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1 <tool id="2021_05_eics_synchronization" name="EICs-individual -> EICs-synchronized" version="0.0.1">
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2
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3 <description> for a series of close mass spectra, e.g. repetitions </description>
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4
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5
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6 <requirements>
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7 <requirement type="package" version="6.0.2">scilab</requirement>
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8 </requirements>
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9
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10
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11 <stdio>
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12 <exit_code range="1:" level="fatal" />
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13 </stdio>
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14
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15
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16 <command>
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17 <![CDATA[
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18 $__root_dir__/packages/scilab-*/bin/scilab-cli -nb -quit -f ${script_file}
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19 ]]>
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20 </command>
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21
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22
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23 <configfiles>
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24 <configfile name="script_file">
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25 <![CDATA[ exec("$__tool_directory__/src/mz_4_extract_final_mz_v3.sci",-1); ...
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26 lasterror(); ...
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27 col=list(); ...
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28 #for $i, $s in enumerate( $series )
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29 x_tr_mz3=glx_tab2div("${s.Xdata.file_name}"); ...
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30 ... // load("${s.Xdata.file_name}"); ... 22avril21
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31 x${i}=x_tr_mz3; ...
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32 col(${i}+1)=x${i}; ...
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33 #end for
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34 ...
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35 [list_eic4_files,mz4_stats]=mz_4_extract_final_mz_v3(col,${delta_mz}); ...
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36 save("${list_eic4_files}",'list_eic4_files'); ...
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37 save("${mz4_stats}",'mz4_stats'); ...
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38 if ~isempty(lasterror(%f)) then ...
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39 write(0,lasterror()); ...
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40 end; ]]>
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41 </configfile>
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42 </configfiles>
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43
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44
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45 <inputs>
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46 <repeat name="series" title="dataset" min="2">
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47 <param name="Xdata" format="tabular" type="data" label="Input file" help="EICs-individual files"/>
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48 </repeat>
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49 <param name="delta_mz" value="0.0024" type="float" label="Threshold for m/z" />
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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="list_eic4_files" format="mat" label="EICs-synchronized"/>
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55 <data name="mz4_stats" format="mat" label="stats on EIC-synchro"/>
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56 </outputs>
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57
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58
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59 <tests>
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60
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61 <test>
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62 <param name="Xdata" value="EICs-individual-1_k3mean.tab"/>
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63 <param name="Xdata" value="EICs-individual-2_k3mean.tab"/>
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64 <param name="Xdata" value="EICs-individual-3_k3mean.tab"/>
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65 <param name="delta_mz" value="0.0024"/>
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66 <output name="list_eic4_files" file="EICs-synchronized.mat" compare="sim_size" delta="1000" />
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67 </test>
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68
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69 </tests>
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70
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71
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72 <help>
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73
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74
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75 .. class:: infomark
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76
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77 **Author** Jean-Claude Boulet (INRAE)
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78
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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 EXTRACTS THE EICS SHARED BY A SERIES OF EIC FILES
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84 =================================================
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85
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86 -----------
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87 Description
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88 -----------
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89
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90 The EICs shared by a series of EICs-individual are identified.
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91
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92 Then, each of the initial EiCs-individual is reprocessed as to keep only the EICs shared by all the series.
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93
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94 The main application is the synchronization of the EICs of repetitions.
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95
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96
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97
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98 -----------
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99 Input files
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100 -----------
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101
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102 At least two EICs-individual
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103
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104 ----------
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105 Parameters
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106 ----------
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107
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108 **Threshold for m/z**
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109
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110 Two m/z values whose difference is larger than this threshold will be considered as different.
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111
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112 Default value: 0.0024
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113
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114
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115 ------------
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116 Output files
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117 ------------
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118
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119
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120 **EICs-shared**
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121
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122 The input files with the same EICs.
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123
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124 A list at the HDF5-scilab .dat format.
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125
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126
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127
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128 **stats on EICs-shared**
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129
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130 Some calculations for the following processings.
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131
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132 </help>
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133
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134
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135 <citations>
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136
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137 </citations>
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138
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139 </tool>
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