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1 <tool id="normalizeMedianNegCntrl" name="Normalize Using Median Negative Controls" version="1.0.0">
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2
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3 <command interpreter="perl">
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4 normalizeMedianNegCntrl.pl $inputFile1 $inputFile2 $outputFile1
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5 </command>
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6
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7 <inputs>
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8 <param format="tabular" name="inputFile1" type="data" label="Select the linear plates file"/>
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9 <param format="tabular" name="inputFile2" type="data" label="Select the plate configuration file"/>
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10 </inputs>
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11
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12 <outputs>
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13 <data format="tabular" name="outputFile1"/>
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14 </outputs>
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15
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16 <tests>
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17 <test>
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18 <param name="inputFile1" value="150615-HR-12015-01A.linear"/>
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19 <param name="inputFile2" value="plate_config.txt"/>
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20 <output name="outputFile1" file="normalized_using_median.tabular"/>
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21 </test>
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22 </tests>
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23
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24 <help>
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25
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26 .. class:: infomark
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27
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28 **What it does**
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29
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30 This program takes a linear plate table and a plate config file as input and then normalizes each plate in the table to the negative controls in the config.
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31 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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32
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33 **Example**
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34
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35 If the plates table consisted of::
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36
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37 #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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38 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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39
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40 and the plates config was::
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41
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42 #Well Type Name
A02 negcontr NT2
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43 B02 negcontr NT2
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44 C02 poscontr ASCIZ
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45 D02 poscontr PARP
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46 E02 negcontr NT2
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47 F02 poscontr ASCIZ
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48 G02 poscontr PARP
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49 H02 negcontr NT2
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50 I02 poscontr ASCIZ
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51 J02 poscontr PARP
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52 K02 negcontr NT2
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53 L02 poscontr ASCIZ
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54 M02 poscontr PARP
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55 N02 negcontr NT2
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56 O02 poscontr ASCIZ
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57 P02 negcontr NT2
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58 A23 negcontr NT2
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59 B23 negcontr NT2
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60 C23 poscontr ASCIZ
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61 D23 poscontr PARP
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62 E23 negcontr NT2
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63 F23 poscontr ASCIZ
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64 G23 poscontr PARP
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65 H23 negcontr NT2
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66 I23 poscontr ASCIZ
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67 J23 poscontr PARP
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68 K23 negcontr NT2
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69 L23 poscontr ASCIZ
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70 M23 poscontr PARP
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71 N23 negcontr NT2
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72 O23 poscontr ASCIZ
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73 P23 negcontr NT2
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74 A01 exclude exclude
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75 A24 exclude exclude
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76 B01 exclude exclude
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77 B24 exclude exclude
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78 C01 exclude exclude
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79 C24 exclude exclude
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80 D01 exclude exclude
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81 D24 exclude exclude
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82 E01 exclude exclude
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83 E24 exclude exclude
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84 F01 exclude exclude
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85 F24 exclude exclude
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86 G01 exclude exclude
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87 G24 exclude exclude
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88 H01 exclude exclude
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89 H24 exclude exclude
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90 I01 exclude exclude
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91 I24 exclude exclude
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92 J01 exclude exclude
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93 J24 exclude exclude
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94 K01 exclude exclude
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95 K24 exclude exclude
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96 L01 exclude exclude
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97 L24 exclude exclude
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98 M01 exclude exclude
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99 M24 exclude exclude
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100 N01 exclude exclude
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101 N24 exclude exclude
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102 O01 exclude exclude
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103 O24 exclude exclude
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104 P01 exclude exclude
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105 P24 exclude exclude
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106
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107 Running the program will give the following output::
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108
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109 #Well Table_1 Table_2
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110 A01 1.03 0.75
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111 A02 1.07 1
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112 A03 1.02 2.38
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113 A04 0.95 0.75
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114 A05 0.99 1.5
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115 A06 0.95 1
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116 A07 1.02 1.12
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117 A08 1.08 0.88
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118 A09 1.01 0.75
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119 A10 1.08 1
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120 ...
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121 P14 1.02 0.75
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122 P15 0.99 0.75
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123 P16 1.09 0.88
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124 P17 0.99 0.75
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125 P18 0.97 0.75
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126 P19 1.06 0.75
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127 P20 0.98 0.75
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128 P21 0.97 0.75
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129 P22 1.12 0.88
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130 P23 0.96 0.75
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131 P24 NA NA
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132
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133 </help>
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134
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135 </tool>
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