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1 <tool id="2021_05_mz_eics_first_extraction" name="MS-centroid -> EICs-individual" version="0.0.2">
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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_3_extract_all_mz2.sci",-1); ...
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25 exec("$__tool_directory__/src/mz_4_scan_mz_raw6.sci",-1); ...
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26 exec("$__tool_directory__/src/mz_5_tr_matrix6bis.sci",-1); ...
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27 exec("$__tool_directory__/src/mz_6bis_durbin_watson.sci",-1); ...
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28 exec("$__tool_directory__/src/mz_6_rescan_mz2.sci",-1); ...
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29 exec("$__tool_directory__/src/mz_7_dwcleaning.sci",-1); ...
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30 exec("$__tool_directory__/src/mz_eic5_step2.sci",-1); ...
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31 lasterror(); ...
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32 load("${resbary}"); ...
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33 if ~isdef('resbary'); ...
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34 error('resbary is not defined'); ...
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35 end; ...
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36 diffmz=${diffmz}; ...
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37 set=${signaleicthresh}; ...
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38 dw=${dw}; ...
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39 x_tr_mz3=mz_eic5_step2(resbary,diffmz,set,dw); ...
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40 ... //save("${x_tr_mz3}",'x_tr_mz3'); ...
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41 div2tab(x_tr_mz3,"${x_tr_mz3}"); ... // 22avril21
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42 if ~isempty(lasterror(%f)); ...
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43 write(0,lasterror()); ...
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44 end; ]]>
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45 </configfile>
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46 </configfiles>
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47
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48
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49 <inputs>
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50 <param name="resbary" format="mat" type="data" label="MS-centroid" />
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51 <param name="diffmz" value="0.0024" type="float" label="Threshold for the m/z values" />
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52 <param name="signaleicthresh" value="30000" type="integer" label="Threshold for the signals" />
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53 <param name="dw" value="1" type="float" label="Threshold for Durbin-Watson" help="to remove noisy EICs" />
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54 </inputs>
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55
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56
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57 <outputs>
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58 <data name="x_tr_mz3" format="tabular" label="EICs-individual" />
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59 </outputs>
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60
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61
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62 <tests>
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63
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64 <test>
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65 <param name="resbary" value="VI2016_AC_4Acentroide-1_k_3mean.mat"/>
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66 <param name="diffmz" value="0.0024"/>
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67 <param name="signaleicthresh" value="30000"/>
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68 <param name="dw" value="1"/>
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69 <output name="x_tr_mz3" file="EICs-individual-1_k3mean.tab" compare="sim_size" delta="1000" />
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70 </test>
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71
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72 </tests>
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73
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74
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75 <help>
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76
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77
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78 **Author** Jean-Claude Boulet (INRAE).
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79
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80
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81 ---------------------------------------------------
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82
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83 ==========================================
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84 EXTRACTION OF EICS FROM A CENTROID MS DATA
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85 ==========================================
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86
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87 -----------
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88 Description
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89 -----------
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90
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91 The HRMS analysis of a samples yields a MS data.
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92
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93 From a centroid MS data, a matrix of (RT x m/z) is extracted.
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94
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95 Each column of this matrix is an EIC = Extracted Ion Chromatogram, i.e. the signals of a given m/z value along the retention times.
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96
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97 ------
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98 Inputs
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99 ------
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100
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101 **MS-centroid**
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102
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103 It is an HDF5-Scilab structure obtained by the previous processings and containing the fields:
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104
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105 - resbary.time: the retention times;
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106
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107 - resbary.mzdata: the mass spectra associated to the RTs.
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108
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109
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110
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111 ----------
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112 Parameters
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113 ----------
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114
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115 Three thresholds have to be determined.
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116
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117
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118 **Threshold for the m/z values**
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119
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120 The difference between two m/z values is compared to the threshold; if lower, the m/z values are considered as the same and merged; if higher the m/z values are considered as different.
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121
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122 Default value: 0.0024.
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123
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124
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125 **Threshold for the signals**
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126
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127 The EICs whose global signal is under this threshold are dropped from the EIC matrix.
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128
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129 Default value: 30000.
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130
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131
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132 **Threshold for Durbin-Watson**
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133
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134 Durbin-Watson values can range between 0 and 2.
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135
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136 EICs with a DW value higher than the threshold are considered as noise and therefore dropped.
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137
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138 Default value: 1.
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139
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140
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141
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142 -----
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143 Oupts
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144 -----
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145
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146 **EIC-individual matrix**
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147
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148 A matrix of signal intensities obtained from a single MS:
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149
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150 - rows are the retention times;
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151
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152 - columns are the m/z values determined by the processing.
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153
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154 The file is a .dat HDF5-Scilab format.
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155
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156 </help>
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157
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158
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159 <citations>
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160
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161 </citations>
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162
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163
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164 </tool>
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165
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166
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167
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168
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169
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