Mercurial > repos > recetox > recetox_aplcms_recover_weaker_signals

annotate macros.xml @ 2:0c56ad04560b draft

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
author recetox
date Mon, 13 Feb 2023 10:26:04 +0000
parents f8f6095377be
children 30d04537d823
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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>
2
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2 <token name="@TOOL_VERSION@">0.10.1</token>
0
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3 <xml name="requirements">
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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>
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8 </xml>
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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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10 <xml name="creator">
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11 <creator>
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12 <person
f8f6095377be planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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13 givenName="Maksym"
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14 familyName="Skoryk"
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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"
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20 url="https://github.com/xtrojak"
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21 identifier="0000-0003-0841-2707" />
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22 <person
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23 givenName="Martin"
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24 familyName="Čech"
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25 url="https://github.com/martenson"
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26 identifier="0000-0002-9318-1781" />
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27 <person
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28 givenName="Jiří"
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29 familyName="Novotný"
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30 url="https://github.com/xtracko"
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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
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38 url="https://www.recetox.muni.cz/"
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39 email="GalaxyToolsDevelopmentandDeployment@space.muni.cz"
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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">
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45 <param name="min_pres" type="float" value="0.5" label="min_pres"
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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." />
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47 <param name="min_run" type="float" value="12" label="min_run"
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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." />
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49 <param name="mz_tol" type="float" value="1e-05" label="mz_tol"
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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. 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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51 <param name="baseline_correct" type="float" value="0" label="baseline_correct"
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52 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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53 <param name="intensity_weighted" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="intensity_weighted"
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54 help="Whether to weight the local density by signal intensities in initial peak detection." />
0
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55 </xml>
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56
2
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57 <xml name="generate_feature_table_params">
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58 <param name="sd_cut_min" type="float" value="0.01" label="sd_cut_min"
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59 help="The minimum standard deviation of a feature to be not eliminated." />
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60 <param name="sd_cut_max" type="float" value="500" label="sd_cut_max"
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61 help="The maximum standard deviation of a feature to be not eliminated." />
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62 <conditional name="shape">
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63 <param name="shape_model" type="select" display="radio" label="shape_model"
0
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64 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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65 <option value="Gaussian">Gaussian</option>
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66 <option value="bi-Gaussian" selected="true">bi-Gaussian</option>
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67 </param>
2
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68 <when value="bi-Gaussian">
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69 <param name="sigma_ratio_lim_min" type="float" value="0.01" label="sigma_ratio_lim_min"
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70 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." />
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71 <param name="sigma_ratio_lim_max" type="float" value="100" label="sigma_ratio_lim_max"
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72 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." />
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73 </when>
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74 </conditional>
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75 <param name="peak_estim_method" type="select" display="radio" label="peak_estim_method"
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76 help="The estimation method for the bi-Gaussian peak model. Two possible values: moment and EM.">
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77 <option value="moment" selected="true">Moment</option>
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78 <option value="EM">EM</option>
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79 </param>
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80 <param name="moment_power" type="float" value="1" label="moment_power"
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81 help="The power parameter for data transformation when fitting the bi-Gaussian or Gaussian mixture model in an EIC." />
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82 <param name="component_eliminate" type="float" value="0.01" label="component_eliminate"
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83 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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84 <param name="BIC_factor" type="float" value="2.0" label="BIC_factor"
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85 help="A factor influencing Bayesian information criterion (BIC) in estimation of RT peak shape. If the value is larger than 1, models with more peaks are penalized more." />
0
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86 </xml>
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87
2
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88 <xml name="compute_clusters_params">
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89 <conditional name="tolerances_input_method">
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90 <param name="input_method" type="select" display="radio" label="Tolerances input method"
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91 help="Tolerances can be entered directly or loaded from a file.">
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92 <option value="direct" selected="true">direct</option>
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93 <option value="file">file</option>
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94 </param>
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95 <when value="direct">
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96 <param name="mz_tol_relative" type="float" optional="true" label="mz_tol_relative"
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97 help="Relative m/z tolerance to use for grouping features." />
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98 <param name="rt_tol_relative" type="float" optional="true" label="rt_tol_relative"
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99 help="Relative retention time tolerance to use for grouping features." />
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100 </when>
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101 <when value="file">
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102 <param label="Input tolerances values" name="input_tolerances" type="data" format="parquet"
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103 help="Table containing tolerance values." />
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104 </when>
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105 </conditional>
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106 <param name="mz_tol_absolute" type="float" label="mz_tol_absolute" value="1e-05"
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107 help="Absolute m/z tolerance to use for grouping features." />
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108 <param name="mz_max_diff" type="float" label="mz_max_diff" value="0.01"
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109 help="Maximum difference between feature m/z values to belong to the same cluster." />
0
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110 </xml>
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111
2
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112 <xml name="recover_weaker_params">
0
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113 <param name="mz_tol" type="float" value="1e-05" label="mz_tol"
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114 help="The m/z tolerance level for the grouping of data points. This value is expressed as the
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115 fraction of the m/z value. This value, multiplied by the m/z value, becomes the cutoff level.
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116 The recommended value is the machine's nominal accuracy level. Divide the ppm value by 1e6.
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117 For FTMS, 1e-5 is recommended." />
2
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118 <param name="recover_mz_range" type="float" optional="true" label="recover_mz_range"
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119 help="The m/z around the feature m/z to search for observations. The default value is NA, in which
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120 case 1.5 times the m/z tolerance in the aligned object will be used." />
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121 <param name="recover_rt_range" type="float" optional="true" label="recover_rt_range"
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122 help="The retention time around the feature retention time to search for observations.
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123 The default value is NA, in which case 0.5 times the retention time tolerance in the aligned
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124 object will be used." />
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125 <param name="use_observed_range" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE"
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126 label="use_observed_range" help="If the value is true, the actual range of the observed locations of
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127 the feature in all the spectra will be used." />
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128 <param name="recover_min_count" type="integer" value="3" label="recover_min_count"
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129 help="The minimum number of raw data points to be considered as a true feature." />
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130 <param name="intensity_weighted" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE"
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131 label="intensity_weighted" help="Whether to weight the local density by signal intensities in initial peak detection." />
0
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132 </xml>
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133
2
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134 <xml name="bandwidth_params">
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135 <param name="bandwidth" type="float" value="0.5" label="bandwidth"
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136 help="A value between zero and one. Multiplying this value to the length of the signal along
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137 the time axis helps determine the bandwidth in the kernel smoother used for peak identification." />
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138 <param name="min_bandwidth" type="float" optional="true" label="min_bandwidth"
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139 help="The minimum bandwidth to use in the kernel smoother." />
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140 <param name="max_bandwidth" type="float" optional="true" label="max_bandwidth"
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141 help="The maximum bandwidth to use in the kernel smoother." />
0
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142 </xml>
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143
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144 <xml name="citations">
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145 <citations>
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146 <citation type="doi">10.1093/bioinformatics/btp291</citation>
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147 <citation type="doi">10.1186/1471-2105-11-559</citation>
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148 <citation type="doi">10.1021/pr301053d</citation>
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149 <citation type="doi">10.1093/bioinformatics/btu430</citation>
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150 <citation type="doi">10.1038/s41598-020-70850-0</citation>
0
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151 <yield />
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152 </citations>
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153 </xml>
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154 </macros>