Mercurial > repos > recetox > recetox_aplcms_align_features

annotate macros.xml @ 3:1e2a13bcb5a7 draft

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
author recetox
date Mon, 03 Apr 2023 14:58:01 +0000
parents abe783e0daca
children c44c73efd6e5
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57c644d3f24c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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1 <macros>
3
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2 <token name="@TOOL_VERSION@">0.10.3</token>
0
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3 <xml name="requirements">
57c644d3f24c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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4 <requirements>
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5 <requirement type="package" version="@TOOL_VERSION@">r-recetox-aplcms</requirement>
2
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6 <requirement type="package" version="2.5.2">pymzml</requirement>
0
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7 </requirements>
57c644d3f24c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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8 </xml>
57c644d3f24c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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9
57c644d3f24c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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10 <xml name="creator">
57c644d3f24c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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11 <creator>
57c644d3f24c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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12 <person
57c644d3f24c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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13 givenName="Maksym"
57c644d3f24c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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14 familyName="Skoryk"
57c644d3f24c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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15 url="https://github.com/maximskorik"
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16 identifier="0000-0003-2056-8018" />
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17 <person
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18 givenName="Matej"
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19 familyName="Troják"
57c644d3f24c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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20 url="https://github.com/xtrojak"
57c644d3f24c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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21 identifier="0000-0003-0841-2707" />
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22 <person
57c644d3f24c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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23 givenName="Martin"
57c644d3f24c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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24 familyName="Čech"
57c644d3f24c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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25 url="https://github.com/martenson"
57c644d3f24c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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26 identifier="0000-0002-9318-1781" />
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27 <person
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28 givenName="Jiří"
57c644d3f24c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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29 familyName="Novotný"
57c644d3f24c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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30 url="https://github.com/xtracko"
57c644d3f24c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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31 identifier="0000-0001-5449-3523" />
2
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32 <person
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33 givenName="Helge"
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34 familyName="Hecht"
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35 url="https://github.com/hechth"
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36 identifier="0000-0001-6744-996X" />
0
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37 <organization
57c644d3f24c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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38 url="https://www.recetox.muni.cz/"
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39 email="GalaxyToolsDevelopmentandDeployment@space.muni.cz"
57c644d3f24c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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40 name="RECETOX MUNI"/>
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41 </creator>
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42 </xml>
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43
2
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44 <xml name="remove_noise_params">
3
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45 <param name="min_pres" type="float" value="0.5" label="Minimal signal presence [fraction of scans]"
2
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46 help="The minimum proportion of presence in the time period for a series of signals grouped by m/z to be considered a peak." />
3
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47 <param name="min_run" type="float" value="12" label="Minimal elution time [unit corresponds to the retention time]"
2
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48 help="The minimum length of elution time for a series of signals grouped by m/z to be considered a peak." />
3
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49 <param name="mz_tol" type="float" value="10" label="m/z tolerance [ppm]"
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50 help="The m/z tolerance level for the grouping of data points. This value is expressed as the fraction of the m/z value.
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51 This value, multiplied by the m/z value, becomes the cutoff level.
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52 The recommended value is the machine's nominal accuracy level (e.g. for FTMS, it is 10)." />
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53 <param name="baseline_correct" type="float" value="0" label="Baseline correction [unit of signal intensity]"
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54 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." />
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55 <param name="intensity_weighted" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Weight intensity"
2
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56 help="Whether to weight the local density by signal intensities in initial peak detection." />
0
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57 </xml>
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58
2
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59 <xml name="generate_feature_table_params">
3
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60 <param name="BIC_factor" type="float" value="2.0" label="BIC factor"
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61 help="A factor influencing Bayesian information criterion (BIC) in estimation of RT peak shape.
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62 If the value is larger than 1, models with more peaks are penalized more." />
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63 <section name="advanced" title="Advanced" expanded="false">
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64 <param name="component_eliminate" type="float" value="0.01" label="Component eliminate"
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65 help="In fitting mixture of bi-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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66 <section name="shape_model" title="Shape model deviations" expanded="true">
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67 <param name="sigma_ratio_lim_min" type="float" optional="true" label="Minimal sigma ratio"
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68 help="The lower limit of the ratio range between the left-standard deviation and the right-standard deviation of the bi-Gaussian function to fit the data." />
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69 <param name="sigma_ratio_lim_max" type="float" optional="true" label="Maximal sigma ratio"
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70 help="The upper limit of the ratio range between the left-standard deviation and the right-standard deviation of the bi-Gaussian function to fit the data." />
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71 </section>
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72 <conditional name="sd_cut">
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73 <param name="sd_cut_bounds" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Standard deviations boundaries."
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74 help="Do not apply any limitations on the standard deviations." />
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75 <when value="FALSE">
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76 <param name="sd_cut_min" type="float" value="0.01" label="Minimal standard deviation"
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77 help="The minimum standard deviation - features with a standard deviation lower than this number are eliminated." />
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78 <param name="sd_cut_max" type="float" value="500" label="Maximal standard deviation"
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79 help="The maximum standard deviation - features with a standard deviation greater than this number are eliminated." />
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80 </when>
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81 </conditional>
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82 <conditional name="peak_estim">
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83 <param name="peak_estim_method" type="select" display="radio" label="Peak estimation method"
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84 help="The estimation method for parameters of the bi-Gaussian peak model. Two possible algorithms: moment and EM (expectation maximization).">
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85 <option value="moment">Moment</option>
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86 <option value="EM" selected="true">EM</option>
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87 </param>
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88 <when value="moment">
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89 <param name="moment_power" type="float" value="1" label="Moment power"
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90 help="The power parameter for data transformation when fitting the bi-Gaussian mixture model in an EIC." />
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91 </when>
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92 </conditional>
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93 </section>
0
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94 </xml>
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95
2
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96 <xml name="compute_clusters_params">
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97 <conditional name="tolerances_input_method">
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98 <param name="input_method" type="select" display="radio" label="Tolerances input method"
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99 help="Tolerances can be entered directly or loaded from a file.">
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100 <option value="direct" selected="true">direct</option>
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101 <option value="file">file</option>
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102 </param>
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103 <when value="direct">
3
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104 <param name="mz_tol_relative" type="float" optional="true" label="Relative m/z tolerance"
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105 help="Relative m/z tolerance to use for grouping features.
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106 If not provided, it is calculated from the data using kernel density estimation." />
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107 <param name="rt_tol_relative" type="float" optional="true" label="Relative rt tolerance [unit corresponds to the retention time]"
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108 help="Relative retention time tolerance to use for grouping features.
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109 If not provided, it is calculated from the data using kernel density estimation." />
2
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110 </when>
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111 <when value="file">
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112 <param label="Input tolerances values" name="input_tolerances" type="data" format="parquet"
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113 help="Table containing tolerance values." />
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114 </when>
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115 </conditional>
3
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116 <param name="mz_tol_absolute" type="float" label="Minimal absolute m/z tolerance [Da]" value="1e-05"
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117 help="During the clustering, an m/z tolerance is computed based on the data and the specified relative tolerance.
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118 This parameter allows the specification of a minimal value of this tolerance." />
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119 <param name="mz_max_diff" type="float" label="Maximal m/z difference [Da]" value="0.01"
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120 help="Maximum allowed difference between feature m/z values to belong to the same cluster." />
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121
0
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122 </xml>
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123
2
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124 <xml name="recover_weaker_params">
3
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125 <param name="mz_tol" type="float" value="10" label="m/z tolerance [ppm]"
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126 help="The m/z tolerance level for the grouping of data points. This value is expressed as the fraction of the m/z value.
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127 This value, multiplied by the m/z value, becomes the cutoff level.
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128 The recommended value is the machine's nominal accuracy level (e.g. for FTMS, it is 10)." />
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129 <param name="recover_mz_range" type="float" optional="true" label="Range for m/z recovery [ppm]"
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130
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131 help="The m/z around the feature m/z to search for observations. If not given, 1.5 times the m/z tolerance
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132 in the aligned object will be used." />
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133 <param name="recover_rt_range" type="float" optional="true" label="Range for rt recovery [unit of retention time]"
2
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134 help="The retention time around the feature retention time to search for observations.
3
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135 If not given, 0.5 times the retention time tolerance in the aligned object will be used." />
2
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136 <param name="use_observed_range" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE"
3
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137 label="Use observed rt range" help="Use the minimal and maximal rt values per feature." />
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138 <param name="recover_min_count" type="integer" value="3" label="Minimal count to recover"
2
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139 help="The minimum number of raw data points to be considered as a true feature." />
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140 <param name="intensity_weighted" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE"
3
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141 label="Weight intensity" help="Whether to weight the local density by signal intensities in initial peak detection." />
0
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142 </xml>
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143
2
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144 <xml name="bandwidth_params">
3
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145 <param name="bandwidth" type="float" value="0.5" label="Bandwidth factor" min="0" max="1"
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146 help="Parameter used to scale down the overall range of retention times (the bandwidth) assumed in the kernel smoother
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147 used for peak identification. The value is between zero and one. The minimal and maximal bandwidth can be limited by explicit values." />
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148 <param name="min_bandwidth" type="float" optional="true" label="Minimal bandwidth [unit corresponds to the retention time]"
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149 help="The lower limit on the resulting bandwidth. If not given, it is estimated based on the overall range of retention times in the profile." />
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150 <param name="max_bandwidth" type="float" optional="true" label="Maximal bandwidth [unit corresponds to the retention time]"
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151 help="The upper limit on the resulting bandwidth. If not given, it is estimated based on the overall range of retention times in the profile" />
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152
0
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153 </xml>
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154
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155 <xml name="citations">
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156 <citations>
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157 <citation type="doi">10.1093/bioinformatics/btp291</citation>
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158 <citation type="doi">10.1186/1471-2105-11-559</citation>
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159 <citation type="doi">10.1021/pr301053d</citation>
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160 <citation type="doi">10.1093/bioinformatics/btu430</citation>
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161 <citation type="doi">10.1038/s41598-020-70850-0</citation>
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57c644d3f24c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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162 <yield />
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163 </citations>
57c644d3f24c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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164 </xml>
57c644d3f24c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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165 </macros>