Mercurial > repos > recetox > recetox_aplcms_recover_weaker_signals

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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 14:57:30 +0000
parents 472dc85ce7c5
children 755ff0afaaff
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472dc85ce7c5 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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1 <macros>
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472dc85ce7c5 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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3 <token name="@GENERAL_HELP@">
472dc85ce7c5 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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4 General Information
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5 ===================
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472dc85ce7c5 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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7 Overview
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8 --------
472dc85ce7c5 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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472dc85ce7c5 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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10 recetox-aplcms is a software package for peak detection in high resolution mass spectrometry (HRMS) data.
472dc85ce7c5 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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11 It supports reading .mzml files in raw profile mode and uses a bi-Gaussian chromatographic peak shape for feature detection and quantification.
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472dc85ce7c5 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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13 recetox-aplcms is based on the apLCMS package developed by Tianwei Yu at Emory University - see the citations and the apLCMS section beneath.
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14 This version includes various software updates and is actively developed and maintained on `GitHub`_.
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15 Please submit eventual bug reports as `issues`_ on the repository.
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17 .. _GitHub: https://github.com/RECETOX/recetox-aplcms
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18 .. _issues: https://github.com/RECETOX/recetox-aplcms/issues/new
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21 Workflow
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22 --------
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24 .. image:: https://raw.githubusercontent.com/RECETOX/galaxytools/aee0dd6cf6c05936269efe4337c50e27cc68e86b/tools/recetox_aplcms/images/scheme.png
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25 :width: 2560
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26 :height: 788
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27 :scale: 40
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28 :alt: A picture of a workflow diagram.
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30 The individual steps of the recetox-aplcms package can be combined in 2 separate workflows processing HRMS data in an unsupervised manner or by including a-priori knowledge.
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31 The workflows consist of the following building blocks:
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33 (1) remove noise - denoise the raw data and extract the EIC
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34 (2) generate feature table - group features in EIC into peaks using peak-shape model
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35 (3) compute clusters - compute mz and rt clusters across samples
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36 (4) compute template - find the template for rt correction
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37 (5) correct time - correct the rt across samples using splines
472dc85ce7c5 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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38 (6) align features - align identical features across samples
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39 (7) recover weaker signals - recover missed features in samples based on the aligned features
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40 (8) merge known table - add known features to detected features table and vice versa
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42 For detailed documentation on the individual steps please see the individual tool wrappers.
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45 apLCMS (Original Reference)
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46 ---------------------------
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48 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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49 tolerance levels are estimated from the data. A run-filter is used to detect peaks and remove noise.
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50 Non-parametric statistical methods are used to find-tune peak selection and grouping. After retention time
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51 correction, a feature table is generated by aligning peaks across spectra. For further information on apLCMS
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52 please refer to https://mypage.cuhk.edu.cn/academics/yutianwei/apLCMS/.
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53 </token>
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55 <token name="@REMOVE_NOISE_HELP@">
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56 recetox-aplcms - remove noise
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57 =============================
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59 This tool is the first step of recetox-aplcms.
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60 It removes noise from the raw data and performs a first clustering step of points with close m/z values into the extracted ion chromatograms (EICs).
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61 Only peaks with a minimum elution length of `min_run` seconds are kept.
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63 Example Output
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64 --------------
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65 The raw data points contained in the scans of the `mzml` file are filtered for noise and grouped into clusters based on m/z values.
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66 See an example output in the table below. The `group_number` column indicates the cluster index.
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68 +----------------------+-------------------+-----------------------+--------------------+
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69 | mz | rt | intensity | group_number |
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70 +======================+===================+=======================+====================+
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71 | 70.01060119055192 | 350.58654 | 21178.330810546875 | 5 |
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72 +----------------------+-------------------+-----------------------+--------------------+
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73 | 70.02334120404554 | 130.175262 | 287869.5478515625 | 10 |
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74 +----------------------+-------------------+-----------------------+--------------------+
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75 | 70.0287408273165 | 134.801352 | 60883.15185546875 | 11 |
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76 +----------------------+-------------------+-----------------------+--------------------+
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77 | 70.02872416715464 | 183.991896 | 9201.574584960938 | 11 |
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78 +----------------------+-------------------+-----------------------+--------------------+
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79 | ... | ... | ... | ... |
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80 +----------------------+-------------------+-----------------------+--------------------+
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81 </token>
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83 <token name="@GENERATE_FEATURE_TABLE_HELP@">
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84 recetox-aplcms - generate feature table
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85 =======================================
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86 The second step in the recetox-aplcms workflow performing peak shape parameter estimation.
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87
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88 This tool takes the grouped features created with `recetox-aplcms-remove-noise` and computes the peak shape in `rt` domain and integrates the peak area.
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89
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90
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91 Example Output
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92 --------------
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93 The output contains the `mz` and `rt` of the peaks as well as the standard deviation in both direction of the peak for the bi-gaussian peak shape.
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94
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95 +----------------------+-------------------+-----------------+-------------------+----------------------+
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96 | mz | rt | sd1 | sd2 | area |
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97 +======================+===================+=================+===================+======================+
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98 | 70.02317542938793 | 142.36033 | 11.436659559 | 14.592754933 | 4159269.24595184 |
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99 +----------------------+-------------------+-----------------+-------------------+----------------------+
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100 | 70.02869594233522 | 205.48765 | 0.263230763 | 0.285101428707 | 8849767.11861127 |
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101 +----------------------+-------------------+-----------------+-------------------+----------------------+
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102 | 78.04643252598305 | 294.01713 | 0.51677558617 | 1.317028944141 | 1333044.50659719 |
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103 +----------------------+-------------------+-----------------+-------------------+----------------------+
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104 | ... | ... | ... | ... | ... |
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105 +----------------------+-------------------+-----------------+-------------------+----------------------+
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106 </token>
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107
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108 <token name="@COMPUTE_CLUSTERS_HELP@">
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109 recetox-aplcms - compute clusters
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110 =================================
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111
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112 Group features with `mz` and `rt` using tolerances within the tolerance into clusters, creating larger features from raw data points.
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113 Custom tolerances for `mz` and `rt` are computed based on the given parameters.
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114 The tool takes a collection of all detected features and computes the clusters over a global feature table, adding the `sample_id` and `cluster` columns to the table.
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115
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116 Example Output
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117 --------------
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118
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119 +----------------------+-------------------+-----------------+-------------------+----------------------+---------------------+---------------+
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120 | mz | rt | sd1 | sd2 | area | sample_id | cluster |
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121 +======================+===================+=================+===================+======================+=====================+===============+
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122 | 70.02317542938793 | 142.36033 | 11.436659559 | 14.592754933 | 4159269.245951841 | 21_qc_no_dil_milliq | 7 |
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123 +----------------------+-------------------+-----------------+-------------------+----------------------+---------------------+---------------+
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124 | 70.02869594233522 | 205.48765 | 0.263230763 | 0.285101428707 | 8849767.11861127 | 21_qc_no_dil_milliq | 9 |
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125 +----------------------+-------------------+-----------------+-------------------+----------------------+---------------------+---------------+
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126 | 78.04643252598305 | 294.01713 | 0.51677558617 | 1.317028944141 | 1333044.506597194 | 21_qc_no_dil_milliq | 13 |
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127 +----------------------+-------------------+-----------------+-------------------+----------------------+---------------------+---------------+
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128 | ... | ... | ... | ... | ... | ... | ... |
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129 +----------------------+-------------------+-----------------+-------------------+----------------------+---------------------+---------------+
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130 </token>
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131
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132 <token name="@CORRECT_TIME_HELP@">
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133 recetox-aplcms - correct time
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134 =============================
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135
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136 Apply spline-based retention time correction to a feature table given the template table and the computed `mz` and `rt` tolerances.
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137
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138 Example Output
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139 --------------
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140 The output has the same format as `compute clusters` but the retention time values are corrected based on the template table.
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141
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142 +----------------------+-------------------+-----------------+-------------------+----------------------+---------------------+---------------+
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143 | mz | rt | sd1 | sd2 | area | sample_id | cluster |
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144 +======================+===================+=================+===================+======================+=====================+===============+
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145 | 70.02317542938793 | 142.36033 | 11.436659559 | 14.592754933 | 4159269.245951841 | 21_qc_no_dil_milliq | 7 |
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146 +----------------------+-------------------+-----------------+-------------------+----------------------+---------------------+---------------+
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147 | 70.02869594233522 | 205.48765 | 0.263230763 | 0.285101428707 | 8849767.11861127 | 21_qc_no_dil_milliq | 9 |
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148 +----------------------+-------------------+-----------------+-------------------+----------------------+---------------------+---------------+
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149 | 78.04643252598305 | 294.01713 | 0.51677558617 | 1.317028944141 | 1333044.506597194 | 21_qc_no_dil_milliq | 13 |
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150 +----------------------+-------------------+-----------------+-------------------+----------------------+---------------------+---------------+
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151 | ... | ... | ... | ... | ... | ... | ... |
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152 +----------------------+-------------------+-----------------+-------------------+----------------------+---------------------+---------------+
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153 </token>
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154 <token name="@COMPUTE_TEMPLATE_HELP@">
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155 recetox-aplcms - compute template
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156 =================================
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157 Compute the template from a set of feature tables, choosing the one with the most features as the template.
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158 </token>
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159
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160 <token name="@RECOVER_WEAKER_SIGNALS_HELP@">
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161 recetox-aplcms - recover weaker signals
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162 =======================================
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163 Second stage peak detection based on the aligned feature table from the `feature alignment` step.
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164 If a feature is contained in the aligned feature table, this step revisits the raw data and searches
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165 for this feature at the retention time obtained by mapping the corrected retention time back to the original sample.
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166
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167 This recovers features which are present in a sample but might have been filtered out initially as noise due to low signal intensity.
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168
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169 Example Output
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170 --------------
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171 The table has the same format as the `compute clusters` output but might contain additional features which have been extracted based
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172 on their presence in the aligned feature table.
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173
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174 +----------------------+-------------------+-----------------+-------------------+----------------------+---------------------+---------------+
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175 | mz | rt | sd1 | sd2 | area | sample_id | cluster |
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176 +======================+===================+=================+===================+======================+=====================+===============+
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177 | 70.02317542938793 | 142.36033 | 11.436659559 | 14.592754933 | 4159269.245951841 | 21_qc_no_dil_milliq | 7 |
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178 +----------------------+-------------------+-----------------+-------------------+----------------------+---------------------+---------------+
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179 | 70.02869594233522 | 205.48765 | 0.263230763 | 0.285101428707 | 8849767.11861127 | 21_qc_no_dil_milliq | 9 |
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180 +----------------------+-------------------+-----------------+-------------------+----------------------+---------------------+---------------+
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181 | 78.04643252598305 | 294.01713 | 0.51677558617 | 1.317028944141 | 1333044.506597194 | 21_qc_no_dil_milliq | 13 |
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182 +----------------------+-------------------+-----------------+-------------------+----------------------+---------------------+---------------+
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183 | ... | ... | ... | ... | ... | ... | ... |
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184 +----------------------+-------------------+-----------------+-------------------+----------------------+---------------------+---------------+
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185 </token>
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186
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187 <token name="@ALIGN_FEATURES_HELP@">
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188 recetox-aplcms - align features
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189 ===============================
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190 This step performs feature alignment after clustering and retention time correction.
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191 The peaks clustered across samples are grouped based on the given tolerances to create an aligned feature table, connecting identical features across samples.
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192 The parameter controls in how many samples a feature has to be detected at least in order to be included in the aligned feature table.
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193
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194 Example Output
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195 --------------
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196 The tool outputs 3 tables: the peak related `metadata`, the `retention times` and the `intensities` for all features across all samples.
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197
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198 Metadata Table
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199 ~~~~~~~~~~~~~~
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200 The `npeaks` column denotes the number of peaks which have been grouped into this feature. The columns with the sample names indicate whether this feature is present in the sample.
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201
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202 +-------+--------------+--------------+---------------+----------------+---------------+---------------+-----------+------------------------+------------------------+------------------------+
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203 | id | mz | mzmin | mzmax | rt | rtmin | rtmax | npeaks | 21_qc_no_dil_milliq | 29_qc_no_dil_milliq | 8_qc_no_dil_milliq |
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204 +=======+==============+==============+===============+================+===============+===============+===========+========================+========================+========================+
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205 | 1 | 70.03707021 | 70.037066 | 70.0370750 | 294.1038014 | 294.0634942 | 294.149985 | 3 | 1 | 1 | 1 |
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206 +-------+--------------+--------------+---------------+----------------+---------------+---------------+-----------+------------------------+------------------------+------------------------+
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207 | 2 | 70.06505677 | 70.065045 | 70.0650676 | 141.9560055 | 140.5762528 | 143.335758 | 2 | 1 | 0 | 1 |
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208 +-------+--------------+--------------+---------------+----------------+---------------+---------------+-----------+------------------------+------------------------+------------------------+
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209 | 57 | 78.04643252 | 78.046429 | 78.0464325 | 294.0063397 | 293.9406777 | 294.072001 | 2 | 1 | 1 | 0 |
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210 +-------+--------------+--------------+---------------+----------------+---------------+---------------+-----------+------------------------+------------------------+------------------------+
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211 | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... |
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212 +-------+--------------+--------------+---------------+----------------+---------------+---------------+-----------+------------------------+------------------------+------------------------+
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213
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214 Intensity Table
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215 ~~~~~~~~~~~~~~~
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216 This table contains the peak area for aligned features in all samples.
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217
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218 +-------+------------------------+------------------------+------------------------+
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219 | id | 21_qc_no_dil_milliq | 29_qc_no_dil_milliq | 8_qc_no_dil_milliq |
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220 +=======+========================+========================+========================+
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221 | 1 | 13187487.20482895 | 7957395.699119729 | 11700594.397257797 |
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222 +-------+------------------------+------------------------+------------------------+
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223 | 2 | 2075168.6398983458 | 0 | 2574362.159289044 |
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224 +-------+------------------------+------------------------+------------------------+
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225 | 57 | 2934524.4406785755 | 1333044.5065971944 | 0 |
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226 +-------+------------------------+------------------------+------------------------+
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227 | ... | ... | ... | ... |
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228 +-------+------------------------+------------------------+------------------------+
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229
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230 Retention Time Table
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231 ~~~~~~~~~~~~~~~~~~~~
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232 This table contains the retention times for all aligned features in all samples.
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233
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234 +-------+------------------------+------------------------+------------------------+
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235 | id | 21_qc_no_dil_milliq | 29_qc_no_dil_milliq | 8_qc_no_dil_milliq |
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236 +=======+========================+========================+========================+
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237 | 1 | 294.09792478513236 | 294.1499853056912 | 294.0634942428341 |
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238 +-------+------------------------+------------------------+------------------------+
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239 | 2 | 140.57625284242982 | 0 | 143.33575827589172 |
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240 +-------+------------------------+------------------------+------------------------+
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241 | 57 | 294.07200187644435 | 293.9406777222317 | 0 |
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242 +-------+------------------------+------------------------+------------------------+
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243 | ... | ... | ... | ... |
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244 +-------+------------------------+------------------------+------------------------+
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245 </token>
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246
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247 <token name="@MERGE_KNOWN_TABLES_HELP@">
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248 recetox-aplcms - merge known table
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249 ==================================
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250
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251 This tool allows merging the detected features back into the table of known features and vice versa.
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252 It is used in the hybrid version of recetox-aplcms to augment the aligned feature table with the suspect peaks
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253 and to augment this table with successfully detected features.
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254 </token>
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255 </macros>