Mercurial > repos > pmac > robustzscorenormalization
diff robustZScoreNormalization.xml @ 0:7ecbc3ec2f55 draft default tip
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| author | pmac |
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| date | Wed, 01 Jun 2016 03:59:51 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/robustZScoreNormalization.xml Wed Jun 01 03:59:51 2016 -0400 @@ -0,0 +1,137 @@ +<tool id="robustZScoreNormalization" name="Calculate Robust Z Score Normalization" version="1.0.0"> + <description>Per Plate</description> + + <command interpreter="perl"> + robustZScoreNormalization.pl $inputFile1 $inputFile2 $outputFile1 + </command> + + <inputs> + <param format="tabular" name="inputFile1" type="data" label="Select the linear plates file"/> + <param format="tabular" name="inputFile2" type="data" label="Select the plate configuration file"/> + </inputs> + + <outputs> + <data format="tabular" name="outputFile1"/> + </outputs> + + <tests> + <test> + <param name="inputFile1" value="150615-HR-12015-01A.linear"/> + <param name="inputFile2" value="plate_config.txt"/> + <output name="outputFile1" file="calc_robust_z.tabular"/> + </test> + </tests> + + + <help> + +.. class:: infomark + +**What it does** + +This program takes a linear plate table and a plate config file as input and then performs Robust Z Score Normalization on the data. +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**. + +**Example** + +If the plates table consisted of:: + + #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 ... + 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 + +and the plates config was:: + + #Well Type Name A02 negcontr NT2 + B02 negcontr NT2 + C02 poscontr ASCIZ + D02 poscontr PARP + E02 negcontr NT2 + F02 poscontr ASCIZ + G02 poscontr PARP + H02 negcontr NT2 + I02 poscontr ASCIZ + J02 poscontr PARP + K02 negcontr NT2 + L02 poscontr ASCIZ + M02 poscontr PARP + N02 negcontr NT2 + O02 poscontr ASCIZ + P02 negcontr NT2 + A23 negcontr NT2 + B23 negcontr NT2 + C23 poscontr ASCIZ + D23 poscontr PARP + E23 negcontr NT2 + F23 poscontr ASCIZ + G23 poscontr PARP + H23 negcontr NT2 + I23 poscontr ASCIZ + J23 poscontr PARP + K23 negcontr NT2 + L23 poscontr ASCIZ + M23 poscontr PARP + N23 negcontr NT2 + O23 poscontr ASCIZ + P23 negcontr NT2 + A01 exclude exclude + A24 exclude exclude + B01 exclude exclude + B24 exclude exclude + C01 exclude exclude + C24 exclude exclude + D01 exclude exclude + D24 exclude exclude + E01 exclude exclude + E24 exclude exclude + F01 exclude exclude + F24 exclude exclude + G01 exclude exclude + G24 exclude exclude + H01 exclude exclude + H24 exclude exclude + I01 exclude exclude + I24 exclude exclude + J01 exclude exclude + J24 exclude exclude + K01 exclude exclude + K24 exclude exclude + L01 exclude exclude + L24 exclude exclude + M01 exclude exclude + M24 exclude exclude + N01 exclude exclude + N24 exclude exclude + O01 exclude exclude + O24 exclude exclude + P01 exclude exclude + P24 exclude exclude + +Running the program will give the following output:: + + #Well Table_1 Table_2 + A01 0.74 -0.67 + A02 1.55 0.67 + A03 0.36 8.09 + A04 -0.96 -0.67 + A05 -0.1 3.37 + A06 -0.97 0.67 + A07 0.54 1.35 + A08 1.72 0 + A09 0.27 -0.67 + A10 1.59 0.67 + ... + P14 0.44 -0.67 + P15 -0.24 -0.67 + P16 1.81 0 + P17 -0.21 -0.67 + P18 -0.64 -0.67 + P19 1.21 -0.67 + P20 -0.44 -0.67 + P21 -0.54 -0.67 + P22 2.44 0 + P23 -0.72 -0.67 + P24 NA NA + + </help> + +</tool>