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1 <tool id="2021_05_features_check_references" name="Features -> checks references" version="0.0.1">
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2
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3 <description> </description>
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4
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5 <requirements>
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6 <requirement type="package" >scilab</requirement>
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7 </requirements>
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8
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9
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10 <stdio>
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11 <exit_code range="1:" level="fatal" />
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12 </stdio>
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13
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14
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15 <command>
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16 <![CDATA[
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17 $__root_dir__/packages/scilab-*/bin/scilab-cli -nb -quit -f ${script_file}
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18 ]]>
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19 </command>
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20
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21
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22 <configfiles>
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23 <configfile name="script_file">
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24 <![CDATA[ exec("$__tool_directory__/src/mz_9_compares_peaks.sci",-1); ...
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25 lasterror(); ...
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26 ... //load "${peaks_list}"; ... // 22avril21
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27 peaks_list=glx_tab2div("${peaks_list}"); ...
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28 ...
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29 load "${peaks_detail}"; ...
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30 x836=glx_tab2div("${peaks_reference}"); ...
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31 diff_mz=${diff_mz}; ...
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32 k=${k}; ...
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33 x_peaks_final=mz_9_compares_peaks(peaks_list,peaks_detail,x836,diff_mz,k); ...
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34 ...
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35 div2tab(x_peaks_final,"${x_peaks_final}"); ...
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36 if ~isempty(lasterror(%f)); ...
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37 write(0,lasterror()); ...
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38 end; ]]>
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39 </configfile>
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40 </configfiles>
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41
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42
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43 <inputs>
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44 <param name="peaks_list" format="tabular" type="data" label="Features list" help="from function EIC->peaks:features" />
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45 <param name="peaks_detail" format="mat" type="data" label="Detailed features" help="from function EIC->peaks:features" />
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46 <param name="peaks_reference" format="tabular" type="data" label="Reference features" help="2columns: mz and RT, with column and line headers" />
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47 <param name="diff_mz" value="0.0050" type="float" label="Threshold for m/z values" />
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48 <param name="k" value="1" type="integer" label="Number of extracted features for each reference feature" help="the closest to the reference peak" />
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49
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50 </inputs>
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51
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52
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53 <outputs>
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54 <data name="x_peaks_final" format="tabular" label="Identified features" />
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55 </outputs>
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56
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57
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58 <tests>
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59
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60 <test>
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61 <param name="peaks_list" value="Peaks_list.tabular"/>
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62 <param name="peaks_detail" value="Peaks_details.mat"/>
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63 <param name="peaks_reference" value="ref_mz_rt.tab"/>
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64 <param name="diff_mz" value="0.0050"/>
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65 <param name="k" value="1"/>
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66 <output name="x_peaks_final">
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67 <assert_contents>
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68 <has_text text="136.0616"/>
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69 <has_text text="229.135"/>
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70 </assert_contents>
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71 </output>
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72 </test>
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73
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74 </tests>
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75
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76
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77 <help>
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78
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79
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80 **Author** Jean-Claude Boulet (INRA).
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81
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82
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83 ---------------------------------------------------
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84
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85 ==================================
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86 FEATURES EXPERIMENTAL VS REFERENCE
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87 ==================================
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88
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89
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90 -----------
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91 Description
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92 -----------
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93
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94 This function checks reference features among experimental features.
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95
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96 -----------
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97 Input files
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98 -----------
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99
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100 **Features list**
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101
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102 The tabular file yielded by the function: EICs -> peaks:features
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103
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104
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105 **Detailed features**
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106
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107 The HDF5-scilab file yielded by the function: EICs -> peaks:features
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108
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109
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110 **Reference features**
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111
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112 A tabular file containing 2 columns: m/z values then retention times
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113
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114 Row labels are the names of the reference features, e.g. chemical compounds
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115
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116
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117
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118 ----------
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119 Parameters
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120 ----------
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121
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122 **Threshold for m/z values**
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123
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124 Observed features are associated to the reference features if 1) the difference in m/z values is under the threshold; 2) the reference RT falls within the range of the observed RTs.
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125
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126 Default: 0.0050
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127
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128 **Number of extracted features for each reference feature**
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129
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130 e.g. if the number is 2, the algorithm will extract the 2 experimental features closest to each reference feature.
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131
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132
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133 ------
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134 Output
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135 ------
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136
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137
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138 **Identified features**
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139
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140 A tabular file with the columns:
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141
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142 - name of the reference feature
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143
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144 - number of the reference feature in the input file: Reference features
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145
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146 - number of the experimental feature in the input files: Features List and Detailed features
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147
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148 - number of identifications= the number of reference features each experimental feature has been attributed to; target = 1
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149
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150 - m/z value of the reference feature
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151
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152 - m/z value of the experimental feature
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153
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154 - difference of m/z values
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155
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156 - RT of the reference feature
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157
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158 - RT of the experimental feature
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159
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160 - difference of RT
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161
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162 - signal of the experimental feature
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163
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164
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165 </help>
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166
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167
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168 <citations>
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169
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170 </citations>
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171
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172
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173 </tool>
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174
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175
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