Mercurial > repos > recetox > recetox_aplcms_unsupervised

annotate aplcms_unsupervised.xml @ 2:3c2a4d95fe06 draft

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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit b6bca87f335b45c6306fef28fd5e8b4877eed3f5"
author recetox
date Thu, 24 Sep 2020 07:23:07 +0000
parents 52cec2e123fa
children b0ba0287b76f
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52cec2e123fa "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit 5305d1a60fe5bf5f1abfec332d432b9d362f1f83"
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1 <tool id="recetox_aplcms_unsupervised" name="apLCMS - Unsupervised" version="@TOOL_VERSION@+galaxy0">
52cec2e123fa "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit 5305d1a60fe5bf5f1abfec332d432b9d362f1f83"
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2 <macros>
52cec2e123fa "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit 5305d1a60fe5bf5f1abfec332d432b9d362f1f83"
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3 <import>aplcms_macros.xml</import>
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4 </macros>
52cec2e123fa "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit 5305d1a60fe5bf5f1abfec332d432b9d362f1f83"
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5
52cec2e123fa "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit 5305d1a60fe5bf5f1abfec332d432b9d362f1f83"
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6 <expand macro="requirements" />
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52cec2e123fa "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit 5305d1a60fe5bf5f1abfec332d432b9d362f1f83"
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8 <command detect_errors="aggressive"><![CDATA[
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9 #set file_str = str('", "').join([str($f) for $f in $files])
52cec2e123fa "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit 5305d1a60fe5bf5f1abfec332d432b9d362f1f83"
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10
52cec2e123fa "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit 5305d1a60fe5bf5f1abfec332d432b9d362f1f83"
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11 Rscript
52cec2e123fa "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit 5305d1a60fe5bf5f1abfec332d432b9d362f1f83"
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12 -e 'x <- apLCMS::unsupervised(
52cec2e123fa "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit 5305d1a60fe5bf5f1abfec332d432b9d362f1f83"
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13 files = c("$file_str"),
52cec2e123fa "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit 5305d1a60fe5bf5f1abfec332d432b9d362f1f83"
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14 min_exp = $noise_filtering.min_exp,
52cec2e123fa "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit 5305d1a60fe5bf5f1abfec332d432b9d362f1f83"
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15 min_pres = $noise_filtering.min_pres,
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16 min_run = $noise_filtering.min_run,
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17 mz_tol = $noise_filtering.mz_tol,
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18 baseline_correct = $noise_filtering.baseline_correct,
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19 baseline_correct_noise_percentile = $noise_filtering.baseline_correct_noise_percentile,
52cec2e123fa "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit 5305d1a60fe5bf5f1abfec332d432b9d362f1f83"
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20 intensity_weighted = $noise_filtering.intensity_weighted,
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21 shape_model = "$feature_detection.shape_model",
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22 BIC_factor = $feature_detection.BIC_factor,
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23 peak_estim_method = "$feature_detection.peak_estim_method",
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24 min_bandwidth = $feature_detection.min_bandwidth,
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25 max_bandwidth = $feature_detection.max_bandwidth,
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26 sd_cut = c($feature_detection.sd_cut_min, $feature_detection.sd_cut_max),
52cec2e123fa "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit 5305d1a60fe5bf5f1abfec332d432b9d362f1f83"
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27 sigma_ratio_lim = c($feature_detection.sigma_ratio_lim_min, $feature_detection.sigma_ratio_lim_max),
52cec2e123fa "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit 5305d1a60fe5bf5f1abfec332d432b9d362f1f83"
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28 component_eliminate = $feature_detection.component_eliminate,
52cec2e123fa "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit 5305d1a60fe5bf5f1abfec332d432b9d362f1f83"
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29 moment_power = $feature_detection.moment_power,
52cec2e123fa "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit 5305d1a60fe5bf5f1abfec332d432b9d362f1f83"
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30 align_chr_tol = $peak_alignment.align_chr_tol,
52cec2e123fa "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit 5305d1a60fe5bf5f1abfec332d432b9d362f1f83"
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31 align_mz_tol = $peak_alignment.align_mz_tol,
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32 max_align_mz_diff = $peak_alignment.max_align_mz_diff,
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33 recover_mz_range = $weak_signal_recovery.recover_mz_range,
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34 recover_chr_range = $weak_signal_recovery.recover_chr_range,
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35 use_observed_range = $weak_signal_recovery.use_observed_range,
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36 recover_min_count = $weak_signal_recovery.recover_min_count
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37 )'
52cec2e123fa "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit 5305d1a60fe5bf5f1abfec332d432b9d362f1f83"
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38 -e 'rhdf5::h5write(x\$final_peaks, "$peaks", "peaks")'
52cec2e123fa "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit 5305d1a60fe5bf5f1abfec332d432b9d362f1f83"
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39 -e 'rhdf5::h5write(x\$aligned_peaks, "$peaks", "aligned_peaks")'
52cec2e123fa "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit 5305d1a60fe5bf5f1abfec332d432b9d362f1f83"
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40 -e 'rhdf5::h5write(x\$corrected_features, "$peaks", "corrected_features")'
52cec2e123fa "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit 5305d1a60fe5bf5f1abfec332d432b9d362f1f83"
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41 -e 'rhdf5::h5write(x\$extracted_features, "$peaks", "extracted_features")'
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42 -e 'rhdf5::h5write(x\$aligned_mz_tolerance, "$peaks", "aligned_mz_tolerance")'
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43 -e 'rhdf5::h5write(x\$aligned_rt_tolerance, "$peaks", "aligned_rt_tolerance")'
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44 ]]></command>
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45
52cec2e123fa "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit 5305d1a60fe5bf5f1abfec332d432b9d362f1f83"
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46 <expand macro="inputs">
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47 <expand macro="noise_filtering" />
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48 <expand macro="feature_detection" />
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49 <expand macro="peak_alignment" />
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50 <expand macro="weak_signal_recovery" />
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51 </expand>
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52
52cec2e123fa "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit 5305d1a60fe5bf5f1abfec332d432b9d362f1f83"
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53 <outputs>
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54 <data name="peaks" format="h5" />
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55 </outputs>
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56
52cec2e123fa "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit 5305d1a60fe5bf5f1abfec332d432b9d362f1f83"
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57 <help>
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58 This is the Unsupervised version of apLCMS which is not relying on any existing knowledge about metabolites or
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59 any historically detected features. For such functionality please use the Hybrid version of apLCMS.
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60
52cec2e123fa "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit 5305d1a60fe5bf5f1abfec332d432b9d362f1f83"
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61 @GENERAL_HELP@
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62 </help>
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63
52cec2e123fa "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit 5305d1a60fe5bf5f1abfec332d432b9d362f1f83"
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64 <expand macro="citations" />
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65 </tool>