Mercurial > repos > recetox > aplcms_unsupervised

annotate aplcms_unsupervised.xml @ 0:7c80b743a2db draft

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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
author recetox
date Sun, 18 Oct 2020 10:35:33 +0000
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children bcc9f27fea2b
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7c80b743a2db "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
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1 <tool id="aplcms_unsupervised" name="apLCMS - Unsupervised" version="@TOOL_VERSION@+galaxy1">
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2 <macros>
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3 <import>aplcms_macros.xml</import>
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4 </macros>
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7c80b743a2db "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
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6 <expand macro="requirements" />
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7c80b743a2db "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
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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 $files])
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7c80b743a2db "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
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11 Rscript
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12 -e 'x <- apLCMS::unsupervised(
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13 files = c("$file_str"),
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14 min_exp = $noise_filtering.min_exp,
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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,
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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, $feature_detection.sd_cut_max),
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27 sigma_ratio_lim = c($feature_detection.sigma_ratio_lim_min, $feature_detection.sigma_ratio_lim_max),
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28 component_eliminate = $feature_detection.component_eliminate,
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29 moment_power = $feature_detection.moment_power,
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30 align_chr_tol = $peak_alignment.align_chr_tol,
7c80b743a2db "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
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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 = $weak_signal_recovery.recover_min_count
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37 )'
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38 -e 'apLCMS::save_peaks_to_hdf("$peaks", x)'
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39 ]]></command>
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41 <expand macro="inputs">
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42 <expand macro="noise_filtering" />
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43 <expand macro="feature_detection" />
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44 <expand macro="peak_alignment" />
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45 <expand macro="weak_signal_recovery" />
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46 </expand>
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7c80b743a2db "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
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48 <outputs>
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49 <data name="peaks" format="h5" />
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50 </outputs>
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51
7c80b743a2db "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
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52 <tests>
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53 <test>
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54 <param name="files" value="mbr_test0.mzml,mbr_test1.mzml,mbr_test2.mzml" ftype="mzml"/>
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55 <output name="peaks" file="peaks_unsupervised.h5" ftype="h5" compare="sim_size" delta="1000"/>
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56 </test>
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57 </tests>
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59 <help>
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60 This is the Unsupervised version of apLCMS which is not relying on any existing knowledge about metabolites or
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61 any historically detected features. For such functionality please use the Hybrid version of apLCMS.
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62
7c80b743a2db "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit ecdfe141b4320e754cc9f3673cc33b7673441ed8"
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63 @GENERAL_HELP@
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64 </help>
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65
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66 <expand macro="citations" />
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67 </tool>