro="peak_alignment" />