Mercurial > repos > recetox > recetox_aplcms_two_step_hybrid

annotate macros.xml @ 0:bd044e7eebbd draft

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
author recetox
date Thu, 26 May 2022 16:45:36 +0000
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children 886d52fd343f
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bd044e7eebbd planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
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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="0.9.4">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 <yield />
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15 <person
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16 givenName="Martin"
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17 familyName="Čech"
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18 url="https://github.com/martenson"
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19 identifier="0000-0002-9318-1781" />
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20 <person
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21 givenName="Jiří"
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22 familyName="Novotný"
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23 url="https://github.com/xtracko"
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24 identifier="0000-0001-5449-3523" />
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25 <organization
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26 url="https://www.recetox.muni.cz/"
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27 email="GalaxyToolsDevelopmentandDeployment@space.muni.cz"
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28 name="RECETOX MUNI"/>
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29 </creator>
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30 </xml>
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31
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32 <xml name="inputs">
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33 <inputs>
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34 <param name="files" type="data" format="mzdata,mzml,mzxml,netcdf" multiple="true" min="3" label="data"
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35 help="Mass spectrometry files for peak extraction." />
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36 <yield />
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37 </inputs>
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38 </xml>
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39
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40 <xml name="history_db">
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41 <param name="known_table" type="data" format="parquet" label="known_table"
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42 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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43 <section name="history_db" title="Known-Table settings">
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44 <param name="match_tol_ppm" type="integer" optional="true" min="0" label="match_tol_ppm (optional)"
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45 help="The ppm tolerance to match identified features to known metabolites/features." />
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46 <param name="new_feature_min_count" type="integer" value="2" min="1" label="new_feature_min_count"
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47 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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48 </section>
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49 </xml>
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50
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51 <xml name="noise_filtering">
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52 <section name="noise_filtering" title="Noise filtering and peak detection">
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53 <yield />
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54 <param name="min_pres" type="float" value="0.5"
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55 label="min_pres"
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56 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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57 <param name="min_run" type="float" value="12"
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58 label="min_run"
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59 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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60 <param name="mz_tol" type="float" value="1e-05"
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61 label="mz_tol"
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62 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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63 <param name="baseline_correct" type="float" value="0" label="baseline_correct"
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64 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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65 <param name="baseline_correct_noise_percentile" type="float" value="0.05"
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66 label="baseline_correct_noise_percentile"
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67 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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68 <param name="intensity_weighted" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE"
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69 label="intensity_weighted"
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70 help="Whether to weight the local density by signal intensities in initial peak detection." />
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71 </section>
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72 </xml>
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73
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74 <xml name="feature_detection">
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75 <section name="feature_detection" title="Feature detection">
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76 <param name="shape_model" type="select" display="radio"
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77 label="shape_model"
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78 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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79 <option value="Gaussian">Gaussian</option>
bd044e7eebbd planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
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80 <option value="bi-Gaussian" selected="true">bi-Gaussian</option>
bd044e7eebbd planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
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81 </param>
bd044e7eebbd planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
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82 <param name="BIC_factor" type="float" value="2.0"
bd044e7eebbd planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
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83 label="BIC_factor"
bd044e7eebbd planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
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84 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." />
bd044e7eebbd planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
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85 <param name="peak_estim_method" type="select" display="radio"
bd044e7eebbd planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
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86 label="peak_estim_method"
bd044e7eebbd planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
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87 help="The estimation method for the bi-Gaussian peak model. Two possible values: moment and EM.">
bd044e7eebbd planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
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88 <option value="moment" selected="true">Moment</option>
bd044e7eebbd planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
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89 <option value="EM">EM</option>
bd044e7eebbd planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
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90 </param>
bd044e7eebbd planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
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91 <param name="min_bandwidth" type="float" optional="true"
bd044e7eebbd planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
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92 label="min_bandwidth (optional)"
bd044e7eebbd planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
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93 help="The minimum bandwidth to use in the kernel smoother." />
bd044e7eebbd planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
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94 <param name="max_bandwidth" type="float" optional="true"
bd044e7eebbd planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
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95 label="max_bandwidth (optional)"
bd044e7eebbd planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
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96 help="The maximum bandwidth to use in the kernel smoother." />
bd044e7eebbd planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
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97 <param name="sd_cut_min" type="float" value="0.01"
bd044e7eebbd planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
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98 label="sd_cut_min"
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99 help="The minimum standard deviation of a feature to be not eliminated." />
bd044e7eebbd planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
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100 <param name="sd_cut_max" type="float" value="500"
bd044e7eebbd planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
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101 label="sd_cut_max"
bd044e7eebbd planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
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102 help="The maximum standard deviation of a feature to be not eliminated." />
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103 <param name="sigma_ratio_lim_min" type="float" value="0.01"
bd044e7eebbd planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
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104 label="sigma_ratio_lim_min"
bd044e7eebbd planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
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105 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." />
bd044e7eebbd planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
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106 <param name="sigma_ratio_lim_max" type="float" value="100"
bd044e7eebbd planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
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107 label="sigma_ratio_lim_max"
bd044e7eebbd planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
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108 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." />
bd044e7eebbd planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
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109 <param name="component_eliminate" type="float" value="0.01"
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110 label="component_eliminate"
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111 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." />
bd044e7eebbd planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
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112 <param name="moment_power" type="float" value="1"
bd044e7eebbd planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
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113 label="moment_power"
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114 help="The power parameter for data transformation when fitting the bi-Gaussian or Gaussian mixture model in an EIC." />
bd044e7eebbd planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
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115 </section>
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116 </xml>
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117
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118 <xml name="peak_alignment">
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119 <section name="peak_alignment" title="Peak Alignment">
bd044e7eebbd planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
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120 <param name="align_chr_tol" type="float" optional="true"
bd044e7eebbd planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
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121 label="align_chr_tol (optional)"
bd044e7eebbd planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
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122 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." />
bd044e7eebbd planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
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123 <param name="align_mz_tol" type="float" optional="true"
bd044e7eebbd planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
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124 label="align_mz_tol (optional)"
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125 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." />
bd044e7eebbd planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
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126 <param name="max_align_mz_diff" type="float" value="0.01"
bd044e7eebbd planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
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127 label="max_align_mz_diff"
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128 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." />
bd044e7eebbd planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
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129 </section>
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130 </xml>
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131
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132 <xml name="weak_signal_recovery">
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133 <section name="weak_signal_recovery" title="Weak Signal Recovery">
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134 <param name="recover_mz_range" type="float" optional="true"
bd044e7eebbd planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
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135 label="recover_mz_range (optional)"
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136 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." />
bd044e7eebbd planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
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137 <param name="recover_chr_range" type="float" optional="true"
bd044e7eebbd planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
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138 label="recover_chr_range (optional)"
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139 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." />
bd044e7eebbd planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
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140 <param name="use_observed_range" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE"
bd044e7eebbd planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
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141 label="use_observed_range"
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142 help="If the value is true, the actual range of the observed locations of the feature in all the spectra will be used." />
bd044e7eebbd planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
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143 <param name="recover_min_count" type="integer" value="3"
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144 label="recover_min_count"
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145 help="The minimum number of raw data points to be considered as a true feature." />
bd044e7eebbd planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
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146 </section>
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147 </xml>
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148 <xml name="multibatch_processing">
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149 <section name="multibatch_processing" title="Multibatch processing">
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150 <param name="min_within_batch_prop_detect" type="float" min="0" max="1" value="0.1"
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151 label="minimum_batchwise_prop_detect"
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152 help="The minimum detection frequency (relative) of a feature for it to be included in the final feature table." />
bd044e7eebbd planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
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153 <param name="min_batch_prop" type="float" min="0" max="1" value="0.5"
bd044e7eebbd planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
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154 label="minimum_batch_prop"
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155 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." />
bd044e7eebbd planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
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156 <param name="batch_align_mz_tol" type="float" min="0" value="0.00001"
bd044e7eebbd planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
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157 label="batch_align_mz_tol"
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158 help="The m/z tolerance level for peak alignment within batch." />
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159 <param name="batch_align_chr_tol" type="float" min="0" value="50.0"
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160 label="batch_align_chr_tol"
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161 help="The retention time tolerance level for peak alignment within batch." />
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162 </section>
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163 </xml>
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164 <xml name="output_format">
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165 <section name="output_format" title="Output Format">
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166 <param name="out_format" type="boolean" checked="false" truevalue="recetox" falsevalue="original" label="Use custom RECETOX output format?" />
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167 </section>
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168 </xml>
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169
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170 <xml name="unsupervised_outputs">
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171 <data name="recovered_feature_sample_table" format="parquet" label="${tool.name} recovered_feature_sample_table on ${on_string}" />
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172 <data name="aligned_feature_sample_table" format="parquet" label="${tool.name} aligned_feature_sample_table on ${on_string}" hidden="true" />
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173 <data name="updated_known_table" format="parquet" label="${tool.name} updated_known_table on ${on_string}"/>
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174 <yield />
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175 </xml>
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176
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177 <xml name="citations">
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178 <citations>
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179 <citation type="doi">10.1093/bioinformatics/btp291</citation>
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180 <citation type="doi">10.1186/1471-2105-11-559</citation>
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181 <citation type="doi">10.1021/pr301053d</citation>
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182 <citation type="doi">10.1093/bioinformatics/btu430</citation>
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183 <yield />
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184 </citations>
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185 </xml>
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186
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187 <token name="@HELP_hybrid@">
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188 <![CDATA[
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189 This is the Hybrid version of apLCMS which is incorporating the knowledge of known metabolites and historically
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190 detected features on the same machinery to help detect and quantify lower-intensity peaks.
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191
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192 CAUTION: To use such knowledge, especially historical data, you must keep using (1) the same chromatography
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193 system (otherwise the retention time will not match), and (2) the same type of samples with similar extraction
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194 technique, such as human serum.
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195
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196 @GENERAL_HELP@
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197 ]]>
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198 </token>
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199
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200 <token name="@HELP_unsupervised@">
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201 <![CDATA[
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202 This is the Unsupervised version of apLCMS which is not relying on any existing knowledge about metabolites or
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203 any historically detected features. For such functionality please use the Hybrid version of apLCMS.
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204
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205 @GENERAL_HELP@
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206 ]]>
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207 </token>
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208
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209 <token name="@HELP_two-step-hybrid@">
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210 <![CDATA[
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211 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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212 effects in multi-batch experiments. As in the Hybrid version, this tool incorporates the knowledge of known metabolites and
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213 historically detected features on the same machinery to help detect and quantify lower-intensity peaks.
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214
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215 **CAUTION**: To use such knowledge, especially historical data, you must keep using (1) the same chromatography
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216 system (otherwise the retention time will not match), and (2) the same type of samples with similar extraction
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217 technique, such as human serum.
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218
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219 @GENERAL_HELP@
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220 ]]>
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221 </token>
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222
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223 <token name="@GENERAL_HELP@">
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224 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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225 tolerance levels are estimated from the data. A run-filter is used to detect peaks and remove noise.
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226 Non-parametric statistical methods are used to find-tune peak selection and grouping. After retention time
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227 correction, a feature table is generated by aligning peaks across spectra. For further information on apLCMS
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228 please refer to https://mypage.cuhk.edu.cn/academics/yutianwei/apLCMS/.
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229 </token>
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230 </macros>