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1 <tool id="robustZScoreNormalization" name="Calculate Robust Z Score Normalization" version="1.0.0">
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2 <description>Per Plate</description>
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3
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4 <command interpreter="perl">
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5 robustZScoreNormalization.pl $inputFile1 $inputFile2 $outputFile1
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6 </command>
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7
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8 <inputs>
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9 <param format="tabular" name="inputFile1" type="data" label="Select the linear plates file"/>
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10 <param format="tabular" name="inputFile2" type="data" label="Select the plate configuration file"/>
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11 </inputs>
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12
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13 <outputs>
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14 <data format="tabular" name="outputFile1"/>
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15 </outputs>
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16
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17 <tests>
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18 <test>
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19 <param name="inputFile1" value="150615-HR-12015-01A.linear"/>
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20 <param name="inputFile2" value="plate_config.txt"/>
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21 <output name="outputFile1" file="calc_robust_z.tabular"/>
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22 </test>
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23 </tests>
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24
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25
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26 <help>
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27
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28 .. class:: infomark
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29
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30 **What it does**
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31
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32 This program takes a linear plate table and a plate config file as input and then performs Robust Z Score Normalization on the data.
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33 The plate config file **must** contain the columns Well, Type and Name in that order. Further the data in column Type must be **exclude**, **negcontr** or **poscontr**.
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34
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35 **Example**
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36
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37 If the plates table consisted of::
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38
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39 #Well Table_1 Table_2
A01 1654 6
A02 1719 8
A03 1624 19
A04 1518 6
A05 1587 12
A06 1517 8
A07 1638 9
A08 1733 7
A09 1617 6
A10 1722 8
...
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40 P14 1630 6
P15 1576 6
P16 1740 7
P17 1578 6
P18 1544 6
P19 1692 6
P20 1560 6
P21 1552 6
P22 1790 7
P23 1537 6
P24 NA NA
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41
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42 and the plates config was::
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43
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44 #Well Type Name
A02 negcontr NT2
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45 B02 negcontr NT2
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46 C02 poscontr ASCIZ
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47 D02 poscontr PARP
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48 E02 negcontr NT2
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49 F02 poscontr ASCIZ
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50 G02 poscontr PARP
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51 H02 negcontr NT2
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52 I02 poscontr ASCIZ
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53 J02 poscontr PARP
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54 K02 negcontr NT2
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55 L02 poscontr ASCIZ
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56 M02 poscontr PARP
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57 N02 negcontr NT2
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58 O02 poscontr ASCIZ
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59 P02 negcontr NT2
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60 A23 negcontr NT2
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61 B23 negcontr NT2
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62 C23 poscontr ASCIZ
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63 D23 poscontr PARP
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64 E23 negcontr NT2
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65 F23 poscontr ASCIZ
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66 G23 poscontr PARP
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67 H23 negcontr NT2
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68 I23 poscontr ASCIZ
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69 J23 poscontr PARP
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70 K23 negcontr NT2
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71 L23 poscontr ASCIZ
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72 M23 poscontr PARP
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73 N23 negcontr NT2
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74 O23 poscontr ASCIZ
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75 P23 negcontr NT2
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76 A01 exclude exclude
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77 A24 exclude exclude
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78 B01 exclude exclude
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79 B24 exclude exclude
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80 C01 exclude exclude
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81 C24 exclude exclude
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82 D01 exclude exclude
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83 D24 exclude exclude
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84 E01 exclude exclude
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85 E24 exclude exclude
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86 F01 exclude exclude
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87 F24 exclude exclude
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88 G01 exclude exclude
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89 G24 exclude exclude
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90 H01 exclude exclude
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91 H24 exclude exclude
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92 I01 exclude exclude
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93 I24 exclude exclude
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94 J01 exclude exclude
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95 J24 exclude exclude
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96 K01 exclude exclude
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97 K24 exclude exclude
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98 L01 exclude exclude
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99 L24 exclude exclude
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100 M01 exclude exclude
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101 M24 exclude exclude
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102 N01 exclude exclude
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103 N24 exclude exclude
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104 O01 exclude exclude
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105 O24 exclude exclude
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106 P01 exclude exclude
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107 P24 exclude exclude
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108
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109 Running the program will give the following output::
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110
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111 #Well Table_1 Table_2
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112 A01 0.74 -0.67
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113 A02 1.55 0.67
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114 A03 0.36 8.09
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115 A04 -0.96 -0.67
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116 A05 -0.1 3.37
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117 A06 -0.97 0.67
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118 A07 0.54 1.35
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119 A08 1.72 0
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120 A09 0.27 -0.67
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121 A10 1.59 0.67
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122 ...
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123 P14 0.44 -0.67
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124 P15 -0.24 -0.67
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125 P16 1.81 0
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126 P17 -0.21 -0.67
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127 P18 -0.64 -0.67
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128 P19 1.21 -0.67
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129 P20 -0.44 -0.67
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130 P21 -0.54 -0.67
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131 P22 2.44 0
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132 P23 -0.72 -0.67
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133 P24 NA NA
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134
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135 </help>
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136
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137 </tool>
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