Mercurial > repos > recetox > aplcms_unsupervised

comparison aplcms_unsupervised.xml @ 1:bcc9f27fea2b draft

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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit 903de3d3bbc57ae9897fa4eea3636e27f67cbdb3"
author recetox
date Tue, 26 Jan 2021 17:10:34 +0000
parents 7c80b743a2db
children 8c6dbef97001
comparison
equal deleted inserted replaced
0:7c80b743a2db 1:bcc9f27fea2b
1 <tool id="aplcms_unsupervised" name="apLCMS - Unsupervised" version="@TOOL_VERSION@+galaxy1"> 1 <tool id="aplcms_unsupervised" name="apLCMS - Unsupervised" version="@TOOL_VERSION@+galaxy2">
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 $files]) 9 #set file_str = str("', '").join([str($f) for $f in $files])
10 10
11 Rscript 11 Rscript
12 -e 'x <- apLCMS::unsupervised( 12 -e "x <- apLCMS::unsupervised(
13 files = c("$file_str"), 13 files = c('$file_str'),
14 min_exp = $noise_filtering.min_exp, 14 min_exp = $noise_filtering.min_exp,
15 min_pres = $noise_filtering.min_pres, 15 min_pres = $noise_filtering.min_pres,
16 min_run = $noise_filtering.min_run, 16 min_run = $noise_filtering.min_run,
17 mz_tol = $noise_filtering.mz_tol, 17 mz_tol = $noise_filtering.mz_tol,
18 baseline_correct = $noise_filtering.baseline_correct, 18 baseline_correct = $noise_filtering.baseline_correct,
19 baseline_correct_noise_percentile = $noise_filtering.baseline_correct_noise_percentile, 19 baseline_correct_noise_percentile = $noise_filtering.baseline_correct_noise_percentile,
20 intensity_weighted = $noise_filtering.intensity_weighted, 20 intensity_weighted = $noise_filtering.intensity_weighted,
21 shape_model = "$feature_detection.shape_model", 21 shape_model = '$feature_detection.shape_model',
22 BIC_factor = $feature_detection.BIC_factor, 22 BIC_factor = $feature_detection.BIC_factor,
23 peak_estim_method = "$feature_detection.peak_estim_method", 23 peak_estim_method = '$feature_detection.peak_estim_method',
24 min_bandwidth = $feature_detection.min_bandwidth, 24 min_bandwidth = $feature_detection.min_bandwidth,
25 max_bandwidth = $feature_detection.max_bandwidth, 25 max_bandwidth = $feature_detection.max_bandwidth,
26 sd_cut = c($feature_detection.sd_cut_min, $feature_detection.sd_cut_max), 26 sd_cut = c($feature_detection.sd_cut_min, $feature_detection.sd_cut_max),
27 sigma_ratio_lim = c($feature_detection.sigma_ratio_lim_min, $feature_detection.sigma_ratio_lim_max), 27 sigma_ratio_lim = c($feature_detection.sigma_ratio_lim_min, $feature_detection.sigma_ratio_lim_max),
28 component_eliminate = $feature_detection.component_eliminate, 28 component_eliminate = $feature_detection.component_eliminate,
31 align_mz_tol = $peak_alignment.align_mz_tol, 31 align_mz_tol = $peak_alignment.align_mz_tol,
32 max_align_mz_diff = $peak_alignment.max_align_mz_diff, 32 max_align_mz_diff = $peak_alignment.max_align_mz_diff,
33 recover_mz_range = $weak_signal_recovery.recover_mz_range, 33 recover_mz_range = $weak_signal_recovery.recover_mz_range,
34 recover_chr_range = $weak_signal_recovery.recover_chr_range, 34 recover_chr_range = $weak_signal_recovery.recover_chr_range,
35 use_observed_range = $weak_signal_recovery.use_observed_range, 35 use_observed_range = $weak_signal_recovery.use_observed_range,
36 recover_min_count = $weak_signal_recovery.recover_min_count 36 recover_min_count = $weak_signal_recovery.recover_min_count,
37 )' 37 cluster = as.integer(\${GALAXY_SLOTS:-1})
38 -e 'apLCMS::save_peaks_to_hdf("$peaks", x)' 38 )"
39 -e "apLCMS::save_peaks_to_hdf('$peaks', x)"
39 ]]></command> 40 ]]></command>
40 41
41 <expand macro="inputs"> 42 <expand macro="inputs">
42 <expand macro="noise_filtering" /> 43 <expand macro="noise_filtering" />
43 <expand macro="feature_detection" /> 44 <expand macro="feature_detection" />