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1 <tool id="2021_05_eics_check_references" name="EICs -> checks reference mz" version="0.0.1">
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2
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3 <description> for 5 determined thresholds for m/z </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> <![CDATA[
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16 $__root_dir__/packages/scilab-*/bin/scilab-cli -nb -quit -f ${script_file}
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17 ]]>
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18 </command>
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19
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20
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21 <configfiles>
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22 <configfile name="script_file"> <![CDATA[ exec("$__tool_directory__/src/mz_0_publi_features4_galaxy.sci",-1); ...
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23 exec("$__tool_directory__/src/mz_6bis_durbin_watson.sci",-1); ...
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24 lasterror(); ...
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25 ...
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26 x_in=glx_tab2div("${xtrmz4}"); ... // 20avril21
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27 [x_bilan,x_synthese,x_tr_mz4]=mz_0_publi_features4_galaxy("${mzref}",x_in, ${electron}); ...
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28 ... //[x_bilan,x_synthese,x_tr_mz4]=mz_0_publi_features4_galaxy("${mzref}", "${xtrmz4}", ${electron}); ...
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29 ...
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30 div2tab(x_bilan, "${xbilan}"); ...
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31 save("${xsynthese}","x_synthese"); ...
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32 save("${x_tr_mz_trouves}","x_tr_mz4"); ...
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33 if ~isempty(lasterror(%f)); ...
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34 write(0,lasterror()); ...
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35 end; ]]>
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36 </configfile>
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37 </configfiles>
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38
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39
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40 <inputs>
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41 <param name="mzref" format="tabular" type="data" label="Reference m/z values" />
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42 <param name="xtrmz4" format="tabular" type="data" label="EICs-mean" />
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43 <param name="electron" size="5" value="0" type="integer" label="Electron mass" help="1=correction of the reference m/z values; 0=no correction" />
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44 </inputs>
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45
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46
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47 <outputs>
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48 <data name="xbilan" format="tabular" label="m/z check-summary" />
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49 <data name="xsynthese" format="mat" label="m/z check-details" />
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50 <data name="x_tr_mz_trouves" format="mat" label="m/z check-matrix" />
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51 </outputs>
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52
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53
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54 <tests>
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55
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56 <test>
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57 <param name="mzref" value="ref_mz.tab"/>
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58 <param name="xtrmz4" value="EICs-merged.tab"/>
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59 <output name="xbilan">
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60 <assert_contents>
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61 <has_text text="0.00034"/>
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62 <has_text text="0.352"/>
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63 </assert_contents>
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64 </output>
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65 </test>
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66
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67 </tests>
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68 <help>
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69
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70
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71 **Author** Jean-Claude Boulet (INRA).
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72
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73
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74 ---------------------------------------------------
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75
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76 =======================================================================
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77 CHECK REFERENCE MZ VALUES AMONG THE EICS-MEAN YIELDED BY THE PROCESSING
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78 =======================================================================
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79
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80 -----------
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81 Description
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82 -----------
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83
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84 A matrix of EICs has been yielded by the function: MS-centroid -> EICs-individual or by the function: several EICs-shared -> one EICs-mean.
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85
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86 The m/z values of these EICs are compared to reference m/z values for 5 pre-determined threshold values for m/z: 0.0005 / 0.0010 / 0.0030 / 0.0050 / 0.0100.
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87
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88 This function is focused on the m/z values, it does not take into account the retention times.
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89
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90
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91
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92 ------
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93 Inputs
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94 ------
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95
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96 **reference m/z values**
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97
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98 A tabular file, to the div format (first columns and rows = labels):
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99
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100 - the first column corresponds to names of chemical compounds;
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101
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102 - the second column contains the exact (reference) m/z values.
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103
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104
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105 **EICs-mean or individual**
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106
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107 A tabular matrix of (RT x m/z); lines are retention times and columns are EICs.
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108
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109
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110 ----------
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111 Parameters
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112 ----------
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113
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114 **correction of the electron mass**
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115
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116 A correction can be applied to the reference m/z values.
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117
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118 - 0: no correction;
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119
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120 - 1: correction = subtraction of 0.00055 in the positive mode.
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121
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122
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123
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124 ------
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125 Output
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126 ------
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127
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128 **summary**
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129
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130 The main results
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131
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132
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133 **details**
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134
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135 A .mat file
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136
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137
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138 **extracted EICs**
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139
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140 An EIC is associated to a reference m/z value if the absolute difference of (EIC minus reference) is under a threshold.
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141
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142 Five threshold values have been pre-determined: 0.0005 / 0.0010 / 0.0030 / 0.0050 / 0.0100
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143
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144 This output contains a list of 5 data, each containing the EICs identified as reference m/z values according to a threshold.
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145
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146 </help>
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147
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148
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149 <citations>
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150
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151 </citations>
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152
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153
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154 </tool>
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