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1 <tool id="V20.10_detrend_sci" name="DT" version="20.05">
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2 <description>Detrend</description>
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3
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4 <requirements>
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5 <requirement type="package" version="6.0.2" >scilab</requirement>
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6 </requirements>
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7
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8 <stdio>
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9 <exit_code range="1:" level="fatal" />
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10 </stdio>
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11
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12 <command><![CDATA[
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13 if [ ! -d /data/singularity ]; then $__root_dir__/packages/scilab-6.1.0/bin/scilab-cli -nb -quit -f $* < ${script_file}; else /usr/local/bin/singularity exec -B /data /data/singularity/scilab.sif scilab-cli -nb -quit -f $* < ${script_file}; fi
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14 ]]>
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15 </command>
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16
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17 <configfiles>
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18 <configfile name="script_file">
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19 lasterror(); ...
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20 if ~isdef('pls') then ...
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21 atomsInstall('FACT'); ...
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22 atomsLoad('FACT'); ...
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23 end; ...
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24 lasterror(%f); ...
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25 x=glx_tab2div("${Xdata.file_name}"); ...
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26 x2=detrending(x,${degre}); ...
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27 div2tab(x2,"${DT}"); ...
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28 if ~isempty(lasterror(%f)) ...
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29 write(0,lasterror()) ...
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30 end
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31 </configfile>
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32 </configfiles>
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33
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34 <inputs>
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35 <param name="Xdata" type="data" format="tabular" label="Select X data" help="Dataset (n x p) containing the n spectra of p variables."/>
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36 <param name="degre" type="integer" value="2" min="0" max="5" label="Degree of the polynom"/>
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37 </inputs>
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38
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39 <outputs>
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40 <data name="DT" format="tabular" label="DT(${Xdata.name})" />
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41 </outputs>
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42
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43 <tests>
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44 <test>
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45 <param name="Xdata" value="test_detrend_input.tabular"/>
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46 <param name="degre" value="2" />
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47
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48 <output name="DT" >
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49 <assert_contents>
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50 <has_text text="0.000838"/>
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51 <has_text text="-0.000194"/>
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52 <has_text text="-0.000131"/>
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53 <has_text text="0.001114"/>
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54 </assert_contents>
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55 </output>
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56
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57 </test>
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58 </tests>
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59
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60 <help>
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61
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62 .. class:: warningmark
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63
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64 **TIP:** If your data is not TAB delimited, use *Convert format data Tools->Convert*
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65
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66 .. class:: infomark
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67
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68 **Authors** Fabien Gogé (IRSTEA), Virginie Rossard (INRA), Eric Latrille (INRA), Jean-Michel Roger (IRSTEA), Jean-Claude Boulet (INRA)
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69
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70
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71 ---------------------------------------------------
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72
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73 =======
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74 DETREND
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75 =======
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76
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77 -----------
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78 Description
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79 -----------
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80
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81
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82 Performs **Detrend**, a baseline correction by orthogonal projection onto a n-order polynomial.
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83 Missing values are not allowed. This scripts uses the FACT-version module.
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84
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85
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86 -----------
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87 Input files
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88 -----------
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89
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90 A matrix of numeric data with headers (tabular format) and decimal separator ".".
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91
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92
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93 +--------+-------+--------+
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94 | Name | 400 | 402 |
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95 +========+=======+========+
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96 |M102T645| 0.63 |0.64 |
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97 +--------+-------+--------+
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98 |M105T604| 0.5 |0.49 |
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99 +--------+-------+--------+
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100
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101 ----------
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102 Parameters
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103 ----------
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104
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105 **Degree of the polynom**
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106
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107 The degree of the polynom used in the Detrend correction
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108
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109 ------------
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110 Output files
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111 ------------
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112
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113 **DT(input.file_name)**
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114
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115 A dataset containing the input file after the Detrend correction; format = tabular.
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116
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117 </help>
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118
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119 <citations>
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120
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121 <citation type="doi">10.1366/0003702894202201</citation>
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122
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123 </citations>
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124
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125
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126 </tool>
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