Mercurial > repos > ethevenot > batchcorrection

changeset 2:57edfd3943ab draft

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planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit a619f606894efd016387a0b6f6bf0d5addc38bc9-dirty
author ethevenot
date Mon, 01 May 2017 08:06:08 -0400
parents 26d058657f66
children 2e3a23dd6c24
files README.md batch_correction.xml determine_bc.xml runit/output/dataMatrix.tsv runit/output/graph_output.pdf runit/output/out_graph.pdf runit/output/preNormSummary.txt runit/output/rdata_output.rdata runit/output/variableMetadata.tsv static/images/batch_correction.png static/images/determine_batch_correction.png
diffstat 11 files changed, 52 insertions(+), 392 deletions(-) [+]
line wrap: on
line diff
--- a/README.md	Sun Apr 09 15:27:17 2017 -0400
+++ b/README.md	Mon May 01 08:06:08 2017 -0400
@@ -7,8 +7,8 @@
 
 ### Description
 
-**Version:** 2.1.0  
-**Date:** 2017-03-20  
+**Version:** 2.1.2  
+**Date:** 2017-04-30  
 **Author:** Jean-François Martin (INRA, AXIOM), Mélanie Pétéra (INRA, PFEM), Marion Landi (INRA, PFEM), Franck Giacomoni (INRA, PFEM), and Etienne A. Thévenot (CEA, LIST)  
 **Email:** [jean-francois.martin(at)toulouse.inra.fr](mailto:jean-francois.martin@toulouse.inra.frr), [melanie.petera(at)clermont.inra.fr](mailto:melanie.petera@clermont.inra.fr), [etienne.thevenot(at)cea.fr](mailto:etienne.thevenot@cea.fr)  
 **Citation:**  
@@ -76,6 +76,12 @@
 
 ### News
 
+##### CHANGES IN VERSION 2.1.2  
+
+INTERNAL MODIFICATIONS  
+
+ * Minor modifications in config file  
+
 ##### CHANGES IN VERSION 2.1.0  
 
 INTERNAL MODIFICATIONS  
--- a/batch_correction.xml	Sun Apr 09 15:27:17 2017 -0400
+++ b/batch_correction.xml	Mon May 01 08:06:08 2017 -0400
@@ -1,4 +1,4 @@
-<tool id="Batch_correction" name="Batch_correction" version="2.1.0">
+<tool id="Batch_correction" name="Batch_correction" version="2.1.2">
   <description>Corrects intensities for signal drift and batch-effects</description>
 
   <requirements>
@@ -292,7 +292,7 @@
 Working example
 ---------------
 
-.. class:: warningmark
+.. class:: infomark
 
 Refer to the corresponding "W4M HowTo" page:
  | `MS data processing - Filters and normalisation &lt;http://workflow4metabolomics.org/sites/workflow4metabolomics.org/files/files/w4e-2016-data_processing.pdf&gt;`_
@@ -309,12 +309,19 @@
 NEWS
 ----
 
+CHANGES IN VERSION 2.1.2  
+========================  
+
+INTERNAL MODIFICATIONS  
+
+Minor modifications in config file  
+
 CHANGES IN VERSION 2.1.0
 ========================
 
 INTERNAL MODIFICATIONS  
 
-For PCA figure display only ("all_loess_" options): missing values are set to the minimum value before PCA computation is performed (with svd)
+For PCA figure display only (**all_loess** options): missing values are set to the minimum value before PCA computation is performed (with svd)
 
 Additional running and installation tests added with planemo, conda, and travis
 
@@ -345,391 +352,5 @@
 	<citation type="doi">10.1021/acs.jproteome.5b00354</citation>
     </citations>
 	
-<!--
 
-example 1:
-
-Input files
-===========
-
-| **To generate the "dataMatrix", "sampleMetadata" and "variableMetadata" files:**
-|   **1) copy/paste the values below in three distinct .txt files**
-|   **2) use the "Get Data" / "Upload File" in the "Tools" (left) panel from the Galaxy page by choosing:**
-|     **Convert spaces to tabs: 'Yes'**
-| 
-
-**dataMatrix file**::
-
-	dataMatrix QC1_001 HU_017 HU_018 HU_020 HU_021 HU_027 HU_028 HU_032 HU_034 QC1_002 HU_037 HU_041 HU_043 HU_044 HU_047 HU_048 QC1_003 HU_049 HU_050 HU_051 HU_052 HU_055 HU_060 HU_061 QC1_004 HU_064 HU_065 HU_066 HU_068 HU_072 HU_077 HU_078 QC1_005 HU_079 HU_083 HU_086 HU_088 HU_089 HU_090 HU_091 HU_093 HU_094 QC1_006 HU_099 HU_100 HU_101 HU_105 HU_107 HU_108 HU_109 HU_110 QC1_007 HU_116 HU_118 HU_123 HU_125 HU_126 HU_127 QC1_008 HU_130 HU_131 HU_132 HU_133 HU_134 HU_138 QC1_009 HU_144 HU_148 HU_149 HU_150 QC1_010 HU_152 HU_154 HU_156 HU_157 HU_158 HU_163 HU_170 HU_171 QC1_011 HU_172 HU_173 HU_174 HU_175 HU_179 HU_180 HU_181 HU_182 QC1_012 HU_184 HU_185 HU_186 HU_189 HU_192 HU_196 QC1_013 HU_200 HU_201 HU_202 HU_204 HU_207 HU_208 HU_209 QC1_014 QC1_015 HU_022 HU_076 HU_166 HU_114 HU_190 HU_139 HU_096 HU_058 HU_031 QC1_016 HU_039 HU_087 HU_143 HU_162 HU_102 HU_188 HU_095 HU_062 QC1_017 HU_063 HU_011 HU_074 HU_122 HU_142 HU_030 HU_187 HU_167 HU_113 QC1_018 HU_081 HU_014 HU_206 HU_119 HU_033 HU_067 HU_140 HU_164 HU_193 HU_112 QC1_019 HU_097 HU_056 HU_195 HU_135 HU_159 HU_070 HU_038 HU_026 QC1_020 HU_098 HU_115 HU_137 HU_019 HU_073 HU_168 HU_191 HU_040 HU_046 QC1_021 HU_103 HU_015 HU_053 HU_121 HU_183 HU_199 HU_042 HU_075 QC1_022 HU_203 HU_024 HU_082 HU_169 HU_129 HU_057 HU_035 HU_194 HU_145 QC1_023 HU_177 HU_025 HU_080 HU_117 HU_136 HU_197 HU_036 HU_054 HU_085 QC1_024 HU_160 HU_092 HU_023 HU_124 HU_147 HU_205 HU_084 HU_120 HU_198 QC1_025 HU_045 HU_029 HU_069 HU_155 HU_106 HU_146 QC1_026
-	met_001 17558910 10657431 13044183 7261208 6909491 2594571 12751984 13522888 13894507 16393604 7865097 3630317 7503242 8537528 5503464 4587754 17599767 8473703 25556162 1332303 13312536 5073342 26036420 4959938 16841618 5608314 29332804 10491655 23448752 19921296 21471497 21223304 17008026 8908921 21091221 51170137 7921432 16085480 13789362 14424243 14714241 8362817 16699474 6133088 26413961 1605625 9660665 35717402 280575 1976782 2568169 15026529 6552813 16307390 12123953 13480559 22963554 12249347 13888520 17165271 17470093 12811880 12013641 18118700 19560902 13687923 25942102 16394638 24333092 12590296 12722221 10992119 6223253 1623756 10758763 2121817 7813434 12500471 12705530 11102165 17869823 9436102 11637518 4185206 3758974 10169281 2777795 5497423 10321096 3558399 944424 7181581 3180237 7866370 8184772 9332856 21413125 4177729 2968557 23287406 6301903 2265236 5640134 8113388 34046147 29268048 43765299 44375419 50601116 4832613 40454119 8126 19479962 11235683 33064844 75260138 36891690 17466250 74160059 32122101 5238560 30163448 10216046 31450577 17301601 11549910 12734389 54057483 3488082 24301846 2046492 23004592 9579482 30075694 7571631 5257922 60032654 15725469 42794552 12202672 10427301 17332850 2558158 66102394 29666404 34174908 36717068 24271602 36414651 37145056 20074559 1865267 5837544 27608715 38999155 21669105 14372963 36030678 24509866 1906953 15589584 18219005 25991397 25068509 21518123 17608775 6613249 4124652 30008362 7839717 16104411 36946332 23198059 6151472 23334545 18392766 27331396 30774819 18461787 42246522 20479189 28817403 21703591 17170407 13809778 11188751 14478896 8256694 2771227 47261207 21462355 24438964 19424590 379608 17107855 14512991 31446516 24437179 18499953 16786178 1370420 23336305 18279598 9162668 29590881 24605602 13020657 30919250 16843645 15320951
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-	
-**sampleMetadata file**::
-	
-	sampleMetadata sampleType injectionOrder batch
-	QC1_001 pool 1 ne1
-	HU_017 sample 2 ne1
-	HU_018 sample 3 ne1
-	HU_020 sample 4 ne1
-	HU_021 sample 5 ne1
-	HU_027 sample 6 ne1
-	HU_028 sample 7 ne1
-	HU_032 sample 8 ne1
-	HU_034 sample 9 ne1
-	QC1_002 pool 10 ne1
-	HU_037 sample 11 ne1
-	HU_041 sample 12 ne1
-	HU_043 sample 13 ne1
-	HU_044 sample 14 ne1
-	HU_047 sample 15 ne1
-	HU_048 sample 16 ne1
-	QC1_003 pool 17 ne1
-	HU_049 sample 18 ne1
-	HU_050 sample 19 ne1
-	HU_051 sample 20 ne1
-	HU_052 sample 21 ne1
-	HU_055 sample 22 ne1
-	HU_060 sample 23 ne1
-	HU_061 sample 24 ne1
-	QC1_004 pool 25 ne1
-	HU_064 sample 26 ne1
-	HU_065 sample 27 ne1
-	HU_066 sample 28 ne1
-	HU_068 sample 29 ne1
-	HU_072 sample 30 ne1
-	HU_077 sample 31 ne1
-	HU_078 sample 32 ne1
-	QC1_005 pool 33 ne1
-	HU_079 sample 34 ne1
-	HU_083 sample 35 ne1
-	HU_086 sample 36 ne1
-	HU_088 sample 37 ne1
-	HU_089 sample 38 ne1
-	HU_090 sample 39 ne1
-	HU_091 sample 40 ne1
-	HU_093 sample 41 ne1
-	HU_094 sample 42 ne1
-	QC1_006 pool 43 ne1
-	HU_099 sample 44 ne1
-	HU_100 sample 45 ne1
-	HU_101 sample 46 ne1
-	HU_105 sample 47 ne1
-	HU_107 sample 48 ne1
-	HU_108 sample 49 ne1
-	HU_109 sample 50 ne1
-	HU_110 sample 51 ne1
-	QC1_007 pool 52 ne1
-	HU_116 sample 53 ne1
-	HU_118 sample 54 ne1
-	HU_123 sample 55 ne1
-	HU_125 sample 56 ne1
-	HU_126 sample 57 ne1
-	HU_127 sample 58 ne1
-	QC1_008 pool 59 ne1
-	HU_130 sample 60 ne1
-	HU_131 sample 61 ne1
-	HU_132 sample 62 ne1
-	HU_133 sample 63 ne1
-	HU_134 sample 64 ne1
-	HU_138 sample 65 ne1
-	QC1_009 pool 66 ne1
-	HU_144 sample 67 ne1
-	HU_148 sample 68 ne1
-	HU_149 sample 69 ne1
-	HU_150 sample 70 ne1
-	QC1_010 pool 71 ne1
-	HU_152 sample 72 ne1
-	HU_154 sample 73 ne1
-	HU_156 sample 74 ne1
-	HU_157 sample 75 ne1
-	HU_158 sample 76 ne1
-	HU_163 sample 77 ne1
-	HU_170 sample 78 ne1
-	HU_171 sample 79 ne1
-	QC1_011 pool 80 ne1
-	HU_172 sample 81 ne1
-	HU_173 sample 82 ne1
-	HU_174 sample 83 ne1
-	HU_175 sample 84 ne1
-	HU_179 sample 85 ne1
-	HU_180 sample 86 ne1
-	HU_181 sample 87 ne1
-	HU_182 sample 88 ne1
-	QC1_012 pool 89 ne1
-	HU_184 sample 90 ne1
-	HU_185 sample 91 ne1
-	HU_186 sample 92 ne1
-	HU_189 sample 93 ne1
-	HU_192 sample 94 ne1
-	HU_196 sample 95 ne1
-	QC1_013 pool 96 ne1
-	HU_200 sample 97 ne1
-	HU_201 sample 98 ne1
-	HU_202 sample 99 ne1
-	HU_204 sample 100 ne1
-	HU_207 sample 101 ne1
-	HU_208 sample 102 ne1
-	HU_209 sample 103 ne1
-	QC1_014 pool 104 ne1
-	QC1_015 pool 105 ne2
-	HU_022 sample 106 ne2
-	HU_076 sample 107 ne2
-	HU_166 sample 108 ne2
-	HU_114 sample 109 ne2
-	HU_190 sample 110 ne2
-	HU_139 sample 111 ne2
-	HU_096 sample 112 ne2
-	HU_058 sample 113 ne2
-	HU_031 sample 114 ne2
-	QC1_016 pool 115 ne2
-	HU_039 sample 116 ne2
-	HU_087 sample 117 ne2
-	HU_143 sample 118 ne2
-	HU_162 sample 119 ne2
-	HU_102 sample 120 ne2
-	HU_188 sample 121 ne2
-	HU_095 sample 122 ne2
-	HU_062 sample 123 ne2
-	QC1_017 pool 124 ne2
-	HU_063 sample 125 ne2
-	HU_011 sample 126 ne2
-	HU_074 sample 127 ne2
-	HU_122 sample 128 ne2
-	HU_142 sample 129 ne2
-	HU_030 sample 130 ne2
-	HU_187 sample 131 ne2
-	HU_167 sample 132 ne2
-	HU_113 sample 133 ne2
-	QC1_018 pool 134 ne2
-	HU_081 sample 135 ne2
-	HU_014 sample 136 ne2
-	HU_206 sample 137 ne2
-	HU_119 sample 138 ne2
-	HU_033 sample 139 ne2
-	HU_067 sample 140 ne2
-	HU_140 sample 141 ne2
-	HU_164 sample 142 ne2
-	HU_193 sample 143 ne2
-	HU_112 sample 144 ne2
-	QC1_019 pool 145 ne2
-	HU_097 sample 146 ne2
-	HU_056 sample 147 ne2
-	HU_195 sample 148 ne2
-	HU_135 sample 149 ne2
-	HU_159 sample 150 ne2
-	HU_070 sample 151 ne2
-	HU_038 sample 152 ne2
-	HU_026 sample 153 ne2
-	QC1_020 pool 154 ne2
-	HU_098 sample 155 ne2
-	HU_115 sample 156 ne2
-	HU_137 sample 157 ne2
-	HU_019 sample 158 ne2
-	HU_073 sample 159 ne2
-	HU_168 sample 160 ne2
-	HU_191 sample 161 ne2
-	HU_040 sample 162 ne2
-	HU_046 sample 163 ne2
-	QC1_021 pool 164 ne2
-	HU_103 sample 165 ne2
-	HU_015 sample 166 ne2
-	HU_053 sample 167 ne2
-	HU_121 sample 168 ne2
-	HU_183 sample 169 ne2
-	HU_199 sample 170 ne2
-	HU_042 sample 171 ne2
-	HU_075 sample 172 ne2
-	QC1_022 pool 173 ne2
-	HU_203 sample 174 ne2
-	HU_024 sample 175 ne2
-	HU_082 sample 176 ne2
-	HU_169 sample 177 ne2
-	HU_129 sample 178 ne2
-	HU_057 sample 179 ne2
-	HU_035 sample 180 ne2
-	HU_194 sample 181 ne2
-	HU_145 sample 182 ne2
-	QC1_023 pool 183 ne2
-	HU_177 sample 184 ne2
-	HU_025 sample 185 ne2
-	HU_080 sample 186 ne2
-	HU_117 sample 187 ne2
-	HU_136 sample 188 ne2
-	HU_197 sample 189 ne2
-	HU_036 sample 190 ne2
-	HU_054 sample 191 ne2
-	HU_085 sample 192 ne2
-	QC1_024 pool 193 ne2
-	HU_160 sample 194 ne2
-	HU_092 sample 195 ne2
-	HU_023 sample 196 ne2
-	HU_124 sample 197 ne2
-	HU_147 sample 198 ne2
-	HU_205 sample 199 ne2
-	HU_084 sample 200 ne2
-	HU_120 sample 201 ne2
-	HU_198 sample 202 ne2
-	QC1_025 pool 203 ne2
-	HU_045 sample 204 ne2
-	HU_029 sample 205 ne2
-	HU_069 sample 206 ne2
-	HU_155 sample 207 ne2
-	HU_106 sample 208 ne2
-	HU_146 sample 209 ne2
-	QC1_026 pool 210 ne2
-
-**variableMetadata file**::
-	
-	variableMetadata variable number
-	met_001 met 1
-	met_002 met 2
-	met_003 met 3
-	met_004 met 4
-	met_005 met 5
-	met_006 met 6
-	met_007 met 7
-	met_008 met 8
-	met_009 met 9
-	met_010 met 10
-
-Parameters
-===========
-
-| **Type of regression model**: 'all_loess_pool'
-| **span**: 1 'default)
-
-Figure output
-=============
-
-| You should obtain with this very simplified dataset the following figure:
-|
-
-.. image:: batchCorrection_workingExampleImage.png
-        :width: 600
-
-
-  
-example 2:
-
-Input files
-===========
-
-| **These two input files can be used in the purview "URL/Text:" of the tool "Get Data/Upload File",**
-| **by checking the box "Convert spaces to tabs: YES"**
-
-Metadata_samples.txt
-	Model input Sample metadata file::
-
-		samples idLIMS serie factor01 factor02 batch injectionOrder sampleType
-		POOL1 POOL1 p p p 01_08_2011 1 p
-		X12588 12588 3 validation 2 01_08_2011 2 s
-		X17736 17736 3 Q1 1 01_08_2011 3 s
-		X15432 15432 3 validation 1 01_08_2011 4 s
-		X17159 17159 3 Q4 1 01_08_2011 5 s
-		X14325 14325 3 validation 2 01_08_2011 6 s
-		X17419 17419 3 Q4 1 01_08_2011 7 s
-		X16437 16437 3 Q4 1 01_08_2011 8 s
-		X16172 16172 3 Q4 2 01_08_2011 9 s
-		X16392 16392 3 Q4 2 01_08_2011 10 s
-		X13875 13875 3 validation 2 01_08_2011 11 s
-		POOL2 POOL2 p p p 01_08_2011 12 p
-		X13117 13117 3 Q4 2 01_08_2011 13 s
-		X13341 13341 3 Q1 2 01_08_2011 14 s
-		X16888 16888 3 Q4 1 01_08_2011 15 s
-		X17489 17489 3 Q4 2 01_08_2011 16 s
-		X12718 12718 3 Q1 2 01_08_2011 17 s
-		X16235 16235 3 Q4 2 01_08_2011 18 s
-		X16878 16878 3 Q1 1 01_08_2011 19 s
-		X12701 12701 3 validation 1 01_08_2011 20 s
-		X16220 16220 3 Q4 2 01_08_2011 21 s
-		X15635 15635 3 Q4 1 01_08_2011 22 s
-
-
-Intensity_matrix.txt
-	Model input Matrix Ions file BEFORE IMPLEMENTATION::
-
-		samples POOL1 X12588 X17736 X15432 X17159 X14325 X17419 X16437 X16172 X16392 X13875 POOL2 X13117 X13341 X16888 X17489 X12718 X16235 X16878 X12701 X16220 X15635
-		ion01 188.4140625 219.729126 122.5697632 123.5487671 805.8852539 183.4683838 37.33084106 151.8625488 97.12005615 91.24694824 69.87762451 195.4349365 112.4111938 136.7092285 159.9987793 172.1585693 0 117.5420532 133.6679688 80.05419922 160.0006104 760.0488281
-		ion02 82.02575684 87.11358643 79.82391357 80.33862305 83.08575439 94.27703857 76.02288818 77.04394531 76.97564697 84.17669678 81.04943848 86.44024658 84.11865234 83.71282959 77.75219727 79.15936279 75.98492432 78.2835083 78.98760986 73.98388672 72.20550537 82.16448975
-		ion03 25.31900024 24.2960968 23.29342651 31.54063416 30.3830719 22.42404175 35.44485474 26.38783264 17.1401825 21.27339172 20.25959778 26.33859253 18.17146301 26.32852173 24.30648804 28.34313965 29.37016296 18.23519897 24.48402405 25.38140869 24.35777283 21.31071472
-		ion04 65.87536621 62.68716431 46.60232544 62.77856445 29.53218079 47.59136963 90.13983154 28.35336304 58.74325562 31.39331055 23.32928467 30.39666748 41.43960571 21.27049255 88.1161499 29.36820984 24.30200195 25.00007629 45.60662842 103.293457 37.46994019 87.09295654
-		ion05 0 103.728544 279.5808214 884.2333448 824.5072072 434.6439081 764.82768 799.0972595 398.4002569 382.5370891 74.55342827 0 636.6596277 514.3863309 741.690017 412.3166491 660.8996555 57.36593795 102.2085264 455.6403091 548.6145486 515.8412195
-		ion06 2711.785156 3465.292969 2469.75 3435.259766 2482.3125 2593.654297 1407.915039 1291.253906 2241.734375 1444.189453 3363.683594 2578.642578 2633.181641 3397.763672 3706.855469 3647.212891 3548.410156 3714.640625 1889.213867 2262.707031 2107.417969 2763.21875
-		ion07 164.9023438 192.40625 140.7609863 192.4053955 139.7540283 140.748291 84.60144043 86.1819458 150.762207 89.90411377 207.5949707 164.0512695 149.8706055 186.336792 214.6140137 202.5360107 214.6877441 195.4482422 117.4679565 127.2941895 142.78479 163.0666504
-
-
-Parameters
-==========
-
-Factor analysis  -> **batch**
-
-Level of details  -> **no**
-
-Model used (linear or not)  -> **Linear**
-
-
-Output files
-============
-
-Norma_rdata_$detail.rdata::
-
-	binary data
-	Download, open with R send res
-
-
-Norma_plots_$detail.pdf
-
-.. image:: Vdk_pdf1.png
-        :width: 800
-        
-.. image:: Vdk_pdf2.png
-        :width: 800
-        
-
-Norma_result_for_simca.tabular::
-
-	samples	idLIMS	serie	factor01	factor02	batch	injectionOrder	sampleType	ion01	ion02	ion03	ion04	ion05	ion06	ion07
-	POOL1	POOL1	p	p	p	01_08_2011	1	p	183.806309736177	78.555522674121	24.2565782732588	67.2059357441544	0	2756.58450391724	158.052416850832
-	POOL2	POOL2	p	p	p	01_08_2011	12	p	190.655485025641	82.783250185879	25.2333869921957	31.0106280849366	0	2621.24237826457	157.236695576441
-	X12588	12588	3	validation	2	01_08_2011	2	s	220.281338788057	87.500123119505	24.4029802274792	62.5632990312483	94.2986763636364	3459.67039593807	193.243760535699
-	X12701	12701	3	validation	1	01_08_2011	20	s	80.2553876257053	74.3121648660553	25.4930666232626	103.089356639338	414.218462818182	2259.03570054876	127.848278698451
-	X12718	12718	3	Q1	2	01_08_2011	17	s	0	76.3220813847312	29.4993682273574	24.2539829611226	600.817868636364	3542.65272205883	215.622242057156
-	X13117	13117	3	Q4	2	01_08_2011	13	s	112.693700265425	84.4919000357226	18.251402938821	41.3577240621519	578.781479727273	2628.90920103769	150.522965863022
-	X13341	13341	3	Q1	2	01_08_2011	14	s	137.052799630498	84.0842765863284	26.4443462044465	21.2284636032788	467.623937181818	3392.25066785752	187.147883253472
-	X13875	13875	3	validation	2	01_08_2011	11	s	70.0532376321925	81.4090675909135	20.3487238346046	23.2831876997425	67.7758438818182	3358.22588611392	208.498595063134
-	X14325	14325	3	validation	2	01_08_2011	6	s	183.929467815501	94.695360623753	22.5226896299416	47.497332543935	395.130825545454	2589.44599169574	141.360943533866
-	X15432	15432	3	validation	1	01_08_2011	4	s	123.859263984884	80.6950981610103	31.6793877676942	62.6545185712173	803.848495272727	3429.68592298187	193.242902316211
-	X15635	15635	3	Q4	1	01_08_2011	22	s	761.958946663093	82.5290665188414	21.4044648499099	86.9208671903241	468.946563181818	2758.73531975414	163.776450823485
-	X16172	16172	3	Q4	2	01_08_2011	9	s	97.3641336556051	77.3172000270102	17.2155856179699	58.6271832180619	362.182051727273	2238.0970735015	151.418448347397
-	X16220	16220	3	Q4	2	01_08_2011	21	s	160.402716323636	72.5258925581935	24.4649275827679	37.3959023125888	498.740498727273	2103.99860111142	143.406307055514
-	X16235	16235	3	Q4	2	01_08_2011	18	s	117.83745429722	78.6308645435113	18.315419286157	24.950677956983	52.1508526818182	3708.61347563638	196.298993992243
-	X16392	16392	3	Q4	2	01_08_2011	10	s	91.4762657301598	84.5502020280356	21.3669776585093	31.3312796509314	347.760990090909	1441.84619925857	90.295450550822
-	X16437	16437	3	Q4	1	01_08_2011	8	s	152.244202534309	77.3858014174909	26.5039180350956	28.2973388561794	726.452054090909	1289.1587961513	86.5570806388865
-	X16878	16878	3	Q1	1	01_08_2011	19	s	134.003896781277	79.3380903129169	24.5917342073347	45.5165130382572	92.9168421818182	1886.14854378149	117.979273835979
-	X16888	16888	3	Q4	1	01_08_2011	15	s	160.400880621802	78.0971960028743	24.4134171806386	87.9420387946402	674.263651818182	3700.84095135577	215.548190721704
-	X17159	17159	3	Q4	1	01_08_2011	5	s	807.910566388206	83.4544189550015	30.5167331579687	29.4738273480161	749.552006545455	2478.28485110605	140.362352983359
-	X17419	17419	3	Q4	1	01_08_2011	7	s	37.4246591541122	76.3602136963513	35.6007838010462	89.9617217868595	695.297890909091	1405.63064191075	84.9696956072378
-	X17489	17489	3	Q4	2	01_08_2011	16	s	172.59123002765	79.510605337691	28.4678268347873	29.3101803926911	374.833317363636	3641.2951457659	203.417614300817
-	X17736	17736	3	Q1	1	01_08_2011	3	s	122.877799698849	80.1781048340628	23.3958989887532	46.5102426333419	254.164383090909	2465.74273425251	141.373694094272
-
-
-Norma_result.tabular::
-
-	POOL1	POOL2	X12588	X12701	X12718	X13117	X13341	X13875	X14325	X15432	X15635	X16172	X16220	X16235	X16392	X16437	X16878	X16888	X17159	X17419	X17489	X17736
-	ion01	183.806309736177	190.655485025641	220.281338788057	80.2553876257053	0	112.693700265425	137.052799630498	70.0532376321925	183.929467815501	123.859263984884	761.958946663093	97.3641336556051	160.402716323636	117.83745429722	91.4762657301598	152.244202534309	134.003896781277	160.400880621802	807.910566388206	37.4246591541122	172.59123002765	122.877799698849
-	ion02	78.555522674121	82.783250185879	87.500123119505	74.3121648660553	76.3220813847312	84.4919000357226	84.0842765863284	81.4090675909135	94.695360623753	80.6950981610103	82.5290665188414	77.3172000270102	72.5258925581935	78.6308645435113	84.5502020280356	77.3858014174909	79.3380903129169	78.0971960028743	83.4544189550015	76.3602136963513	79.510605337691	80.1781048340628
-	ion03	24.2565782732588	25.2333869921957	24.4029802274792	25.4930666232626	29.4993682273574	18.251402938821	26.4443462044465	20.3487238346046	22.5226896299416	31.6793877676942	21.4044648499099	17.2155856179699	24.4649275827679	18.315419286157	21.3669776585093	26.5039180350956	24.5917342073347	24.4134171806386	30.5167331579687	35.6007838010462	28.4678268347873	23.3958989887532
-	ion04	67.2059357441544	31.0106280849366	62.5632990312483	103.089356639338	24.2539829611226	41.3577240621519	21.2284636032788	23.2831876997425	47.497332543935	62.6545185712173	86.9208671903241	58.6271832180619	37.3959023125888	24.950677956983	31.3312796509314	28.2973388561794	45.5165130382572	87.9420387946402	29.4738273480161	89.9617217868595	29.3101803926911	46.5102426333419
-	ion05	0	0	94.2986763636364	414.218462818182	600.817868636364	578.781479727273	467.623937181818	67.7758438818182	395.130825545454	803.848495272727	468.946563181818	362.182051727273	498.740498727273	52.1508526818182	347.760990090909	726.452054090909	92.9168421818182	674.263651818182	749.552006545455	695.297890909091	374.833317363636	254.164383090909
-	ion06	2756.58450391724	2621.24237826457	3459.67039593807	2259.03570054876	3542.65272205883	2628.90920103769	3392.25066785752	3358.22588611392	2589.44599169574	3429.68592298187	2758.73531975414	2238.0970735015	2103.99860111142	3708.61347563638	1441.84619925857	1289.1587961513	1886.14854378149	3700.84095135577	2478.28485110605	1405.63064191075	3641.2951457659	2465.74273425251
-	ion07	158.052416850832	157.236695576441	193.243760535699	127.848278698451	215.622242057156	150.522965863022	187.147883253472	208.498595063134	141.360943533866	193.242902316211	163.776450823485	151.418448347397	143.406307055514	196.298993992243	90.295450550822	86.5570806388865	117.979273835979	215.548190721704	140.362352983359	84.9696956072378	203.417614300817	141.373694094272
--->
 </tool>
--- a/determine_bc.xml	Sun Apr 09 15:27:17 2017 -0400
+++ b/determine_bc.xml	Mon May 01 08:06:08 2017 -0400
@@ -1,4 +1,4 @@
-<tool id="Determine_BC" name="Determine_batch_correction" version="2.1.0">
+<tool id="Determine_BC" name="Determine_batch_correction" version="2.1.2">
   <description>to choose between linear, lowess and loess methods</description>
 
   <requirements>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/runit/output/dataMatrix.tsv	Mon May 01 08:06:08 2017 -0400
@@ -0,0 +1,11 @@
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