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1 <tool id="2021_05_features_extract" name="EICs -> Peaks:features" version="0.0.1">
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2 <description> extracts the peaks (m/z x TR) from the EICs </description>
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3
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4 <requirements>
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5 <requirement type="package" >scilab</requirement>
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6 </requirements>
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7
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8
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9 <stdio>
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10 <exit_code range="1:" level="fatal" />
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11 </stdio>
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12
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13
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14 <command> <![CDATA[
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15 $__root_dir__/packages/scilab-*/bin/scilab-cli -nb -quit -f ${script_file}
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16 ]]>
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17 </command>
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18
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19
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20 <configfiles>
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21 <configfile name="script_file">
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22 <![CDATA[ exec("$__tool_directory__/src/mz_8_peakpicking_dw.sci",-1); ...
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23 exec("$__tool_directory__/src/mz_6bis_durbin_watson.sci",-1); ...
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24 lasterror(); ...
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25 option=${option}; ...
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26 if option==1 then ... // liste ou fichier .dat
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27 load("${list_eic4_files}"); ...
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28 list_var=who_user(%f); ...
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29 n=size(list_var,1); ...
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30 for i=1:n;
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31 execstr(msprintf("type_tmp=type(%s);",list_var(i))); ...
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32 if type_tmp==15 then ...
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33 execstr(msprintf("x_tr_mz4=%s;",list_var(i))); ...
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34 break;...
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35 end; ...
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36 end; ...
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37 ...
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38 elseif option==2 then ... // tabular
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39 x_tr_mz4=glx_tab2div("${list_eic4_files}"); ...
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40 end; ...
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41 ...
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42 if isdef('x_tr_mz3'); ...
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43 x_tr_mz4=x_tr_mz3; ...
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44 end; ...
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45 ...
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46 if typeof(x_tr_mz4)=="list"; ...
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47 x_tr_mz4_i=x_tr_mz4(${no}); ...
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48 elseif typeof(x_tr_mz4)=="div"; ...
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49 x_tr_mz4_i=x_tr_mz4; ...
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50 end; ...
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51 ...
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52 [peaks_list,peaks_detail]=mz_8_peakpicking_dw(x_tr_mz4_i,[1:$],${plage_tr},${plage_min_tr},${dw_max},${signal_min},0); ...
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53 ...
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54 peaks_list.i='eic n0 '+ peaks_list.i; ...
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55 div2tab(peaks_list,"${peaks_list}"); ... // 20avril21
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56 ... // save("${peaks_list}",'peaks_list'); ...
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57 save("${peaks_detail}",'peaks_detail'); ...
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58 ...
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59 if ~isempty(lasterror(%f)); ...
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60 write(0,lasterror()); ...
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61 end; ]]>
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62 </configfile>
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63 </configfiles>
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64
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65
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66 <inputs>
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67 <param name="list_eic4_files" format="mat,tabular" type="data" label="EICs files" help="a list of several files, or a single matrix EIC matrix (RT x m/z)" />
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68 <param name="option" value="2" type="integer" min="1" max="2" label="Type of data" help="1= a list from the function: EIVs -> check reference mz; 2= an EIC matrix, e.g. from the function: EICs-synchronized -> EICs-merged" />
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69 <param name="no" size="5" value="1" type="integer" label="Number" help="if list, from 1 to 5 " />
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70 <param name="plage_tr" size="5" value="0.3" type="float" label="Maximum range of RT " help="in minutes" />
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71 <param name="plage_min_tr" size="5" value="0.05" type="float" label="Minimum range of RT " help="in minutes" />
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72 <param name="dw_max" size="5" value="1" type="float" label="Threshold for Durbin-Watson" help="a value between 0 and 2" />
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73 <param name="signal_min" size="5" value="100000" type="float" label="Threshold for the signal max" help="peaks with signal max under this value are dropped" />
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74
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75 </inputs>
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76
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77
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78 <outputs>
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79 <data name="peaks_list" format="tabular" label="Peaks list"/>
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80 <data name="peaks_detail" format="mat" label="Peaks details" />
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81 </outputs>
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82
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83
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84 <tests>
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85
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86 <test>
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87 <param name="list_eic4_files" value="x4_list.dat"/>
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88 <param name="option" value="1"/>
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89 <param name="no" value="3"/>
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90 <param name="plage_tr" value="0.3"/>
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91 <param name="plage_min_tr" value="0.05"/>
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92 <param name="dw_max" value="1"/>
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93 <param name="signal_min" value="100000"/>
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94 <output name="peaks_list">
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95 <assert_contents>
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96 <has_text text="0.2020"/>
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97 <has_text text="0.8740"/>
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98 <has_text text="3.2942"/>
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99 </assert_contents>
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100 </output>
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101 </test>
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102
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103 <test>
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104 <param name="list_eic4_files" value="x4.tab"/>
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105 <param name="option" value="2"/>
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106 <param name="plage_tr" value="0.3"/>
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107 <param name="plage_min_tr" value="0.05"/>
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108 <param name="dw_max" value="1"/>
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109 <param name="signal_min" value="100000"/>
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110 <output name="peaks_list">
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111 <assert_contents>
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112 <has_text text="0.2020"/>
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113 <has_text text="0.8740"/>
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114 <has_text text="3.2942"/>
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115 </assert_contents>
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116 </output>
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117 </test>
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118
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119 </tests>
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120
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121
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122 <help>
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123
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124
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125 **Authors** Jean-Claude Boulet (INRA).
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126
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127
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128 ---------------------------------------------------
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129
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130 =========================
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131 PEAKS:FEATURES EXTRACTION
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132 =========================
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133
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134 -----------
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135 Description
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136 -----------
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137
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138 A feature or peak is a signal recorded for a given m/z value and a range of retention times.
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139
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140 This function extracts the peaks of each EIC from an EIC matrix.
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141
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142 Note: this features extraction algorithm does not claim novelty nor higher performances. But it corresponds well to our outputs. For a basic use.
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143
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144
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145
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146 -----
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147 Input
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148 -----
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149
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150 **EICs files**
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151
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152 - a matrix from e.g. the function: EICs-synchronized -> EICs-merged
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153
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154 - or a list yielded by the function: EICs -> checks reference mz
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155
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156
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157 ----------
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158 Parameters
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159 ----------
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160
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161 **Number**
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162
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163 In case of a list, the number to select, from 1 to 5, corresponding to the m/z thresholds of 0.0005, 0.0010, 0.0030, 0.0050 and 0.0100 respectively
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164
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165 **Maximum range of retention time**
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166
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167 Default value: 0.3
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168
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169
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170 **Minimum range of retention time**
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171
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172 Default value: 0.05
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173
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174 **Threshold for Durbin-Watson**
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175
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176 Default value: 1
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177
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178
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179 -------
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180 Outputs
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181 -------
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182
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183 **Peaks list**
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184
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185 A file of 4 columns: RT min, RT max, m/z value and signal
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186
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187 **Peaks detail**
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188
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189 The file, format HDF5-scilab, contains a list.
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190
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191 Each element of the list is associated to a peak, i.e. a line of the Peaks List output.
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192
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193 Each element of the list contains a column vector of the signals recorded along a range of retention times, identified by the line labels. The column label is the m/z value of the peak.
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194
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195 </help>
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196
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197
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198 <citations>
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199
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200 </citations>
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201
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202
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203 </tool>
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