Mercurial > repos > recetox > recetox_aplcms_unsupervised

annotate recetox_aplcms_macros.xml @ 6:7e0838248fbd draft

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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 636146595a7067d7062961dbfa834f366c342156"
author recetox
date Sun, 20 Jun 2021 09:14:36 +0000
parents d06ec5e6721c
children 6925295ae5c3
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1b9140057e5a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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1 <macros>
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2 <token name="@TOOL_VERSION@">0.9.3</token>
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1b9140057e5a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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4 <xml name="requirements">
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5 <requirements>
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7e0838248fbd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 636146595a7067d7062961dbfa834f366c342156"
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6 <requirement type="package" version="4.1.0">r-base</requirement>
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7 <requirement type="package" version="4.0.1">r-arrow</requirement>
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8 <requirement type="package" version="0.9.3">r-recetox-aplcms</requirement>
1b9140057e5a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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9 </requirements>
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10 </xml>
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1b9140057e5a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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12 <xml name="inputs">
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13 <inputs>
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14 <param name="files" type="data" format="mzdata,mzml,mzxml,netcdf" multiple="true" min="3" label="data"
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15 help="Mass spectrometry files for peak extraction." />
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16 <yield />
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17 </inputs>
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18 </xml>
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20 <xml name="history_db">
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21 <param name="known_table" type="data" format="parquet" label="known_table"
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22 help="A data table containing the known metabolite ions and previously found features. The table must contain these 18 columns: chemical_formula (optional), HMDB_ID (optional), KEGG_compound_ID (optional), neutral.mass (optional), ion.type (the ion form - optional), m.z (either theoretical or mean observed m/z value of previously found features), Number_profiles_processed (the total number of processed samples to build this database), Percent_found (the percentage of historically processed samples in which the feature appeared), mz_min (minimum observed m/z value), mz_max (maximum observed m/z value), RT_mean (mean observed retention time), RT_sd (standard deviation of observed retention time), RT_min (minimum observed retention time), RT_max (maximum observed retention time), int_mean.log. (mean observed log intensity), int_sd.log. (standard deviation of observed log intensity), int_min.log. (minimum observed log intensity), int_max.log. (maximum observed log intensity)." />
1b9140057e5a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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23 <section name="history_db" title="Known-Table settings">
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24 <param name="match_tol_ppm" type="integer" optional="true" min="0" label="match_tol_ppm (optional)"
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25 help="The ppm tolerance to match identified features to known metabolites/features." />
1b9140057e5a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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26 <param name="new_feature_min_count" type="integer" value="2" min="1" label="new_feature_min_count"
1b9140057e5a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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27 help="The minimum number of occurrences of a historically unseen (unknown) feature to add this feature into the database of known features." />
1b9140057e5a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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28 </section>
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29 </xml>
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31 <xml name="noise_filtering">
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32 <section name="noise_filtering" title="Noise filtering and peak detection">
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33 <param name="min_exp" type="integer" min="1" value="2"
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34 label="min_exp"
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35 help="If a feature is to be included in the final feature table, it must be present in at least this number of spectra." />
1b9140057e5a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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36 <param name="min_pres" type="float" value="0.5"
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37 label="min_pres"
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38 help="The minimum proportion of presence in the time period for a series of signals grouped by m/z to be considered a peak." />
1b9140057e5a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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39 <param name="min_run" type="float" value="12"
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40 label="min_run"
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41 help="The minimum length of elution time for a series of signals grouped by m/z to be considered a peak." />
1b9140057e5a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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42 <param name="mz_tol" type="float" value="1e-05"
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43 label="mz_tol"
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44 help="The m/z tolerance level for the grouping of data points. This value is expressed as the fraction of the m/z value. This value, multiplied by the m/z value, becomes the cutoff level. The recommended value is the machine's nominal accuracy level. Divide the ppm value by 1e6. For FTMS, 1e-5 is recommended." />
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45 <param name="baseline_correct" type="float" value="0" label="baseline_correct"
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46 help="After grouping the observations, the highest intensity in each group is found. If the highest is lower than this value, the entire group will be deleted. The default value is NA, in which case the program uses a percentile of the height of the noise groups. If given a value, the value will be used as the threshold, and baseline.correct.noise.percentile will be ignored." />
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47 <param name="baseline_correct_noise_percentile" type="float" value="0.05"
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48 label="baseline_correct_noise_percentile"
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49 help="The percentile of signal strength of those EIC that don't pass the run filter, to be used as the baseline threshold of signal strength." />
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50 <param name="intensity_weighted" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE"
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51 label="intensity_weighted"
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52 help="Whether to weight the local density by signal intensities in initial peak detection." />
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53 </section>
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54 </xml>
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56 <xml name="feature_detection">
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57 <section name="feature_detection" title="Feature detection">
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58 <param name="shape_model" type="select" display="radio"
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59 label="shape_model"
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60 help="The mathematical model for the shape of a peak. There are two choices - bi-Gaussian and Gaussian. When the peaks are asymmetric, the bi-Gaussian is better.">
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61 <option value="Gaussian">Gaussian</option>
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62 <option value="bi-Gaussian" selected="true">bi-Gaussian</option>
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63 </param>
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64 <param name="BIC_factor" type="float" value="2.0"
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65 label="BIC_factor"
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66 help="The factor that is multiplied on the number of parameters to modify the BIC criterion. If larger than 1, models with more peaks are penalized more." />
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67 <param name="peak_estim_method" type="select" display="radio"
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68 label="peak_estim_method"
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69 help="The estimation method for the bi-Gaussian peak model. Two possible values: moment and EM.">
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70 <option value="moment" selected="true">Moment</option>
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71 <option value="EM">EM</option>
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72 </param>
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73 <param name="min_bandwidth" type="float" optional="true"
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74 label="min_bandwidth (optional)"
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75 help="The minimum bandwidth to use in the kernel smoother." />
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76 <param name="max_bandwidth" type="float" optional="true"
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77 label="max_bandwidth (optional)"
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78 help="The maximum bandwidth to use in the kernel smoother." />
1b9140057e5a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
recetox
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diff changeset
79 <param name="sd_cut_min" type="float" value="0.01"
1b9140057e5a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
recetox
parents:
diff changeset
80 label="sd_cut_min"
1b9140057e5a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
recetox
parents:
diff changeset
81 help="The minimum standard deviation of a feature to be not eliminated." />
1b9140057e5a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
recetox
parents:
diff changeset
82 <param name="sd_cut_max" type="float" value="500"
1b9140057e5a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
recetox
parents:
diff changeset
83 label="sd_cut_max"
1b9140057e5a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
recetox
parents:
diff changeset
84 help="The maximum standard deviation of a feature to be not eliminated." />
1b9140057e5a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
recetox
parents:
diff changeset
85 <param name="sigma_ratio_lim_min" type="float" value="0.01"
1b9140057e5a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
recetox
parents:
diff changeset
86 label="sigma_ratio_lim_min"
1b9140057e5a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
recetox
parents:
diff changeset
87 help="The lower limit of the believed ratio range between the left-standard deviation and the right-standard deviation of the bi-Gaussian function used to fit the data." />
1b9140057e5a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
recetox
parents:
diff changeset
88 <param name="sigma_ratio_lim_max" type="float" value="100"
1b9140057e5a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
recetox
parents:
diff changeset
89 label="sigma_ratio_lim_max"
1b9140057e5a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
recetox
parents:
diff changeset
90 help="The upper limit of the believed ratio range between the left-standard deviation and the right-standard deviation of the bi-Gaussian function used to fit the data." />
1b9140057e5a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
recetox
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diff changeset
91 <param name="component_eliminate" type="float" value="0.01"
1b9140057e5a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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92 label="component_eliminate"
1b9140057e5a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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diff changeset
93 help="In fitting mixture of bi-Gaussian (or Gaussian) model of an EIC, when a component accounts for a proportion of intensities less than this value, the component will be ignored." />
1b9140057e5a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
recetox
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diff changeset
94 <param name="moment_power" type="float" value="1"
1b9140057e5a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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95 label="moment_power"
1b9140057e5a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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96 help="The power parameter for data transformation when fitting the bi-Gaussian or Gaussian mixture model in an EIC." />
1b9140057e5a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
recetox
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diff changeset
97 </section>
1b9140057e5a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
recetox
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diff changeset
98 </xml>
1b9140057e5a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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99
1b9140057e5a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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diff changeset
100 <xml name="peak_alignment">
1b9140057e5a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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101 <section name="peak_alignment" title="Peak Alignment">
1b9140057e5a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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102 <param name="align_chr_tol" type="float" optional="true"
1b9140057e5a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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103 label="align_chr_tol (optional)"
1b9140057e5a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
recetox
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diff changeset
104 help="The retention time tolerance level for peak alignment. The default is NA, which allows the program to search for the tolerance level based on the data." />
1b9140057e5a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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diff changeset
105 <param name="align_mz_tol" type="float" optional="true"
1b9140057e5a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
recetox
parents:
diff changeset
106 label="align_mz_tol (optional)"
1b9140057e5a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
recetox
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diff changeset
107 help="The m/z tolerance level for peak alignment. The default is NA, which allows the program to search for the tolerance level based on the data. The tolerance is given in absolute numbers, not scaled, i.e. for 10ppm tolerance enter '1e-05'. This value, multiplied by the m/z value, becomes the cutoff level." />
1b9140057e5a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
recetox
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diff changeset
108 <param name="max_align_mz_diff" type="float" value="0.01"
1b9140057e5a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
recetox
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diff changeset
109 label="max_align_mz_diff"
1b9140057e5a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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diff changeset
110 help="As the m/z tolerance is expressed in relative terms (ppm), it may not be suitable when the m/z range is wide. This parameter limits the tolerance in absolute terms. It mostly influences feature matching in higher m/z range." />
1b9140057e5a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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diff changeset
111 </section>
1b9140057e5a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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112 </xml>
1b9140057e5a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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113
1b9140057e5a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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114 <xml name="weak_signal_recovery">
1b9140057e5a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
recetox
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115 <section name="weak_signal_recovery" title="Weak Signal Recovery">
1b9140057e5a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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116 <param name="recover_mz_range" type="float" optional="true"
1b9140057e5a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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117 label="recover_mz_range (optional)"
1b9140057e5a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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diff changeset
118 help="The m/z around the feature m/z to search for observations. The default value is NA, in which case 1.5 times the m/z tolerance in the aligned object will be used." />
1b9140057e5a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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119 <param name="recover_chr_range" type="float" optional="true"
1b9140057e5a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
recetox
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120 label="recover_chr_range (optional)"
1b9140057e5a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
recetox
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diff changeset
121 help="The retention time around the feature retention time to search for observations. The default value is NA, in which case 0.5 times the retention time tolerance in the aligned object will be used." />
1b9140057e5a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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122 <param name="use_observed_range" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE"
1b9140057e5a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
recetox
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123 label="use_observed_range"
1b9140057e5a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
recetox
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124 help="If the value is true, the actual range of the observed locations of the feature in all the spectra will be used." />
1b9140057e5a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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125 <param name="recover_min_count" type="integer" value="3"
1b9140057e5a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
recetox
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126 label="recover_min_count"
1b9140057e5a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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127 help="The minimum number of raw data points to be considered as a true feature." />
1b9140057e5a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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128 </section>
1b9140057e5a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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129 </xml>
1b9140057e5a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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130
1b9140057e5a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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diff changeset
131 <xml name="unsupervised_outputs">
1b9140057e5a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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132 <data name="recovered_feature_sample_table" format="parquet" label="${tool.name} recovered_feature_sample_table on ${on_string}" />
1b9140057e5a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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133 <data name="aligned_feature_sample_table" format="parquet" label="${tool.name} aligned_feature_sample_table on ${on_string}" hidden="true" />
1b9140057e5a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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134 <collection name="corrected_features" type="list" label="${tool.name} corrected_features on ${on_string}">
1b9140057e5a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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135 <discover_datasets pattern="__designation__" directory="corrected" format="parquet" />
1b9140057e5a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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136 </collection >
1b9140057e5a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
recetox
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137 <collection name="extracted_features" type="list" label="${tool.name} extracted_features on ${on_string}">
1b9140057e5a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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138 <discover_datasets pattern="__designation__" directory="extracted" format="parquet" />
1b9140057e5a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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139 </collection >
1b9140057e5a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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140 </xml>
1b9140057e5a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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141
1b9140057e5a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
recetox
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142 <token name="@GENERAL_HELP@">
1b9140057e5a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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143 apLCMS is a software which generates a feature table from a batch of LC/MS spectra. The m/z and retention time
1b9140057e5a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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144 tolerance levels are estimated from the data. A run-filter is used to detect peaks and remove noise.
1b9140057e5a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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145 Non-parametric statistical methods are used to find-tune peak selection and grouping. After retention time
1b9140057e5a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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146 correction, a feature table is generated by aligning peaks across spectra. For further information on apLCMS
1b9140057e5a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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147 please refer to https://mypage.cuhk.edu.cn/academics/yutianwei/apLCMS/.
1b9140057e5a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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148 </token>
1b9140057e5a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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149
1b9140057e5a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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150 <xml name="citations">
1b9140057e5a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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151 <citations>
1b9140057e5a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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152 <citation type="doi">10.1093/bioinformatics/btp291</citation>
1b9140057e5a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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153 <citation type="doi">10.1186/1471-2105-11-559</citation>
1b9140057e5a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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154 <citation type="doi">10.1021/pr301053d</citation>
1b9140057e5a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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155 <citation type="doi">10.1093/bioinformatics/btu430</citation>
1b9140057e5a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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156 </citations>
1b9140057e5a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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157 </xml>
1b9140057e5a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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158 </macros>