Mercurial > repos > recetox > recetox_aplcms_recover_weaker_signals

annotate macros.xml @ 0:f8f6095377be draft

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
author recetox
date Fri, 10 Jun 2022 10:14:03 +0000
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children 0c56ad04560b
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f8f6095377be planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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1 <macros>
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2 <token name="@TOOL_VERSION@">0.9.4</token>
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3 <xml name="requirements">
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4 <requirements>
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5 <requirement type="package" version="4.1.0">r-base</requirement>
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6 <requirement type="package" version="4.0.1">r-arrow</requirement>
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7 <requirement type="package" version="@TOOL_VERSION@">r-recetox-aplcms</requirement>
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8 <requirement type="package" version="1.0.7">r-dplyr</requirement>
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9 </requirements>
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10 </xml>
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11
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12 <xml name="creator">
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13 <creator>
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14 <person
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15 givenName="Maksym"
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16 familyName="Skoryk"
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17 url="https://github.com/maximskorik"
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18 identifier="0000-0003-2056-8018" />
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19 <person
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20 givenName="Matej"
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21 familyName="Troják"
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22 url="https://github.com/xtrojak"
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23 identifier="0000-0003-0841-2707" />
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24 <person
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25 givenName="Martin"
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26 familyName="Čech"
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27 url="https://github.com/martenson"
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28 identifier="0000-0002-9318-1781" />
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29 <person
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30 givenName="Jiří"
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31 familyName="Novotný"
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32 url="https://github.com/xtracko"
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33 identifier="0000-0001-5449-3523" />
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34 <organization
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35 url="https://www.recetox.muni.cz/"
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36 email="GalaxyToolsDevelopmentandDeployment@space.muni.cz"
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37 name="RECETOX MUNI"/>
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38 </creator>
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39 </xml>
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40
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41 <xml name="inputs">
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42 <inputs>
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43 <param name="files" type="data" format="mzdata,mzml,mzxml,netcdf" multiple="true" min="3" label="data"
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44 help="Mass spectrometry files for peak extraction." />
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45 <yield />
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46 </inputs>
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47 </xml>
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48
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49 <xml name="history_db">
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50 <param name="known_table" type="data" format="parquet" label="known_table"
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51 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)." />
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52 <section name="history_db" title="Known-Table settings">
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53 <param name="match_tol_ppm" type="integer" optional="true" min="0" label="match_tol_ppm (optional)"
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54 help="The ppm tolerance to match identified features to known metabolites/features." />
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55 <param name="new_feature_min_count" type="integer" value="2" min="1" label="new_feature_min_count"
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56 help="The minimum number of occurrences of a historically unseen (unknown) feature to add this feature into the database of known features." />
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57 </section>
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58 </xml>
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59
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60 <xml name="noise_filtering">
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61 <section name="noise_filtering" title="Noise filtering and peak detection">
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62 <yield />
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63 <param name="min_pres" type="float" value="0.5"
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64 label="min_pres"
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65 help="The minimum proportion of presence in the time period for a series of signals grouped by m/z to be considered a peak." />
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66 <param name="min_run" type="float" value="12"
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67 label="min_run"
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68 help="The minimum length of elution time for a series of signals grouped by m/z to be considered a peak." />
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69 <param name="mz_tol" type="float" value="1e-05"
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70 label="mz_tol"
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71 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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72 <param name="baseline_correct" type="float" value="0" label="baseline_correct"
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73 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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74 <param name="baseline_correct_noise_percentile" type="float" value="0.05"
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75 label="baseline_correct_noise_percentile"
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76 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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77 <param name="intensity_weighted" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE"
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78 label="intensity_weighted"
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79 help="Whether to weight the local density by signal intensities in initial peak detection." />
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80 </section>
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81 </xml>
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82
f8f6095377be planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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diff changeset
83 <xml name="feature_detection">
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diff changeset
84 <section name="feature_detection" title="Feature detection">
f8f6095377be planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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85 <param name="shape_model" type="select" display="radio"
f8f6095377be planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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86 label="shape_model"
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diff changeset
87 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.">
f8f6095377be planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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88 <option value="Gaussian">Gaussian</option>
f8f6095377be planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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89 <option value="bi-Gaussian" selected="true">bi-Gaussian</option>
f8f6095377be planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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diff changeset
90 </param>
f8f6095377be planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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diff changeset
91 <param name="BIC_factor" type="float" value="2.0"
f8f6095377be planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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diff changeset
92 label="BIC_factor"
f8f6095377be planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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diff changeset
93 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." />
f8f6095377be planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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94 <param name="peak_estim_method" type="select" display="radio"
f8f6095377be planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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95 label="peak_estim_method"
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96 help="The estimation method for the bi-Gaussian peak model. Two possible values: moment and EM.">
f8f6095377be planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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97 <option value="moment" selected="true">Moment</option>
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98 <option value="EM">EM</option>
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diff changeset
99 </param>
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100 <param name="min_bandwidth" type="float" optional="true"
f8f6095377be planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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101 label="min_bandwidth (optional)"
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diff changeset
102 help="The minimum bandwidth to use in the kernel smoother." />
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103 <param name="max_bandwidth" type="float" optional="true"
f8f6095377be planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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diff changeset
104 label="max_bandwidth (optional)"
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diff changeset
105 help="The maximum bandwidth to use in the kernel smoother." />
f8f6095377be planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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diff changeset
106 <param name="sd_cut_min" type="float" value="0.01"
f8f6095377be planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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107 label="sd_cut_min"
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108 help="The minimum standard deviation of a feature to be not eliminated." />
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109 <param name="sd_cut_max" type="float" value="500"
f8f6095377be planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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110 label="sd_cut_max"
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diff changeset
111 help="The maximum standard deviation of a feature to be not eliminated." />
f8f6095377be planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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112 <param name="sigma_ratio_lim_min" type="float" value="0.01"
f8f6095377be planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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113 label="sigma_ratio_lim_min"
f8f6095377be planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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114 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." />
f8f6095377be planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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115 <param name="sigma_ratio_lim_max" type="float" value="100"
f8f6095377be planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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116 label="sigma_ratio_lim_max"
f8f6095377be planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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diff changeset
117 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." />
f8f6095377be planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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118 <param name="component_eliminate" type="float" value="0.01"
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119 label="component_eliminate"
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120 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." />
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121 <param name="moment_power" type="float" value="1"
f8f6095377be planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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122 label="moment_power"
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123 help="The power parameter for data transformation when fitting the bi-Gaussian or Gaussian mixture model in an EIC." />
f8f6095377be planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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124 </section>
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diff changeset
125 </xml>
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126
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127 <xml name="peak_alignment">
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128 <section name="peak_alignment" title="Peak Alignment">
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129 <param name="align_chr_tol" type="float" optional="true"
f8f6095377be planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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130 label="align_chr_tol (optional)"
f8f6095377be planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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131 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." />
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132 <param name="align_mz_tol" type="float" optional="true"
f8f6095377be planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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133 label="align_mz_tol (optional)"
f8f6095377be planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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134 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." />
f8f6095377be planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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135 <param name="max_align_mz_diff" type="float" value="0.01"
f8f6095377be planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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136 label="max_align_mz_diff"
f8f6095377be planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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137 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." />
f8f6095377be planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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138 </section>
f8f6095377be planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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139 </xml>
f8f6095377be planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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140
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141 <xml name="weak_signal_recovery">
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142 <section name="weak_signal_recovery" title="Weak Signal Recovery">
f8f6095377be planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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143 <param name="recover_mz_range" type="float" optional="true"
f8f6095377be planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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144 label="recover_mz_range (optional)"
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145 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." />
f8f6095377be planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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146 <param name="recover_chr_range" type="float" optional="true"
f8f6095377be planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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147 label="recover_chr_range (optional)"
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148 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." />
f8f6095377be planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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149 <param name="use_observed_range" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE"
f8f6095377be planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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150 label="use_observed_range"
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151 help="If the value is true, the actual range of the observed locations of the feature in all the spectra will be used." />
f8f6095377be planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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152 <param name="recover_min_count" type="integer" value="3"
f8f6095377be planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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153 label="recover_min_count"
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154 help="The minimum number of raw data points to be considered as a true feature." />
f8f6095377be planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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155 </section>
f8f6095377be planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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156 </xml>
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157 <xml name="multibatch_processing">
f8f6095377be planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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158 <section name="multibatch_processing" title="Multibatch processing">
f8f6095377be planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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159 <param name="min_within_batch_prop_detect" type="float" min="0" max="1" value="0.1"
f8f6095377be planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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160 label="minimum_batchwise_prop_detect"
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161 help="The minimum detection frequency (relative) of a feature for it to be included in the final feature table." />
f8f6095377be planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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162 <param name="min_batch_prop" type="float" min="0" max="1" value="0.5"
f8f6095377be planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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163 label="minimum_batch_prop"
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164 help="The minimum proportion of batches that must have a given feature. The features that are less abundant than the value won't be reported." />
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165 <param name="batch_align_mz_tol" type="float" min="0" value="0.00001"
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166 label="batch_align_mz_tol"
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167 help="The m/z tolerance level for peak alignment within batch." />
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168 <param name="batch_align_chr_tol" type="float" min="0" value="50.0"
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169 label="batch_align_chr_tol"
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170 help="The retention time tolerance level for peak alignment within batch." />
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171 </section>
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172 </xml>
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173
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174 <xml name="mz_tol_macro">
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175 <param name="mz_tol" type="float" value="1e-05" label="mz_tol"
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176 help="The m/z tolerance level for the grouping of data points. This value is expressed as the
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177 fraction of the m/z value. This value, multiplied by the m/z value, becomes the cutoff level.
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178 The recommended value is the machine's nominal accuracy level. Divide the ppm value by 1e6.
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179 For FTMS, 1e-5 is recommended." />
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180 </xml>
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181
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182 <xml name="output_format">
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183 <section name="output_format" title="Output Format">
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184 <param name="out_format" type="boolean" checked="false" truevalue="recetox" falsevalue="original" label="Use custom RECETOX output format?" />
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185 </section>
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186 </xml>
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187
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188 <xml name="unsupervised_outputs">
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189 <data name="recovered_feature_sample_table" format="parquet" label="${tool.name} recovered_feature_sample_table on ${on_string}" />
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190 <data name="aligned_feature_sample_table" format="parquet" label="${tool.name} aligned_feature_sample_table on ${on_string}" hidden="true" />
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191 <yield />
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192 </xml>
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193
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194 <xml name="citations">
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195 <citations>
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196 <citation type="doi">10.1093/bioinformatics/btp291</citation>
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197 <citation type="doi">10.1186/1471-2105-11-559</citation>
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198 <citation type="doi">10.1021/pr301053d</citation>
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199 <citation type="doi">10.1093/bioinformatics/btu430</citation>
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200 <yield />
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201 </citations>
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202 </xml>
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203
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204 <token name="@HELP_hybrid@">
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205 <![CDATA[
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206 This is the Hybrid version of apLCMS which is incorporating the knowledge of known metabolites and historically
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207 detected features on the same machinery to help detect and quantify lower-intensity peaks.
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208
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209 CAUTION: To use such knowledge, especially historical data, you must keep using (1) the same chromatography
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210 system (otherwise the retention time will not match), and (2) the same type of samples with similar extraction
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211 technique, such as human serum.
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212
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213 @GENERAL_HELP@
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214 ]]>
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215 </token>
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216
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217 <token name="@HELP_unsupervised@">
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218 <![CDATA[
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219 This is the Unsupervised version of apLCMS which is not relying on any existing knowledge about metabolites or
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220 any historically detected features. For such functionality please use the Hybrid version of apLCMS.
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221
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222 @GENERAL_HELP@
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223 ]]>
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224 </token>
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225
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226 <token name="@HELP_two-step-hybrid@">
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227 <![CDATA[
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228 This is the **Two-Step Hybrid** version of **apLCMS**. This tool is improved upon the Hybrid version by accounting for the batch
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229 effects in multi-batch experiments. As in the Hybrid version, this tool incorporates the knowledge of known metabolites and
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230 historically detected features on the same machinery to help detect and quantify lower-intensity peaks.
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231
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232 **CAUTION**: To use such knowledge, especially historical data, you must keep using (1) the same chromatography
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233 system (otherwise the retention time will not match), and (2) the same type of samples with similar extraction
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234 technique, such as human serum.
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235
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236 @GENERAL_HELP@
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237 ]]>
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238 </token>
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239
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240 <token name="@GENERAL_HELP@">
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241 apLCMS is a software which generates a feature table from a batch of LC/MS spectra. The m/z and retention time
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242 tolerance levels are estimated from the data. A run-filter is used to detect peaks and remove noise.
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243 Non-parametric statistical methods are used to find-tune peak selection and grouping. After retention time
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244 correction, a feature table is generated by aligning peaks across spectra. For further information on apLCMS
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245 please refer to https://mypage.cuhk.edu.cn/academics/yutianwei/apLCMS/.
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246 </token>
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247 </macros>