Mercurial > repos > ethevenot > heatmap

--- a/README.md	Tue Aug 02 06:26:41 2016 -0400
+++ b/README.md	Sat Aug 06 12:18:15 2016 -0400
@@ -1,12 +1,14 @@
-## Heatmap of the data matrix
-#### A Galaxy module from the [Workflow4metabolomics](http://workflow4metabolomics.org) project
+Heatmap of the data matrix
+==========================
+
+A Galaxy module from the [Workflow4metabolomics](http://workflow4metabolomics.org) infrastructure

 Status: [![Build Status](https://travis-ci.org/workflow4metabolomics/heatmap.svg?branch=master)](https://travis-ci.org/workflow4metabolomics/heatmap).

 ### Description

-**Version:** 2.2.0
-**Date:** 2016-07-30
+**Version:** 2.2.2
+**Date:** 2016-08-04
 **Author:** Etienne A. Thevenot (CEA, LIST, MetaboHUB, W4M Core Development Team)
 **Email:** [etienne.thevenot(at)cea.fr](mailto:etienne.thevenot@cea.fr)
 **Citation:** Thevenot E.A., Roux A., Xu Y., Ezan E. and Junot C. (2015). Analysis of the human adult urinary metabolome variations with age, body mass index and gender by implementing a comprehensive workflow for univariate and OPLS statistical analyses. *Journal of Proteome Research*, **14**:3322-3335. [doi:10.1021/acs.jproteome.5b00354](http://dx.doi.org/10.1021/acs.jproteome.5b00354)
@@ -16,45 +18,52 @@

 ### Installation

-* Configuration file: **heatmap_config.xml**
+* Configuration file: `heatmap_config.xml`
 * Image files:
-    + **static/images/heatmap_workflowPositionImage.png**
-    + **static/images/heatmap_workingExampleImage.png**
-* Wrapper file: **heatmap_wrapper.R**
+    + `static/images/heatmap_workflowPositionImage.png`
+    + `static/images/heatmap_workingExampleImage.png`
+* Wrapper file: `heatmap_wrapper.R`
 * R packages
-    + **batch** from CRAN
-> install.packages("batch", dep=TRUE)
+    + **batch** from CRAN
+
+    ```r
+    install.packages("batch", dep=TRUE)
+    ```

 ### Tests

-The code in the wrapper can be tested by running the **tests/heatmap_tests.R** in R
+The code in the wrapper can be tested by running the `runit/heatmap_runtests.R` R file
+
+### Working example
+
+See the **W4M00001a_sacurine-subset-statistics** shared history in the **Shared Data/Published Histories** menu (https://galaxy.workflow4metabolomics.org/history/list_published)

-### News
+### News
+
+##### CHANGES IN VERSION 2.2.2
+
+INTERNAL MODIFICATION
+
+ * Minor internal modifications

 ##### CHANGES IN VERSION 2.2.0

 NEW FEATURES

-    o Default method for the correlation coefficient is now 'pearson', instead of 'spearman' previously (the latter can still be selected in the advanced parameters)
-
-    o The 1-abs(correlation) dissimilarity is now available (in addition to the default '1-correlation') in case the sign of correlations between samples and between variables does not matter, as well as the euclidean, maximum, manhattan, canberra, binary, and minkowski dissimilarities
+ * Default method for the correlation coefficient is now 'pearson', instead of 'spearman' previously (the latter can still be selected in the advanced parameters)

-    o A new red-green color scale is available
+ * The 1-abs(correlation) dissimilarity is now available (in addition to the default '1-correlation') in case the sign of correlations between samples and between variables does not matter, as well as the euclidean, maximum, manhattan, canberra, binary, and minkowski dissimilarities

-***
-
+ * A new red-green color scale is available
+
 ##### CHANGES IN VERSION 2.1.2

 INTERNAL MODIFICATION

-    o Creating additional files for planemo and travis validation
+ * Creating additional files for planemo and travis validation

-***
-
 ##### CHANGES IN VERSION 2.0.2

 INTERNAL MODIFICATION

-    o Creating tests for R code
-
-***
\ No newline at end of file
+ * Creating tests for R code
\ No newline at end of file
--- a/heatmap_config.xml	Tue Aug 02 06:26:41 2016 -0400
+++ b/heatmap_config.xml	Sat Aug 06 12:18:15 2016 -0400
@@ -1,13 +1,18 @@
-<tool id="Heatmap" name="Heatmap" version="2.2.0">
+<tool id="Heatmap" name="Heatmap" version="2.2.2">
   <description>Heatmap of the dataMatrix</description>

   <requirements>
     <requirement type="package" version="3.2.2">R</requirement>
     <requirement type="package">r-batch</requirement>
   </requirements>
-
+
+  <stdio>
+    <exit_code range="1:" level="fatal" />
+  </stdio>
+
   <command><![CDATA[
   Rscript $__tool_directory__/heatmap_wrapper.R
+
   dataMatrix_in "$dataMatrix_in"
   sampleMetadata_in "$sampleMetadata_in"
   variableMetadata_in "$variableMetadata_in"
@@ -292,7 +297,7 @@

 .. class:: infomark

-See the **W4M00001a_sacurine-subset-statistics** shared history in the **Shared Data/Published Histories** menu
+See the **W4M00001a_sacurine-subset-statistics** shared history in the **Shared Data/Published Histories** menu (https://galaxy.workflow4metabolomics.org/history/list_published)

 ---------------------------------------------------

@@ -300,6 +305,13 @@
 NEWS
 ----

+CHANGES IN VERSION 2.2.2
+========================
+
+INTERNAL MODIFICATIONS
+
+Minor internal modifications
+
 CHANGES IN VERSION 2.2.0
 ========================

@@ -322,11 +334,21 @@
 CHANGES IN VERSION 2.1.1
 ========================

+INTERNAL MODIFICATIONS
+
 Internal replacement of the as.hclust function which happened to produce error messages

  </help>

  <citations>
+   <citation type="bibtex">@Manual{,
+   title = {R: A Language and Environment for Statistical Computing},
+   author = {{R Core Team}},
+   organization = {R Foundation for Statistical Computing},
+   address = {Vienna, Austria},
+   year = {2016},
+   url = {https://www.R-project.org/},
+   }</citation>
    <citation type="bibtex">@Article{Thevenot2015,
    Title                    = {Analysis of the human adult urinary metabolome variations with age, body mass index and gender by implementing a comprehensive workflow for univariate and OPLS statistical analyses},
    Author                   = {Thevenot, Etienne A. and Roux, Aurelie and Xu, Ying and Ezan, Eric and Junot, Christophe},
@@ -339,7 +361,8 @@

    Doi                      = {10.1021/acs.jproteome.5b00354},
    Url                      = {http://pubs.acs.org/doi/full/10.1021/acs.jproteome.5b00354}
-   }</citation>
+   }</citation>
+   <citation type="doi">10.1093/bioinformatics/btu813</citation>
  </citations>

 </tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/runit/exa1/dataMatrix.tsv	Sat Aug 06 12:18:15 2016 -0400
@@ -0,0 +1,39 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/runit/exa1/sampleMetadata.tsv	Sat Aug 06 12:18:15 2016 -0400
@@ -0,0 +1,7 @@
+sampleMetadata	smeta1	smeta2
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+S4	182894	3142179
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/runit/exa1/variableMetadata.tsv	Sat Aug 06 12:18:15 2016 -0400
@@ -0,0 +1,39 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/runit/exa2/dataMatrix.tsv	Sat Aug 06 12:18:15 2016 -0400
@@ -0,0 +1,117 @@
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+V30	12.75	14.38	8.06	13.79	15.45	7.33	16.09	14.9	12.84	3.34	8.78	11.42	9.47	12.32	7.87	7.82	9.61	1.87	8.15	11.43	13.59	8.63	11.36	8.74	10.62	15.01	10.94	2.45
+V31	152.24	143.82	99.08	127.98	140.79	77.54	137.85	112.09	123.92	25.64	107.74	112.76	89.79	107.46	71.99	82.81	95.43	16.35	78.04	79.82	132.59	126.74	133.86	82.86	109.23	124.44	108.45	24.55
+V32	938.99	725.51	504.85	599.76	701.02	393.83	668.81	533.32	633.26	165.95	562.51	557.52	415.33	598.74	338.85	352.62	470.93	115.55	385.39	327.2	589.46	648.36	743.1	360.36	591.98	574.85	527.59	150.99
+V33	2988.64	2781	2451.36	2290.88	2497.75	1772.76	2434.42	2222.88	2429.96	365.39	2071.07	2358.74	1919.88	2141.82	1236.79	1292.48	1836.8	465.52	1668.16	1167.73	2095.17	3286.45	2900.66	1323.11	2346.08	2245.29	2129.08	735.12
+V34	1644.27	1378.93	970.38	1310.7	1277.11	838.94	1276.17	1038.97	1216.93	256.38	1070.93	1248.62	908.78	1301.31	795.45	690.35	1002.58	246.43	1039.85	738.11	1609.77	1444.48	1417.84	843.04	1359.28	1512.42	1245.6	326.87
+V35	34.28	28.91	29.9	31.11	38.88	17.48	39.24	23.23	30.38	7.43	19.24	32.68	22.86	29.83	13.98	13.69	22.05	7.96	21.14	30.86	25.14	34.58	29.31	14.04	32.27	29.3	27.08	6.72
+V36	34.69	25.94	25.12	31.06	34.84	18.45	27.52	20.78	27.3	6.01	16.27	32.31	21.57	24.55	15.88	13.34	20.65	7.03	16.83	25.77	27.02	38.17	26.83	15.03	36.42	32.65	27.34	8.39
+V37	53.33	33.39	38.28	56	18.46	33.81	39.24	25.03	37.19	12.79	19.02	29.64	29.32	36.33	21.06	26.69	27.01	6.3	24.3	49.3	23.38	133.19	49.05	20.55	57.23	32.46	48.68	36.85
+V38	55.46	32.06	38.14	73.93	17.66	27.63	40.29	24.64	38.73	18.25	17.06	30.63	28.54	39.35	15.18	27.94	26.45	9.01	22.52	62.43	17.96	222	42.3	16.94	65.81	35.65	60.7	67.84
+V39	1615.79	832.94	948.85	1163.14	780.73	932.8	827.92	651.39	969.19	300.59	651.84	688.09	704.96	886.23	511.33	657.76	683.37	120.74	872.17	1307.25	802.54	2032.41	1544.2	758.36	1356.28	1432.05	1263.16	435.85
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+V41	3995.34	1888.42	2393.66	1835.16	1684.97	1796.85	1192.55	1091.08	1984.75	909.69	1763.01	1285.69	1150.88	1126.86	1048.41	1193.59	1261.41	257.87	1437.84	1248.8	1395.5	2019.26	3393.17	1548.47	2189.84	2792.08	2003.12	761.04
+V42	6200.76	2703.73	3569.72	2967.38	2647.22	2701.52	1896.29	1731.65	3052.28	1397.8	2729.69	1770.64	1689.06	1813.5	1552.25	1977.75	1922.15	419.79	2262.29	1830.99	2226.75	2961.28	5042.17	2440.05	3329.37	4602.08	3086.87	1171.63
+V43	2766.76	1286.7	1535.67	1776.16	1043.65	1253.94	1165.85	989.89	1477.33	581.17	1081.96	962.62	1015.15	1217.68	877.56	1123.53	1046.42	120.87	1150.86	1405.41	1211.44	2590.33	1996.95	1466.31	2124.7	2561.89	1813.49	583.43
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+V45	361.49	289.55	263.82	424.39	250.66	201.69	240.88	240.95	284.18	73.44	248.27	273.46	216.48	217.64	165.11	174.49	215.91	41.61	227.97	327.36	274.12	615.76	379.63	251.66	345.47	506.13	366.01	133.46
+V46	2607.82	2000.16	1671.95	2357.94	1683.26	1571.32	1935.52	1840.49	1958.56	359.59	1995.27	1867.04	1691.03	1610.68	1121.25	1356.18	1606.91	323.82	1288.12	2384.86	1957.6	4620.77	2142.9	2097.88	2778.2	3638.56	2613.61	1057.86
+V47	4306.74	3278.54	2766.81	3676.12	2584.89	2707.8	3218.81	3013.78	3194.19	573.31	3189.42	3307.49	2902.72	2845.79	2162.9	2270.99	2779.88	470.14	2005.07	3846.66	3287.96	7678.68	3441.2	3648.6	4534.31	6234.27	4334.59	1807.15
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+V49	2846.27	2112.17	2074.85	2484.04	2030.38	2892.38	2323.34	2689.36	2431.6	349.58	1659.98	3637.59	1615.48	2586.62	2360.5	1413.49	2212.28	835.81	1208.92	2272.05	2841.18	5130.58	4188	2879.36	2853.44	5754.18	3390.96	1517.17
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+V53	352.51	261.05	248.74	309.45	289.73	416.53	266.85	428.71	321.69	70.28	236.94	537.25	193.5	326	319.28	189.21	300.36	130.33	152.84	203.76	442.22	511.73	516.04	437.43	331.36	880.17	434.44	225.04
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+V61	30316.42	25360.24	24223.65	23154.87	18133.87	22307.77	23062.85	23590.21	23768.74	3389.17	15197.09	21838.91	19822.74	25644.43	20471.11	22104.93	20846.53	3426.18	25946.74	31472.14	23168.38	33432.4	20220.09	23962.44	22402.54	56752.04	29669.59	11842.22
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+V63	5345.95	2464.9	3091.4	2805.39	3415.52	2539.93	3108.55	3202.34	3246.75	909.16	3585.55	2965.11	2611.3	2390.26	2831.05	3065.67	2908.16	412.12	2899.18	2910.75	2276.04	2502.17	3031.16	2991.49	2581.47	8752.35	3493.07	2141.79
+V64	5292.96	4008.72	4012.44	3886.04	3647.09	4488.47	3153.78	4115.83	4075.66	624.71	3329.53	3032.83	2312.02	3514.26	3087.36	3808.11	3180.69	512.3	5079.61	5010.13	3983.6	3431.06	4013.46	4214.52	3237.19	10957.47	4990.88	2498.27
+V65	25444.34	13558.49	16493.22	12642.32	18907.52	18009.06	14231.51	18620.1	17238.32	4086.37	19094.31	14715.79	12230.13	14978.12	11587.05	17803.28	15068.11	2966.33	20658.33	15965.36	15559.69	10040.91	15401.79	19709.15	13056.25	46168.25	19569.97	11265.33
+V66	13899.53	8944.63	10159.96	11074.5	10592.6	8214.08	10176.94	9842.82	10363.13	1692.08	10224.02	8347.23	9132.47	9222.4	7107.34	10746.74	9130.03	1305.62	12811.74	12563.23	8865.71	12920.36	8100.75	11165.92	10182.24	27260.68	12983.83	6047.39
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+V68	821.85	585.07	674.53	840.2	718.19	574.86	651.98	653.13	689.98	98.6	706.95	560.39	503.06	591.94	388.25	697.71	574.72	120.85	1200.77	898.01	617.64	580.33	598.67	661.06	518.03	1915.59	873.76	476.91
+V69	5665.21	3978.35	4089.75	6323.17	5026.21	3349.48	4344.41	4708.65	4685.65	964.71	5080.09	3035.72	3840.01	3568.7	2368.7	4560.78	3742.33	988.46	7508.69	6081.63	3875.94	4956.96	3618.8	4029.91	4201.27	11407.44	5710.08	2652.15
+V70	22886.12	12566.47	13528.14	14763.84	14470.03	10368.79	13211.34	16198.81	14749.19	3707.08	18464.21	12968.59	14976.46	11752.16	9218.14	15570.81	13825.06	3229.53	15895.44	17072.56	12786.98	16896.42	8923.53	16188.56	14585.89	34726.7	17134.51	7604.44
+V71	11423.67	7260.23	8970.27	7850.77	7000.97	7015.29	6913.61	7283.92	7964.84	1553.03	6763.98	8126.89	6577.43	7492.23	8528.18	8010.27	7583.16	782.55	8054.41	8188.51	6660.61	8871.33	7225.66	8376.3	7110.27	20520.68	9375.97	4562.98
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+V76	27989.88	27031.11	27818.36	26202.32	31496.87	31500.9	29211.25	33237.97	29311.08	2502.57	30111.45	28276.59	27232.92	31880.59	26296.06	28183.17	28663.46	2023.76	31918.73	34538.92	29086.99	27914.54	27498.1	39484.04	33320.98	43351.62	33389.24	5645.12
+V77	6033.59	5638.84	5757.39	5676.17	6856.34	6971.39	5687.13	8714.58	6416.93	1072.27	6824.08	6173.48	5757.01	6766.91	5862.96	6737.69	6353.69	483.48	7038.06	7289.71	6550.93	6474.58	6456.35	8406.92	5959.81	9192.51	7171.11	1101.49
+V78	7531.71	9766.33	7917.05	7066.02	12533.47	8597.12	10418.97	11146.66	9372.17	1920.47	9102.5	9784.31	7945.3	9496.2	8096.37	6447.88	8478.76	1239.67	6847.86	10800.66	8877.01	9466.25	7931.75	8909.79	9603.09	8932.52	8921.12	1169.52
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+V80	2868.85	5047.99	6140.96	3806.85	7216.89	5022.46	5256.06	7169.93	5316.25	1519.33	6397.22	6182.99	4471.19	4996.46	5044.24	3879.66	5161.96	972.74	4630.92	5302.12	5241.23	6062.4	4313.43	6004.09	4748.38	3915.5	5027.26	767.88
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+V87	4401.04	2934.89	3681.01	6152.67	2603.61	2332.57	5978.46	1842.04	3740.79	1638.59	2181.44	2571.46	2344.9	3162.33	1741.34	4144.96	2691.07	852.26	2984.39	3569.27	1848.09	3728.68	4482.7	3372.3	3045.7	5581.86	3576.62	1103.72
+V88	4420.06	1904.34	2745.79	4347.63	2944.8	1893.85	4677.78	1650.45	3073.09	1248.88	2285.76	1717.32	1691.2	1981.19	1265.7	3952.21	2148.9	946	1923.49	2689.61	1150.01	2382.48	3544.16	2397.09	2072.07	4295.69	2556.82	977.41
+V89	2025.01	1309.69	1534.02	1724.7	997.37	1112.13	1504.17	1062.01	1408.64	356.9	1060.36	1233.53	1053.84	1231.26	1037.81	1653.63	1211.74	234.19	1373.49	870.32	1061.5	971.79	1322.44	1953.7	1160.28	3600.17	1539.21	897.22
+V90	7867.46	4397.17	5500.73	6128.55	4480.76	4361.83	6223.22	3656.82	5327.07	1374.86	5401.66	4479.81	3795.24	4545.42	3955.3	6335.78	4752.2	958.89	5860.18	3637.58	3601.16	3030.4	5119.26	7934.1	3942.76	12438.43	5695.48	3154
+V91	15420.21	6374.06	8675.69	9187.97	9400.76	7612.14	11663.12	6741.51	9384.43	2960.52	10596.69	7079.71	6181.61	7096.04	6025.42	12463.24	8240.45	2652.77	9551.32	5992.62	5097.49	4421.58	9300.09	12959.02	6316.93	21213.88	9356.62	5563.45
+V92	6810.22	3429.58	4299.33	6127.84	4075.32	3344.66	5125.32	3028.74	4530.12	1375.11	4175.7	3140.88	3084.36	3031.18	2636.89	6669.27	3789.71	1500.91	3604.49	2605.3	2145.3	2993.63	4287.71	5353.81	3153.44	9144.78	4161.06	2250.33
+V93	0	354.36	350.3	379.16	287.08	292.88	444.09	303.69	301.44	132.41	207.65	392.54	274.35	267.83	257.3	382.95	297.1	74.08	238.86	145.6	268.33	189	452.98	351.16	243.21	1063.47	369.08	296.38
+V94	2856.36	2456.4	2540.2	3367.98	2179.99	1475.83	2299.58	2163.25	2417.45	552.18	1869.28	2155.91	1924.65	1709.17	1633.53	3130.02	2070.43	550.12	1852.97	935.78	2010.54	1819.26	2184.75	2451.9	1909.68	5332.67	2312.19	1296.17
+V95	24091.97	15443.29	15942.72	17970	12145.72	10870.02	14682.71	15930	15884.55	4008.56	13247.25	15454.42	13712.53	11623.37	9969.61	19752.29	13959.91	3398.12	9621.47	5782.84	11913.08	12015.65	12566.22	17116.78	13006.74	34928.36	14618.89	8804.83
+V96	60793.4	33382.53	33715.73	32764.43	24127.78	25432.17	29776.84	35260.09	34406.62	11394.51	28888.49	34024.7	31279.19	25136.41	21490.99	42646.24	30577.67	7389.9	16961.84	12299.55	24074.2	26183.98	25604.38	38438.79	28979.32	78126.8	31333.61	20446.85
+V97	17570.51	9240.64	9721.88	10284.94	6788.15	7088.16	9220.42	9323.72	9904.8	3334.56	7668.14	9513.44	7976.91	7000.53	6579.27	12453.69	8532	2170.52	4915.75	3693.18	6545.25	7271.72	7741.63	11272.66	8234.6	21625.05	8912.48	5612.76
+V98	0	149.15	135.65	144.37	124.09	117.76	110.31	127.3	113.58	47.7	128.4	127.61	126.27	136.02	105.67	160.41	130.73	17.73	118.88	107.55	121.9	120.41	133.07	129.53	119.35	0	106.34	43.64
+V99	314.71	233.89	257.32	290.71	136.54	131.91	212.71	151.12	216.11	70.67	144.84	161.98	199.1	177.26	109.83	276.15	178.19	56.71	136.06	92.56	133.57	240.27	196.46	181.17	175.41	0	144.44	73.62
+V100	1063.57	888.31	802.4	899.21	524.53	465.73	990.79	508.3	767.86	235.42	425.38	531.11	631.35	755.31	380.35	795.06	586.43	170.6	399.27	323.3	426.24	771.87	698.1	557.47	570.57	1826.56	696.67	480.86
+V101	2587.9	1673.54	1654.1	1984.41	1404.72	1474.72	2767.56	1490.35	1879.66	525.82	725.28	1591.13	1128.98	1962.5	1210.7	1571.45	1365.01	433.48	897.88	885.71	1024.88	1264.44	2472.8	1515.25	1349.88	4852	1782.85	1340.9
+V102	3565.72	1975.42	2013.22	2140.6	1668.46	2455.07	3602.33	2361.46	2472.79	726.93	769.9	2420.79	1099.54	1908.1	1814.65	1765.41	1629.73	596.03	990.98	1185.95	1435.53	1123.37	4179.54	2564.22	1660.72	6490.51	2453.85	1944.54
+V103	0	48.29	0	0	0	0	70.19	0	14.81	28.04	0	0	0	0	0	0	0	0	0	123.9	0	0	0	0	0	5.93	16.23	43.56
+V104	0	123.49	65.51	80.81	98.52	68.99	195.36	83.25	89.49	55.5	97.05	128.29	99.81	113.05	120.62	0	93.14	47.16	119.68	367.75	78.17	59.42	81.7	79.25	121.63	0	113.45	109.53
+V105	0	85.23	0	0	0	0	168.05	0	31.66	62.66	0	0	0	0	0	0	0	0	0	233.87	0	0	0	0	0	0	29.23	82.69
+V106	0	183.94	76.89	113	125.6	0	370.73	0	108.77	125.97	150.38	121.92	135.84	186.45	103.87	0	116.41	63.52	154.21	496.94	107.83	94.48	106.85	0	141.87	0	137.77	156.29
+V107	423.7	0	164.21	507.86	578.77	522.85	0	346.55	317.99	234.19	0	299.3	343.68	661.93	499.17	759.59	427.28	274.44	363.88	432.47	486.04	383.04	381.67	0	497.37	0	318.06	202.18
+V108	4.6	2.76	2.42	3.59	3.85	3.27	5.32	4.47	3.79	0.98	4.96	3.56	3.84	4.62	5.72	5.58	4.72	0.89	3.99	4.66	4.99	4.79	4.25	2.82	3.33	4.09	4.11	0.74
+V109	1.46	1.14	1.27	1.13	1.52	1.57	1.35	1.14	1.32	0.18	1.18	1.28	1.13	1.2	1.14	1.63	1.26	0.19	1.32	0.9	1.14	1.6	1.07	1.42	1.87	0.91	1.28	0.34
+V110	0.52	0.55	0	0.49	0	0	0	0.51	0.26	0.28	0.35	0.38	0.56	0.44	0	0.55	0.38	0.2	0.32	0.37	0.35	0.52	0	0.44	0.44	0.28	0.34	0.16
+V111	0.4	0	0	0.43	0.32	0	0	0.39	0.19	0.21	0.3	0.37	0	0.4	0	0.42	0.25	0.2	0	0.36	0.25	0.47	0	0.39	0.38	0	0.23	0.2
+V112	0.76	0.49	0.43	0.64	0.49	0.48	0.23	0.71	0.53	0.17	0.47	0.52	0.59	0.62	0.38	0.65	0.54	0.1	0.32	0.49	0.38	0.55	0.49	0.6	0.64	0.47	0.49	0.11
+V113	0.61	0.58	0.53	0.53	0.45	0.31	0.15	0.51	0.46	0.15	0.36	0.51	0.44	0.45	0.48	0.66	0.48	0.1	0.33	0.53	0.37	0.61	0.36	0.51	0.67	0.33	0.46	0.13
+V114	0	0	0	0	0.09	0	0	0.12	0.03	0.05	0	0.1	0	0	0	0	0.02	0.04	0	0	0.1	0	0.12	0.11	0	0	0.04	0.06
+V115	0	0	0	0	0	0	0	0.13	0.02	0.04	0	0.11	0	0	0	0	0.02	0.05	0	0	0	0	0.15	0.12	0	0	0.03	0.06
+V116	1.76	1.89	1.43	1.19	1.34	1.64	0	2.33	1.44	0.68	1.16	2.16	0	1.74	2.23	1.12	1.4	0.83	0	1.47	1.37	1.34	2.27	1.83	1.51	1.43	1.4	0.65
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/runit/exa2/sampleMetadata.tsv	Sat Aug 06 12:18:15 2016 -0400
@@ -0,0 +1,29 @@
+sampleMetadata	meta1
+S1	A
+S2	A
+S3	A
+S4	A
+S5	A
+S6	A
+S7	A
+S8	A
+S9	B
+S10	B
+S11	B
+S12	B
+S13	B
+S14	B
+S15	B
+S16	C
+S17	C
+S18	C
+S19	C
+S20	C
+S21	C
+S22	C
+S23	C
+S24	C
+S25	BC
+S26	AB
+S27	BC
+S28	AC
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/runit/exa2/variableMetadata.tsv	Sat Aug 06 12:18:15 2016 -0400
@@ -0,0 +1,117 @@
+variableMetadata	meta2
+V1	ER
+V2	GGG
+V3	GGG
+V4	GGG
+V5	GGG
+V6	CE
+V7	CE
+V8	CE
+V9	TG
+V10	TG
+V11	TG
+V12	TG
+V13	TG
+V14	AM
+V15	AM
+V16	AM
+V17	AM
+V18	AM
+V19	AM
+V20	AM
+V21	AM
+V22	AM
+V23	AM
+V24	AM
+V25	AM
+V26	AM
+V27	AM
+V28	AM
+V29	AM
+V30	AM
+V31	AM
+V32	ER
+V33	ER
+V34	ER
+V35	ER
+V36	ER
+V37	CER
+V38	CER
+V39	CER
+V40	CER
+V41	CER
+V42	CER
+V43	CER
+V44	CER
+V45	CER
+V46	CER
+V47	PP
+V48	PP
+V49	PP
+V50	PP
+V51	PP
+V52	PP
+V53	PP
+V54	PP
+V55	PP
+V56	PP
+V57	PP
+V58	PP
+V59	PP
+V60	PP
+V61	PP
+V62	PP
+V63	PP
+V64	CC
+V65	CC
+V66	CC
+V67	CC
+V68	CC
+V69	CC
+V70	CC
+V71	CC
+V72	CC
+V73	CC
+V74	CC
+V75	CC
+V76	CC
+V77	CC
+V78	CC
+V79	CC
+V80	CC
+V81	CC
+V82	CC
+V83	CC
+V84	CC
+V85	SM
+V86	SM
+V87	SM
+V88	SM
+V89	SM
+V90	SM
+V91	SM
+V92	SM
+V93	SM
+V94	SM
+V95	SM
+V96	PI
+V97	PI
+V98	PI
+V99	PI
+V100	PI
+V101	PI
+V102	PI
+V103	PI
+V104	PI
+V105	PI
+V106	PI
+V107	NG
+V108	NG
+V109	NG
+V110	SO
+V111	SO
+V112	SO
+V113	SO
+V114	SO
+V115	SO
+V116	SO
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/runit/heatmap_runtests.R	Sat Aug 06 12:18:15 2016 -0400
@@ -0,0 +1,105 @@
+#!/usr/bin/env Rscript
+
+## Package
+##--------
+
+library(RUnit)
+
+## Constants
+##----------
+
+testOutDirC <- "output"
+argVc <- commandArgs(trailingOnly = FALSE)
+scriptPathC <- sub("--file=", "", argVc[grep("--file=", argVc)])
+
+
+## Functions
+##-----------
+
+## Reading tables (matrix or data frame)
+readTableF <- function(fileC, typeC = c("matrix", "dataframe")[1]) {
+
+    	file.exists(fileC) || stop(paste0("No output file \"", fileC ,"\"."))
+
+        switch(typeC,
+               matrix = return(t(as.matrix(read.table(file = fileC,
+                   header = TRUE,
+                   row.names = 1,
+                   sep = "\t",
+                   stringsAsFactors = FALSE)))),
+               dataframe = return(read.table(file = fileC,
+                   header = TRUE,
+                   row.names = 1,
+                   sep = "\t",
+                   stringsAsFactors = FALSE)))
+
+}
+
+## Call wrapper
+wrapperCallF <- function(paramLs) {
+
+	## Set program path
+    	wrapperPathC <- file.path(dirname(scriptPathC), "..", "heatmap_wrapper.R")
+
+	## Set arguments
+	argLs <- NULL
+	for (parC in names(paramLs))
+		argLs <- c(argLs, parC, paramLs[[parC]])
+
+	## Call
+	wrapperCallC <- paste(c(wrapperPathC, argLs), collapse = " ")
+
+        if(.Platform$OS.type == "windows")
+            wrapperCallC <- paste("Rscript", wrapperCallC)
+
+	wrapperCodeN <- system(wrapperCallC)
+
+	if (wrapperCodeN != 0)
+		stop("Error when running heatmap_wrapper.R.")
+
+	## Get output
+	outLs <- list()
+	if ("dataMatrix_out" %in% names(paramLs))
+            outLs[["datMN"]] <- readTableF(paramLs[["dataMatrix_out"]], "matrix")
+	if ("sampleMetadata_out" %in% names(paramLs))
+            outLs[["samDF"]] <- readTableF(paramLs[["sampleMetadata_out"]], "dataframe")
+	if ("variableMetadata_out" %in% names(paramLs))
+            outLs[["varDF"]] <- readTableF(paramLs[["variableMetadata_out"]], "dataframe")
+        if("information" %in% names(paramLs))
+            outLs[["infVc"]] <- readLines(paramLs[["information"]])
+
+	return(outLs)
+}
+
+## Setting default parameters
+defaultArgF <- function(testInDirC) {
+
+    defaultArgLs <- list()
+    if(file.exists(file.path(dirname(scriptPathC), testInDirC, "dataMatrix.tsv")))
+        defaultArgLs[["dataMatrix_in"]] <- file.path(dirname(scriptPathC), testInDirC, "dataMatrix.tsv")
+    if(file.exists(file.path(dirname(scriptPathC), testInDirC, "sampleMetadata.tsv")))
+        defaultArgLs[["sampleMetadata_in"]] <- file.path(dirname(scriptPathC), testInDirC, "sampleMetadata.tsv")
+    if(file.exists(file.path(dirname(scriptPathC), testInDirC, "variableMetadata.tsv")))
+        defaultArgLs[["variableMetadata_in"]] <- file.path(dirname(scriptPathC), testInDirC, "variableMetadata.tsv")
+
+    defaultArgLs[["dataMatrix_out"]] <- file.path(dirname(scriptPathC), testOutDirC, "dataMatrix.tsv")
+    defaultArgLs[["sampleMetadata_out"]] <- file.path(dirname(scriptPathC), testOutDirC, "sampleMetadata.tsv")
+    defaultArgLs[["variableMetadata_out"]] <- file.path(dirname(scriptPathC), testOutDirC, "variableMetadata.tsv")
+    defaultArgLs[["figure"]] <- file.path(dirname(scriptPathC), testOutDirC, "figure.pdf")
+    defaultArgLs[["information"]] <- file.path(dirname(scriptPathC), testOutDirC, "information.txt")
+
+    defaultArgLs
+
+}
+
+## Main
+##-----
+
+## Create output folder
+file.exists(testOutDirC) || dir.create(testOutDirC)
+
+## Run tests
+test.suite <- defineTestSuite('tests', dirname(scriptPathC), testFileRegexp = paste0('^.*_tests\\.R$'), testFuncRegexp = '^.*$')
+isValidTestSuite(test.suite)
+test.results <- runTestSuite(test.suite)
+print(test.results)
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/runit/heatmap_tests.R	Sat Aug 06 12:18:15 2016 -0400
@@ -0,0 +1,57 @@
+test_input_cut4 <- function() {
+
+    testDirC <- "input"
+    argLs <- list(disC = "1-cor",
+                  cutSamN = "4",
+                  cutVarN = "3",
+                  corMetC = "spearman",
+                  aggMetC = "ward",
+                  colC = "blueOrangeRed",
+                  scaL = "TRUE",
+                  cexN = "0.8")
+
+    argLs <- c(defaultArgF(testDirC), argLs)
+    outLs <- wrapperCallF(argLs)
+
+    checkEqualsNumeric(outLs[['samDF']][13, 'heat_clust'], 4)
+
+}
+
+test_exa1_cut3 <- function() {
+
+    testDirC <- "exa1"
+    argLs <- list(disC = "1-cor",
+                  cutSamN = "3",
+                  cutVarN = "4",
+                  corMetC = "spearman",
+                  aggMetC = "ward",
+                  colC = "blueOrangeRed",
+                  scaL = "TRUE",
+                  cexN = "1")
+
+    argLs <- c(defaultArgF(testDirC), argLs)
+    outLs <- wrapperCallF(argLs)
+
+    checkEqualsNumeric(outLs[['varDF']]['V24', 'heat_clust'], 4)
+
+}
+
+test_exa2_cut4 <- function() {
+
+    testDirC <- "exa2"
+    argLs <- list(disC = "1-cor",
+                  cutSamN = "1",
+                  cutVarN = "1",
+                  corMetC = "spearman",
+                  aggMetC = "ward",
+                  colC = "blueOrangeRed",
+                  scaL = "TRUE",
+                  cexN = "1")
+
+    argLs <- c(defaultArgF(testDirC), argLs)
+    outLs <- wrapperCallF(argLs)
+
+    checkEquals(outLs[['varDF']]['V31', 'meta2'], 'AM')
+
+}
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/runit/input/dataMatrix.tsv	Sat Aug 06 12:18:15 2016 -0400
@@ -0,0 +1,16 @@
+dataMatrix	HU_017	HU_028	HU_034	HU_051	HU_060	HU_078	HU_091	HU_093	HU_099	HU_110	HU_130	HU_134	HU_138	HU_149	HU_152	HU_175	HU_178	HU_185	HU_204	HU_208
+HMDB03193	76043	412165	44943	27242	436566	173175	242549	57066	559869	3732	339188	471368	262271	127285	451270	212500	79673	NA	891129	43907
+HMDB01101	30689	6877586	52217	3158	10789748	229568	4763576	3878773	976436	831937	608298	1605075	72021	442510	1107705	1464339	31250	2724553	72900	32742
+HMDB10348	47259	544877	60885	34582	529874	168264	176500	76457	610110	16262	279156	524468	451573	591487	433529	161069	214392	13781	1580343	39315
+HMDB59717	357351	1030464	301983	67604	306862	1028110	1530493	270027	1378535	289677	808334	1132813	871209	895435	715190	1563158	784738	146195	994336	239030
+HMDB00822	483755	579287	1132413	157113	1577570	1469735	1085454	477909	814755	245417	610681	763706	2406336	827531	992508	569605	355321	150259	1334200	271010
+HMDB13189	2644620	727587	1661412	619181	136278	2755434	593863	837865	3526136	2003278	1608814	3446611	1941527	113937	3132404	2893445	2092753	1034666	1517319	841661
+HMDB00299	250551	1046138	456162	159386	1013302	808657	614370	250403	768004	242085	504108	1014041	1362408	1057660	1110050	566050	411886	142233	1992420	284775
+HMDB00191	560002	771533	575790	392284	888498	785428	645785	591569	960658	910201	639437	1092885	1409045	2292023	1246459	1945577	710519	773384	1061418	622898
+HMDB00518	34236	58249	85944	NA	342102	129886	175800	13154	230242	NA	440223	315368	10657	419508	48673	28361	514579	23108	867108	73831
+HMDB00715	1252089	2547452	905408	371059	4983588	5140022	2658555	814523	2558923	859466	4184204	3865723	3236644	2615560	3820724	3577833	2295288	625924	7517724	1341900
+HMDB01032	2569205	26023086	1604999	430453	8103558	26222916	257139	675754	59906109	263055	31151730	18648127	14989438	1554658	20249262	5588731	871010	15920	9120781	44276
+HMDB00208	747080	13420742	595872	1172376	7172632	3143654	4059767	1433702	5593888	5402629	2477288	3346077	4230072	7621236	8960828	10335722	7037373	1574738	3359238	2540044
+HMDB04824	374028	1144386	539206	178517	1046190	959381	605191	310260	1253319	477259	477995	825691	1157093	1089284	1411802	1020206	782673	346761	1824553	387811
+HMDB00512	53304	319783	280560	85009	1333877	556003	590779	209285	342532	198512	569970	525240	246282	1140422	542345	1171008	827723	222953	438839	85554
+HMDB00251	368600	616555	94936	622468	180988	293988	352855	767894	268331	167246	310918	1248919	577184	10985	335711	403815	80614	63393	454489	616061
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/runit/input/sampleMetadata.tsv	Sat Aug 06 12:18:15 2016 -0400
@@ -0,0 +1,21 @@
+sampleMetadata	injectionOrder	mode	age	bmi	gender
+HU_017	2	pos	41	23.03	M
+HU_028	7	pos	41	23.92	F
+HU_034	9	pos	52	23.37	M
+HU_051	20	pos	24	23.23	F
+HU_060	24	pos	55	28.72	F
+HU_078	34	pos	46	25.18	M
+HU_091	42	pos	61	26.12	M
+HU_093	43	pos	53	21.71	M
+HU_099	46	pos	23	21.3	M
+HU_110	53	pos	50	20.9	F
+HU_130	63	pos	33	26.06	M
+HU_134	67	pos	48	22.89	M
+HU_138	68	pos	42	21.88	M
+HU_149	72	pos	35	19.49	F
+HU_152	75	pos	26	17.58	F
+HU_175	87	pos	35	21.26	F
+HU_178	88	pos	60	32.87	F
+HU_185	95	pos	42	21.09	F
+HU_204	104	pos	31	29.06	M
+HU_208	106	pos	27	18.61	F
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/runit/input/variableMetadata.tsv	Sat Aug 06 12:18:15 2016 -0400
@@ -0,0 +1,16 @@
+variableMetadata	name
+HMDB03193	Testosterone_glucuronide
+HMDB01101	p-Anisic_acid
+HMDB10348	Dehydroepiandrosterone_3-glucuronide
+HMDB59717	Glu-Val
+HMDB00822	p-Hydroxymandelic_acid
+HMDB13189	3-Indole_carboxylic_acid_glucuronide
+HMDB00299	Xanthosine
+HMDB00191	L-Aspartic_acid
+HMDB00518	Chenodeoxycholic_acid
+HMDB00715	Kynurenic_acid
+HMDB01032	Dehydroepiandrosterone_sulfate
+HMDB00208	Oxoglutaric_acid
+HMDB04824	N2,N2-Dimethylguanosine
+HMDB00512	N-Acetyl-L-phenylalanine
+HMDB00251	Taurine
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/runit/output/dataMatrix.tsv	Sat Aug 06 12:18:15 2016 -0400
@@ -0,0 +1,16 @@
+dataMatrix	HU_051	HU_208	HU_178	HU_130	HU_175	HU_099	HU_152	HU_204	HU_017	HU_138	HU_034	HU_078	HU_060	HU_149	HU_028	HU_093	HU_134	HU_091	HU_110	HU_185
+HMDB13189	619181	841661	2092753	1608814	2893445	3526136	3132404	1517319	2644620	1941527	1661412	2755434	136278	113937	727587	837865	3446611	593863	2003278	1034666
+HMDB00251	622468	616061	80614	310918	403815	268331	335711	454489	368600	577184	94936	293988	180988	10985	616555	767894	1248919	352855	167246	63393
+HMDB01101	3158	32742	31250	608298	1464339	976436	1107705	72900	30689	72021	52217	229568	10789748	442510	6877586	3878773	1605075	4763576	831937	2724553
+HMDB00191	392284	622898	710519	639437	1945577	960658	1246459	1061418	560002	1409045	575790	785428	888498	2292023	771533	591569	1092885	645785	910201	773384
+HMDB00208	1172376	2540044	7037373	2477288	10335722	5593888	8960828	3359238	747080	4230072	595872	3143654	7172632	7621236	13420742	1433702	3346077	4059767	5402629	1574738
+HMDB59717	67604	239030	784738	808334	1563158	1378535	715190	994336	357351	871209	301983	1028110	306862	895435	1030464	270027	1132813	1530493	289677	146195
+HMDB00512	85009	85554	827723	569970	1171008	342532	542345	438839	53304	246282	280560	556003	1333877	1140422	319783	209285	525240	590779	198512	222953
+HMDB00518	NA	73831	514579	440223	28361	230242	48673	867108	34236	10657	85944	129886	342102	419508	58249	13154	315368	175800	NA	23108
+HMDB00822	157113	271010	355321	610681	569605	814755	992508	1334200	483755	2406336	1132413	1469735	1577570	827531	579287	477909	763706	1085454	245417	150259
+HMDB00715	371059	1341900	2295288	4184204	3577833	2558923	3820724	7517724	1252089	3236644	905408	5140022	4983588	2615560	2547452	814523	3865723	2658555	859466	625924
+HMDB01032	430453	44276	871010	31151730	5588731	59906109	20249262	9120781	2569205	14989438	1604999	26222916	8103558	1554658	26023086	675754	18648127	257139	263055	15920
+HMDB00299	159386	284775	411886	504108	566050	768004	1110050	1992420	250551	1362408	456162	808657	1013302	1057660	1046138	250403	1014041	614370	242085	142233
+HMDB04824	178517	387811	782673	477995	1020206	1253319	1411802	1824553	374028	1157093	539206	959381	1046190	1089284	1144386	310260	825691	605191	477259	346761
+HMDB03193	27242	43907	79673	339188	212500	559869	451270	891129	76043	262271	44943	173175	436566	127285	412165	57066	471368	242549	3732	NA
+HMDB10348	34582	39315	214392	279156	161069	610110	433529	1580343	47259	451573	60885	168264	529874	591487	544877	76457	524468	176500	16262	13781
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/runit/output/essai.tsv	Sat Aug 06 12:18:15 2016 -0400
@@ -0,0 +1,21 @@
+sampleMetadata	injectionOrder	mode	age	bmi	gender	heat_clust
+HU_017	2	pos	41	23.03	M	1
+HU_034	9	pos	52	23.37	M	1
+HU_204	104	pos	31	29.06	M	2
+HU_134	67	pos	48	22.89	M	2
+HU_099	46	pos	23	21.3	M	2
+HU_078	34	pos	46	25.18	M	2
+HU_130	63	pos	33	26.06	M	2
+HU_028	7	pos	41	23.92	F	2
+HU_138	68	pos	42	21.88	M	2
+HU_152	75	pos	26	17.58	F	2
+HU_051	20	pos	24	23.23	F	3
+HU_208	106	pos	27	18.61	F	3
+HU_110	53	pos	50	20.9	F	3
+HU_178	88	pos	60	32.87	F	3
+HU_149	72	pos	35	19.49	F	3
+HU_175	87	pos	35	21.26	F	3
+HU_060	24	pos	55	28.72	F	4
+HU_091	42	pos	61	26.12	M	4
+HU_093	43	pos	53	21.71	M	4
+HU_185	95	pos	42	21.09	F	4
Binary file runit/output/figure.pdf has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/runit/output/information.txt	Sat Aug 06 12:18:15 2016 -0400
@@ -0,0 +1,24 @@
+
+Start of the 'Heatmap' module: Tue 02 Aug 2016 11:48:22 AM
+
+Arguments used:
+
+                     value
+dataMatrix_in        "tests/input/dataMatrix.tsv"
+sampleMetadata_in    "tests/input/sampleMetadata.tsv"
+variableMetadata_in  "tests/input/variableMetadata.tsv"
+dataMatrix_out       "tests/output/dataMatrix.tsv"
+sampleMetadata_out   "tests/output/sampleMetadata.tsv"
+variableMetadata_out "tests/output/variableMetadata.tsv"
+figure               "tests/output/figure.pdf"
+information          "tests/output/information.txt"
+disC                 "1-cor"
+cutSamN              "4"
+cutVarN              "3"
+corMetC              "spearman"
+aggMetC              "ward"
+colC                 "blueOrangeRed"
+scaL                 "TRUE"
+cexN                 "0.8"
+
+End of the 'Heatmap' Galaxy module call: Tue 02 Aug 2016 11:48:22 AM
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/runit/output/sampleMetadata.tsv	Sat Aug 06 12:18:15 2016 -0400
@@ -0,0 +1,21 @@
+sampleMetadata	injectionOrder	mode	age	bmi	gender	heat_clust
+HU_051	20	pos	24	23.23	F	3
+HU_208	106	pos	27	18.61	F	3
+HU_178	88	pos	60	32.87	F	1
+HU_130	63	pos	33	26.06	M	1
+HU_175	87	pos	35	21.26	F	1
+HU_099	46	pos	23	21.3	M	1
+HU_152	75	pos	26	17.58	F	1
+HU_204	104	pos	31	29.06	M	1
+HU_017	2	pos	41	23.03	M	1
+HU_138	68	pos	42	21.88	M	1
+HU_034	9	pos	52	23.37	M	1
+HU_078	34	pos	46	25.18	M	1
+HU_060	24	pos	55	28.72	F	4
+HU_149	72	pos	35	19.49	F	4
+HU_028	7	pos	41	23.92	F	2
+HU_093	43	pos	53	21.71	M	2
+HU_134	67	pos	48	22.89	M	2
+HU_091	42	pos	61	26.12	M	2
+HU_110	53	pos	50	20.9	F	2
+HU_185	95	pos	42	21.09	F	2
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/runit/output/variableMetadata.tsv	Sat Aug 06 12:18:15 2016 -0400
@@ -0,0 +1,16 @@
+variableMetadata	name	heat_clust
+HMDB13189	3-Indole_carboxylic_acid_glucuronide	3
+HMDB00251	Taurine	3
+HMDB01101	p-Anisic_acid	2
+HMDB00191	L-Aspartic_acid	2
+HMDB00208	Oxoglutaric_acid	2
+HMDB59717	Glu-Val	2
+HMDB00512	N-Acetyl-L-phenylalanine	2
+HMDB00518	Chenodeoxycholic_acid	1
+HMDB00822	p-Hydroxymandelic_acid	1
+HMDB00715	Kynurenic_acid	1
+HMDB01032	Dehydroepiandrosterone_sulfate	1
+HMDB00299	Xanthosine	1
+HMDB04824	N2,N2-Dimethylguanosine	1
+HMDB03193	Testosterone_glucuronide	1
+HMDB10348	Dehydroepiandrosterone_3-glucuronide	1
--- a/tests/exa1/dataMatrix.tsv	Tue Aug 02 06:26:41 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,39 +0,0 @@
-dataMatrix	S1	S2	S3	S4	S5	S6
-V1	196502	237810	198284	182894	105331	132150
-V2	2544571	2614302	2451909	3142179	3768416	3713752
-V3	1230784	1161975	1143745	1150915	1344578	1220503
-V4	1630089	1818363	1563465	2387030	3502620	2954208
-V5	2184963	2374515	1974647	2313226	1782744	1860757
-V6	5262172	6365930	5010369	9109487	6410977	6378638
-V7	2232587	2745906	2200995	3832216	2708070	2869295
-V8	483320	660332	433486	1062013	677822	748514
-V9	112905	136174	123604	162138	240686	195271
-V10	179154	195001	180519	98623	132470	123032
-V11	175220	169515	158401	111215	103539	159727
-V12	46503	55313	76310	46932	92318	43629
-V13	113796	91557	95960	92685	140973	112898
-V14	540798	596737	511783	876548	1626199	1385367
-V15	140806	135469	145016	229518	434119	398941
-V16	1334798	1318651	1308783	2345055	4068874	3565724
-V17	1083792	1145232	916864	838363	1678307	1304234
-V18	91671	101007	79999	85402	146939	126314
-V19	274181	282331	292645	394175	330817	293481
-V20	879658	809068	903330	1273966	959314	938277
-V21	608434	662366	727426	920178	1106194	1201520
-V22	1600960	1545158	1608816	1880288	2246189	2069613
-V23	2171614	2239769	2106004	2565354	4913676	4072322
-V24	4045143	3862213	4053630	7352540	5574415	6185035
-V25	202805	182042	165499	57267	86611	89320
-V26	586997	667911	522193	748212	595063	659353
-V27	229790	256287	253497	1189248	1025521	746948
-V28	1644853	1759382	1760494	3379214	4572430	4386799
-V29	8491372	9275641	8655578	12105700	13265172	13484917
-V30	724039	730730	640992	1475658	1191085	1213210
-V31	86524840	89500400	88593487	183705591	150949959	169189091
-V32	26916143	30167854	28256416	39049936	45546213	47237473
-V33	2683733	2654918	2386486	4786536	3622659	3879731
-V34	3919797	4529379	3595989	7965534	5963667	6339219
-V35	84384696	90691983	83322980	51888441	86013709	79735533
-V36	95751916	101056674	92760886	129551865	109580811	118980909
-V37	374328	416298	355931	255675	371223	338701
-V38	2219529	2333885	2206832	903780	981633	1136522
--- a/tests/exa1/sampleMetadata.tsv	Tue Aug 02 06:26:41 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,7 +0,0 @@
-sampleMetadata	smeta1	smeta2
-S1	196502	2544571
-S2	237810	2614302
-S3	198284	2451909
-S4	182894	3142179
-S5	105331	3768416
-S6	132150	3713752
--- a/tests/exa1/variableMetadata.tsv	Tue Aug 02 06:26:41 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,39 +0,0 @@
-variableMetadata	vmeta1	vmeta2	vmeta3	vmeta4	vmeta5	vmeta6
-V1	196502	237810	198284	182894	105331	132150
-V2	2544571	2614302	2451909	3142179	3768416	3713752
-V3	1230784	1161975	1143745	1150915	1344578	1220503
-V4	1630089	1818363	1563465	2387030	3502620	2954208
-V5	2184963	2374515	1974647	2313226	1782744	1860757
-V6	5262172	6365930	5010369	9109487	6410977	6378638
-V7	2232587	2745906	2200995	3832216	2708070	2869295
-V8	483320	660332	433486	1062013	677822	748514
-V9	112905	136174	123604	162138	240686	195271
-V10	179154	195001	180519	98623	132470	123032
-V11	175220	169515	158401	111215	103539	159727
-V12	46503	55313	76310	46932	92318	43629
-V13	113796	91557	95960	92685	140973	112898
-V14	540798	596737	511783	876548	1626199	1385367
-V15	140806	135469	145016	229518	434119	398941
-V16	1334798	1318651	1308783	2345055	4068874	3565724
-V17	1083792	1145232	916864	838363	1678307	1304234
-V18	91671	101007	79999	85402	146939	126314
-V19	274181	282331	292645	394175	330817	293481
-V20	879658	809068	903330	1273966	959314	938277
-V21	608434	662366	727426	920178	1106194	1201520
-V22	1600960	1545158	1608816	1880288	2246189	2069613
-V23	2171614	2239769	2106004	2565354	4913676	4072322
-V24	4045143	3862213	4053630	7352540	5574415	6185035
-V25	202805	182042	165499	57267	86611	89320
-V26	586997	667911	522193	748212	595063	659353
-V27	229790	256287	253497	1189248	1025521	746948
-V28	1644853	1759382	1760494	3379214	4572430	4386799
-V29	8491372	9275641	8655578	12105700	13265172	13484917
-V30	724039	730730	640992	1475658	1191085	1213210
-V31	86524840	89500400	88593487	183705591	150949959	169189091
-V32	26916143	30167854	28256416	39049936	45546213	47237473
-V33	2683733	2654918	2386486	4786536	3622659	3879731
-V34	3919797	4529379	3595989	7965534	5963667	6339219
-V35	84384696	90691983	83322980	51888441	86013709	79735533
-V36	95751916	101056674	92760886	129551865	109580811	118980909
-V37	374328	416298	355931	255675	371223	338701
-V38	2219529	2333885	2206832	903780	981633	1136522
--- a/tests/exa2/dataMatrix.tsv	Tue Aug 02 06:26:41 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,117 +0,0 @@
-dataMatrix	S1	S2	S3	S4	S5	S6	S7	S8	S9	S10	S11	S12	S13	S14	S15	S16	S17	S18	S19	S20	S21	S22	S23	S24	S25	S26	S27	S28
-V1	1484.78	1106.3	1217.84	1441.38	1213.63	1302.49	1412.79	1322.28	1258.89	1365.49	1146.78	1243	1242.47	1250.61	1307.52	1423.59	1290.51	1126.64	1421.23	1235.75	1084.56	1252.87	1254.74	1584.64	1474.43	1283.85	1347.74	1557.35
-V2	0	0	0	13.14	0	0	0	16.36	0	0	11.8	0	0	0	0	12.34	12.45	0	0	6.87	6.41	0	15.53	12.87	0	14.58	0	0
-V3	0	5.93	7.82	16.41	7.58	9.54	8.25	20.52	5.89	6.27	20.86	5.2	8.97	10.93	6.51	21.06	25.05	0	0	11.79	16.97	7.23	19.58	20.56	11.07	20.87	0	6.18
-V4	10.86	12.56	7.93	14.32	10.64	11.38	8.24	15.8	11.75	11.29	12	6.34	8.05	16.12	13.33	18.81	24.44	8.26	6.99	9.76	10.29	9.11	19.32	26.55	15.58	17.38	3.31	7.2
-V5	9.49	5.72	6.96	5.48	6.38	9.57	6.31	8.67	8.21	9.1	9.23	9.68	7.1	6.89	4.39	7.98	11.58	7.71	10.99	8.67	13.18	7.19	10.96	5.86	7.98	10.39	4.69	11.78
-V6	43.5	19.95	34.96	31.98	31.27	49.9	38.17	26.44	27.19	40.64	40.9	47	26.26	30.31	20.64	49.54	49.06	26.73	64.56	43.29	80.61	38.08	42.01	37.22	26.37	25.97	25.2	41.05
-V7	333.79	311.77	321.24	391.51	297.03	263.85	246.39	221.76	447.49	418.79	300.37	414.43	262.68	244.09	213.24	423.97	523.16	344.76	413.98	402.45	251.38	225.47	300.48	230.58	301.51	246.9	361.04	375.51
-V8	49.48	20.81	27.33	17.44	15.39	14.84	17.67	13.41	29.27	63.13	34.04	23.41	25.16	16.2	11.68	42.53	31.46	12.83	38.02	40.28	25.77	12.44	41.05	15.25	23.21	27.11	25.98	22.33
-V9	2.56	1.18	1.07	1.39	2.59	2.53	1.98	3.84	1.61	1.72	1.76	1.73	0.63	2.13	2.02	2.44	0	1.24	1.22	1.87	7.83	4.15	5.88	4.77	5.77	7.81	0	1.67
-V10	6.37	4.55	2.63	5.09	6.29	6.32	6.31	6.61	4.35	5.98	4.79	6.3	1.24	6.98	5.09	6.64	7.21	3.63	4.14	5.47	19.45	8.4	9.41	10.83	10.78	11.98	1.29	3.86
-V11	11.9	21.21	10.67	19.08	17.84	10.64	13.61	10.41	17.75	17.87	13.24	15.27	7.83	18.66	13.5	18.67	26.37	14.46	13.18	18.29	26.21	10.65	16.46	21.52	19.57	17.89	8.81	10.4
-V12	4.38	8.56	4.95	8.83	5.87	3.53	5.15	0.45	7.67	5.85	5.32	4.88	4.55	5.87	5.12	6.16	10.97	6.67	4.69	6.11	7.33	3.34	5.44	8.94	5.83	5.07	5.77	3.8
-V13	0.78	1.17	0.61	1.21	0.89	0	0.56	0.45	1.04	1.03	0	0.71	0.62	0.78	0	1.25	0	0.63	1.1	1.16	1.13	0	0.87	1.05	1.06	0.63	0.36	0.82
-V14	1511.11	1158.59	1529.32	1471.39	1654.17	2320.94	2630.11	2148.49	1248.21	1590.03	1120.83	1388.4	1523.12	2293.02	0	1566.36	1543.42	842.31	1421.66	1850.9	2870.84	2338.83	1979.28	3581.78	1757.49	2983.66	2967.62	1392.97
-V15	638.35	560.78	803.6	597.71	719.25	805.09	773.49	777.4	566.6	780.02	607.71	493.24	655.73	880.88	0	768.64	625.98	451.52	443.79	745.64	692.9	839.58	727.49	1376.26	622.72	1421.07	997.77	827.06
-V16	165.37	51.55	130.59	57.95	98.46	310.56	233.32	147.43	39.69	109.04	0	101.57	0	97.94	0	107.15	90.92	0	177.32	137.54	432.77	267.66	128.29	331.03	144.05	118.52	162.61	64.33
-V17	1586.23	2103.69	1926.52	1614.01	2166.04	2284.19	2506.01	2040.02	1327.06	1705.97	1461.31	1649.21	1759.17	2442.95	0	1875.52	1881.42	1512.88	1520.67	1981.82	3021.6	2389.78	2088.67	4697.26	1646.11	3269.32	2805.59	2315.4
-V18	243.32	227.33	349.71	195.5	327.78	307.89	703.12	197.9	0	234.07	330.09	246.26	256.2	419.19	0	265.17	192.4	188.52	255.13	481.91	462.41	216.66	336.29	478.85	152.09	424.2	257.62	198.53
-V19	1921.6	2015.61	2872.21	2975.67	2406.07	2438.08	2381.42	2789.98	2881.8	2119.69	1953.23	1880.63	1985.58	1819.19	0	2343.84	2473.67	1909.11	1798.62	2824.34	1735	2429.73	1958.41	4299.39	2609.31	3374.62	2824.95	3079.01
-V20	539.06	432.85	724.98	347.76	380.87	522.5	444.07	550.04	502.86	576.95	744.34	410.58	415.64	321.36	0	805.68	451.18	292.67	471.68	793.63	804.05	679.41	0	1047.85	444.04	444.5	547.87	738.82
-V21	288.7	0	0	0	0	0	0	0	0	144.5	0	0	0	154.85	0	119.48	0	0	0	0	0	0	0	179.2	0	208.44	0	0
-V22	273.95	149.66	287.92	0	327.34	0	717.56	0	0	311.8	0	121.95	0	172.76	0	238.66	161.38	0	0	0	0	0	608.86	398.84	173.3	462.34	347.64	312.02
-V23	614.701	98.849	0	217.085	320.044	246.769	107.187	114.252	185.453	0	0	179.589	0	0	0	169.996	58.781	133.231	209.81	106.94	159.654	97.758	160.071	0	131.035	0	169.996	0
-V24	7.329	7.035	6.437	5.973	6.656	0	0	6.663	7.697	7.511	6.876	7.531	6.817	6.579	5.978	0	7.191	7.57	6.105	6.994	6.84	0	0	0	7.322	7.182	0	5.935
-V25	28.846	26.604	26.246	0	25.943	0	24.929	0	29.452	27.652	28.324	28.299	0	0	24.957	0	28.278	28.029	25.955	27.292	27.437	24.795	0	0	0	26.468	0	0
-V26	16.71	15.574	15.343	0	0	14.629	0	16.021	18.624	16.703	16.82	15.859	15.086	14.725	14.543	0	16.698	16.782	14.461	16.186	16.36	0	0	14.682	0	14.853	0	14.503
-V27	187.78	134.86	104.51	164.53	145.23	101.57	194.53	143.99	147.12	34.35	110	105.84	95.85	160.24	97.8	108.21	112.99	23.83	110.36	146.6	127.22	132.54	134.6	123.13	156.39	138.56	133.67	14.17
-V28	20.22	14.96	11.79	17.94	16.79	11.55	22.08	17.8	16.64	3.74	13.56	12.82	11.43	19.05	11.62	12.97	13.58	2.8	13.44	17.3	15.87	14.87	16.1	14.06	16.01	17.45	15.64	1.43
-V29	75.78	77.98	38.21	69.93	86.6	35.94	93.92	70.68	68.63	21.05	45.99	55.4	45.65	58.75	39.82	34.02	46.6	9.28	29.73	65.55	65.73	62.13	56.75	35.83	61.46	60.77	54.74	13.94
-V30	12.75	14.38	8.06	13.79	15.45	7.33	16.09	14.9	12.84	3.34	8.78	11.42	9.47	12.32	7.87	7.82	9.61	1.87	8.15	11.43	13.59	8.63	11.36	8.74	10.62	15.01	10.94	2.45
-V31	152.24	143.82	99.08	127.98	140.79	77.54	137.85	112.09	123.92	25.64	107.74	112.76	89.79	107.46	71.99	82.81	95.43	16.35	78.04	79.82	132.59	126.74	133.86	82.86	109.23	124.44	108.45	24.55
-V32	938.99	725.51	504.85	599.76	701.02	393.83	668.81	533.32	633.26	165.95	562.51	557.52	415.33	598.74	338.85	352.62	470.93	115.55	385.39	327.2	589.46	648.36	743.1	360.36	591.98	574.85	527.59	150.99
-V33	2988.64	2781	2451.36	2290.88	2497.75	1772.76	2434.42	2222.88	2429.96	365.39	2071.07	2358.74	1919.88	2141.82	1236.79	1292.48	1836.8	465.52	1668.16	1167.73	2095.17	3286.45	2900.66	1323.11	2346.08	2245.29	2129.08	735.12
-V34	1644.27	1378.93	970.38	1310.7	1277.11	838.94	1276.17	1038.97	1216.93	256.38	1070.93	1248.62	908.78	1301.31	795.45	690.35	1002.58	246.43	1039.85	738.11	1609.77	1444.48	1417.84	843.04	1359.28	1512.42	1245.6	326.87
-V35	34.28	28.91	29.9	31.11	38.88	17.48	39.24	23.23	30.38	7.43	19.24	32.68	22.86	29.83	13.98	13.69	22.05	7.96	21.14	30.86	25.14	34.58	29.31	14.04	32.27	29.3	27.08	6.72
-V36	34.69	25.94	25.12	31.06	34.84	18.45	27.52	20.78	27.3	6.01	16.27	32.31	21.57	24.55	15.88	13.34	20.65	7.03	16.83	25.77	27.02	38.17	26.83	15.03	36.42	32.65	27.34	8.39
-V37	53.33	33.39	38.28	56	18.46	33.81	39.24	25.03	37.19	12.79	19.02	29.64	29.32	36.33	21.06	26.69	27.01	6.3	24.3	49.3	23.38	133.19	49.05	20.55	57.23	32.46	48.68	36.85
-V38	55.46	32.06	38.14	73.93	17.66	27.63	40.29	24.64	38.73	18.25	17.06	30.63	28.54	39.35	15.18	27.94	26.45	9.01	22.52	62.43	17.96	222	42.3	16.94	65.81	35.65	60.7	67.84
-V39	1615.79	832.94	948.85	1163.14	780.73	932.8	827.92	651.39	969.19	300.59	651.84	688.09	704.96	886.23	511.33	657.76	683.37	120.74	872.17	1307.25	802.54	2032.41	1544.2	758.36	1356.28	1432.05	1263.16	435.85
-V40	1699.27	766.05	997.32	1114.23	990.02	987.62	890.66	680.92	1015.76	309.1	716.86	590.9	623.14	866.72	485.55	674.31	659.58	128.63	766	948.5	764.57	1414.08	1579.67	769.54	1269.34	1677.86	1148.7	383.33
-V41	3995.34	1888.42	2393.66	1835.16	1684.97	1796.85	1192.55	1091.08	1984.75	909.69	1763.01	1285.69	1150.88	1126.86	1048.41	1193.59	1261.41	257.87	1437.84	1248.8	1395.5	2019.26	3393.17	1548.47	2189.84	2792.08	2003.12	761.04
-V42	6200.76	2703.73	3569.72	2967.38	2647.22	2701.52	1896.29	1731.65	3052.28	1397.8	2729.69	1770.64	1689.06	1813.5	1552.25	1977.75	1922.15	419.79	2262.29	1830.99	2226.75	2961.28	5042.17	2440.05	3329.37	4602.08	3086.87	1171.63
-V43	2766.76	1286.7	1535.67	1776.16	1043.65	1253.94	1165.85	989.89	1477.33	581.17	1081.96	962.62	1015.15	1217.68	877.56	1123.53	1046.42	120.87	1150.86	1405.41	1211.44	2590.33	1996.95	1466.31	2124.7	2561.89	1813.49	583.43
-V44	1808.56	1052.58	1064.38	1465.2	861.99	1062.52	1290.66	962.53	1196.05	311.32	811.08	1038.58	980.55	1253.84	820.41	794.37	949.8	179.67	766.54	1582.99	1107.43	3061.94	1384.89	1171.4	1849.11	2223.83	1643.52	731.04
-V45	361.49	289.55	263.82	424.39	250.66	201.69	240.88	240.95	284.18	73.44	248.27	273.46	216.48	217.64	165.11	174.49	215.91	41.61	227.97	327.36	274.12	615.76	379.63	251.66	345.47	506.13	366.01	133.46
-V46	2607.82	2000.16	1671.95	2357.94	1683.26	1571.32	1935.52	1840.49	1958.56	359.59	1995.27	1867.04	1691.03	1610.68	1121.25	1356.18	1606.91	323.82	1288.12	2384.86	1957.6	4620.77	2142.9	2097.88	2778.2	3638.56	2613.61	1057.86
-V47	4306.74	3278.54	2766.81	3676.12	2584.89	2707.8	3218.81	3013.78	3194.19	573.31	3189.42	3307.49	2902.72	2845.79	2162.9	2270.99	2779.88	470.14	2005.07	3846.66	3287.96	7678.68	3441.2	3648.6	4534.31	6234.27	4334.59	1807.15
-V48	2757.36	1972.09	1921.97	2047.43	2307.53	3450.36	2481.9	3192.32	2516.37	573.41	1605.23	4187.86	1340.3	2548.83	2241.75	1147.41	2178.56	1120.09	946.32	1988.3	3012.52	4348.05	4947.77	2894.49	2605.46	6227.79	3371.34	1704.39
-V49	2846.27	2112.17	2074.85	2484.04	2030.38	2892.38	2323.34	2689.36	2431.6	349.58	1659.98	3637.59	1615.48	2586.62	2360.5	1413.49	2212.28	835.81	1208.92	2272.05	2841.18	5130.58	4188	2879.36	2853.44	5754.18	3390.96	1517.17
-V50	63.24	68.39	44.94	64.93	37.36	31.18	60.74	35.49	50.78	15.1	52.13	43.34	53.45	55.07	31.66	31.25	44.48	10.88	33.05	60.72	34.37	209.37	55.71	37.41	51.12	69.22	68.87	58.26
-V51	1745.37	1185.09	1129.87	1082.42	1354.59	1492.4	1089.89	1391.1	1308.84	232.89	1028.07	1955.9	729.97	1004.49	961.76	574.74	1042.49	481.45	420.8	926.39	1134.46	2690.76	2585.95	984.56	1268.87	2558.63	1571.3	896.32
-V52	2325.89	1572.13	1488.2	1298.49	1823.74	2252.49	1456.85	2073.13	1786.37	391.59	1356.24	2938.31	868.29	1287.9	1431.16	730.25	1435.36	788.12	531.96	1115.79	1682.73	2924.65	3710.59	1520.02	1620.38	3734.6	2105.09	1202.01
-V53	352.51	261.05	248.74	309.45	289.73	416.53	266.85	428.71	321.69	70.28	236.94	537.25	193.5	326	319.28	189.21	300.36	130.33	152.84	203.76	442.22	511.73	516.04	437.43	331.36	880.17	434.44	225.04
-V54	216.14	119.32	400.57	336.36	56.47	89.37	155.36	49.48	177.88	130.48	97.22	114.95	135.48	117.64	76.58	160.44	117.05	29.18	83.99	83.8	18.56	195.87	181.22	21.21	196.54	152.66	116.73	74.64
-V55	3354.74	1889.02	3463.96	2595.51	1095.04	1188.43	1840.09	983.93	2051.34	989.95	1188.04	1824.94	1599.03	1844.36	1384.25	1654.65	1582.54	256.02	1244.41	1674.07	559.55	2535.71	2199.75	710.19	2034.19	3209.59	1770.93	909.24
-V56	689.37	323.77	632.5	615.72	142.49	199.66	291.67	166.84	382.75	226.87	180.91	296.75	246.47	305.63	207.47	338.53	262.63	61.25	203.85	288.31	71.53	584.03	353.14	107.89	389.42	519.26	314.68	183.74
-V57	6414.27	4067.65	4605.44	4227.56	3397.35	4016.57	3910.51	3544.13	4272.94	943.77	3394.68	4289.36	3906.95	4409.8	3951.68	4184.76	4022.87	363.34	3950.15	6095.62	3268.86	5116.94	4149.28	5007.15	4429.98	9674.53	5211.56	1994.81
-V58	6266.36	3952.06	4638.28	5920.74	2062.48	2497.54	4169.02	3215.66	4090.27	1503.58	1974.3	2964.15	3022.96	3735.08	2495.87	3708.52	2983.48	685.38	2577.02	5480.39	1887.75	9838.32	2801.7	2511.25	3945.65	6713.94	4469.5	2726.1
-V59	2080.03	874.53	1695.81	1374.04	1394.91	765.07	1135.71	1004.63	1290.59	440.83	1819.62	1091.7	968.82	881.98	936.64	1111.28	1135.01	347.02	942.22	791.46	436.14	1258.84	1124.31	632.85	885.87	2287.78	1044.93	565.34
-V60	4019.07	2882.43	2920.72	2773.03	2331.94	2583.34	2238.8	2947.54	2837.11	547.71	2278.86	2457.49	2253.88	2589.84	2426.05	2732.92	2456.51	183.15	2860.57	3738.87	2620.94	4076.27	2372.31	3116.74	2923.46	6850.52	3569.96	1439.67
-V61	30316.42	25360.24	24223.65	23154.87	18133.87	22307.77	23062.85	23590.21	23768.74	3389.17	15197.09	21838.91	19822.74	25644.43	20471.11	22104.93	20846.53	3426.18	25946.74	31472.14	23168.38	33432.4	20220.09	23962.44	22402.54	56752.04	29669.59	11842.22
-V62	62402.87	35366.22	42321.8	31258.28	45712.77	37769.84	37522.2	43278.66	41954.08	9480.21	43459.12	35791.78	33007.49	37555.87	30867.86	39466.54	36691.44	4528.68	42271.25	38040.41	33835.98	31348.66	36815.48	42979.08	35687.18	100505.6	45185.45	22694.47
-V63	5345.95	2464.9	3091.4	2805.39	3415.52	2539.93	3108.55	3202.34	3246.75	909.16	3585.55	2965.11	2611.3	2390.26	2831.05	3065.67	2908.16	412.12	2899.18	2910.75	2276.04	2502.17	3031.16	2991.49	2581.47	8752.35	3493.07	2141.79
-V64	5292.96	4008.72	4012.44	3886.04	3647.09	4488.47	3153.78	4115.83	4075.66	624.71	3329.53	3032.83	2312.02	3514.26	3087.36	3808.11	3180.69	512.3	5079.61	5010.13	3983.6	3431.06	4013.46	4214.52	3237.19	10957.47	4990.88	2498.27
-V65	25444.34	13558.49	16493.22	12642.32	18907.52	18009.06	14231.51	18620.1	17238.32	4086.37	19094.31	14715.79	12230.13	14978.12	11587.05	17803.28	15068.11	2966.33	20658.33	15965.36	15559.69	10040.91	15401.79	19709.15	13056.25	46168.25	19569.97	11265.33
-V66	13899.53	8944.63	10159.96	11074.5	10592.6	8214.08	10176.94	9842.82	10363.13	1692.08	10224.02	8347.23	9132.47	9222.4	7107.34	10746.74	9130.03	1305.62	12811.74	12563.23	8865.71	12920.36	8100.75	11165.92	10182.24	27260.68	12983.83	6047.39
-V67	23512.63	13724.09	15652.33	13277.44	14818.7	9962.66	15178.26	16531.8	15332.24	3861.68	16746.25	14037.72	17098.1	13131.82	11032.59	15239.5	14547.66	2299.46	12753.96	18982.74	12462.65	21193.96	9974.96	15787.58	16677.68	36925.01	18094.82	8438.68
-V68	821.85	585.07	674.53	840.2	718.19	574.86	651.98	653.13	689.98	98.6	706.95	560.39	503.06	591.94	388.25	697.71	574.72	120.85	1200.77	898.01	617.64	580.33	598.67	661.06	518.03	1915.59	873.76	476.91
-V69	5665.21	3978.35	4089.75	6323.17	5026.21	3349.48	4344.41	4708.65	4685.65	964.71	5080.09	3035.72	3840.01	3568.7	2368.7	4560.78	3742.33	988.46	7508.69	6081.63	3875.94	4956.96	3618.8	4029.91	4201.27	11407.44	5710.08	2652.15
-V70	22886.12	12566.47	13528.14	14763.84	14470.03	10368.79	13211.34	16198.81	14749.19	3707.08	18464.21	12968.59	14976.46	11752.16	9218.14	15570.81	13825.06	3229.53	15895.44	17072.56	12786.98	16896.42	8923.53	16188.56	14585.89	34726.7	17134.51	7604.44
-V71	11423.67	7260.23	8970.27	7850.77	7000.97	7015.29	6913.61	7283.92	7964.84	1553.03	6763.98	8126.89	6577.43	7492.23	8528.18	8010.27	7583.16	782.55	8054.41	8188.51	6660.61	8871.33	7225.66	8376.3	7110.27	20520.68	9375.97	4562.98
-V72	15637.27	10686.69	12884.29	7658.22	11941.71	16143.55	12067.08	13664.64	12585.43	2720.13	8240.99	12552.56	6342.23	11346.03	11072.08	8526.86	9680.13	2345.48	10280.75	9082.97	11453.12	8256.47	14972.26	12789.22	8817.57	34220.75	13734.14	8577.94
-V73	135.27	87.47	100.36	112.7	84.8	79.57	89.6	87.62	97.17	18.55	90.81	70.86	83.71	83.59	71.35	94.23	82.42	9.69	140.04	119.03	80.9	117.49	74.17	97.09	93.08	275.42	124.65	64.66
-V74	14754.19	9880.17	10295.05	8265.04	9657.1	14237.48	10965.97	14015.39	11508.8	2467.86	7500.76	12549.98	5789.86	8750.01	8146.62	7193.56	8321.8	2299.97	8467.08	8028.29	8820.04	6808.25	13820.28	11066.16	7654.05	27388.57	11506.59	6795.54
-V75	5044.67	4123.9	3380.68	3943.65	4810.8	3194.4	5781.71	4796.76	4384.57	880.42	3954.38	4991.5	3876.63	4266.2	4298.95	3072.12	4076.63	630.29	4034.2	4324.63	2909.16	3440.2	4620.79	2600.36	4008.27	5293.72	3903.92	890.76
-V76	27989.88	27031.11	27818.36	26202.32	31496.87	31500.9	29211.25	33237.97	29311.08	2502.57	30111.45	28276.59	27232.92	31880.59	26296.06	28183.17	28663.46	2023.76	31918.73	34538.92	29086.99	27914.54	27498.1	39484.04	33320.98	43351.62	33389.24	5645.12
-V77	6033.59	5638.84	5757.39	5676.17	6856.34	6971.39	5687.13	8714.58	6416.93	1072.27	6824.08	6173.48	5757.01	6766.91	5862.96	6737.69	6353.69	483.48	7038.06	7289.71	6550.93	6474.58	6456.35	8406.92	5959.81	9192.51	7171.11	1101.49
-V78	7531.71	9766.33	7917.05	7066.02	12533.47	8597.12	10418.97	11146.66	9372.17	1920.47	9102.5	9784.31	7945.3	9496.2	8096.37	6447.88	8478.76	1239.67	6847.86	10800.66	8877.01	9466.25	7931.75	8909.79	9603.09	8932.52	8921.12	1169.52
-V79	3370.7	4671.45	3614.71	3446.79	5356.27	4618.38	4037.77	7068.76	4523.1	1239.4	4406.1	4263.32	3463.28	4600.41	3959.76	3752.84	4074.29	427.18	3553.62	5079.92	4848.24	4350.41	4002.13	5329.31	3919.06	4823.83	4488.31	627.07
-V80	2868.85	5047.99	6140.96	3806.85	7216.89	5022.46	5256.06	7169.93	5316.25	1519.33	6397.22	6182.99	4471.19	4996.46	5044.24	3879.66	5161.96	972.74	4630.92	5302.12	5241.23	6062.4	4313.43	6004.09	4748.38	3915.5	5027.26	767.88
-V81	1281.17	2380.08	2630.57	1937.7	2948.17	2691.06	2049.1	4141.95	2507.47	842.56	2926.15	2622.13	1919.88	2621.26	2455.64	2368.02	2485.52	336.42	2351.46	2619.77	3160.6	2527.13	2012.54	3985.57	2068.56	2219.55	2618.15	662.38
-V82	2146.74	3932.04	7069.54	3549.09	7827.98	6430.48	4776.82	6935.8	5333.56	2022.04	6914.18	5835.39	4308.74	5546.11	4125.61	3316.45	5007.75	1321.86	5274.98	6382.23	4334.58	7275.77	4046.02	6099.75	5484.72	2524.77	5177.85	1504.1
-V83	1907.68	3559.05	5257.18	3193.54	6000.27	5750.61	3999.64	7589.13	4657.14	1824.28	6055.9	5410.81	3697.01	5334.87	4176.24	3397.35	4678.7	1069.69	5656.93	5396.48	4561.55	5252.67	3739.43	5920.38	4914.96	2876.17	4789.82	1031.33
-V84	1563.87	3853.97	8432.18	3998.8	8762.48	7300.71	5457.68	7690.55	5882.53	2579.31	7568.64	6990.02	4975.96	6365.79	4614.85	3298.13	5635.56	1615.25	6009.26	8596.72	5386.72	9056.14	3895.21	8087.23	6738.97	2065.6	6229.48	2415.73
-V85	3302.09	7922.23	14839.62	8695.1	14895.67	16252.17	9849.17	16439.95	11524.5	4784.86	15467.28	13457.69	9570.14	14436.95	11137.53	7751.42	11970.17	2992.62	14886.11	19383.47	13977.26	15573.95	8041.42	19837.99	14672.95	5478.44	13981.45	4998.55
-V86	0	296.05	366.33	1166.3	169.79	130.5	910.02	161.2	400.02	414.37	118.7	194.08	229.06	300.62	98.91	317.51	209.81	90.62	117.23	575.01	90.37	827.4	371.26	112.71	288.72	0	297.84	283.19
-V87	4401.04	2934.89	3681.01	6152.67	2603.61	2332.57	5978.46	1842.04	3740.79	1638.59	2181.44	2571.46	2344.9	3162.33	1741.34	4144.96	2691.07	852.26	2984.39	3569.27	1848.09	3728.68	4482.7	3372.3	3045.7	5581.86	3576.62	1103.72
-V88	4420.06	1904.34	2745.79	4347.63	2944.8	1893.85	4677.78	1650.45	3073.09	1248.88	2285.76	1717.32	1691.2	1981.19	1265.7	3952.21	2148.9	946	1923.49	2689.61	1150.01	2382.48	3544.16	2397.09	2072.07	4295.69	2556.82	977.41
-V89	2025.01	1309.69	1534.02	1724.7	997.37	1112.13	1504.17	1062.01	1408.64	356.9	1060.36	1233.53	1053.84	1231.26	1037.81	1653.63	1211.74	234.19	1373.49	870.32	1061.5	971.79	1322.44	1953.7	1160.28	3600.17	1539.21	897.22
-V90	7867.46	4397.17	5500.73	6128.55	4480.76	4361.83	6223.22	3656.82	5327.07	1374.86	5401.66	4479.81	3795.24	4545.42	3955.3	6335.78	4752.2	958.89	5860.18	3637.58	3601.16	3030.4	5119.26	7934.1	3942.76	12438.43	5695.48	3154
-V91	15420.21	6374.06	8675.69	9187.97	9400.76	7612.14	11663.12	6741.51	9384.43	2960.52	10596.69	7079.71	6181.61	7096.04	6025.42	12463.24	8240.45	2652.77	9551.32	5992.62	5097.49	4421.58	9300.09	12959.02	6316.93	21213.88	9356.62	5563.45
-V92	6810.22	3429.58	4299.33	6127.84	4075.32	3344.66	5125.32	3028.74	4530.12	1375.11	4175.7	3140.88	3084.36	3031.18	2636.89	6669.27	3789.71	1500.91	3604.49	2605.3	2145.3	2993.63	4287.71	5353.81	3153.44	9144.78	4161.06	2250.33
-V93	0	354.36	350.3	379.16	287.08	292.88	444.09	303.69	301.44	132.41	207.65	392.54	274.35	267.83	257.3	382.95	297.1	74.08	238.86	145.6	268.33	189	452.98	351.16	243.21	1063.47	369.08	296.38
-V94	2856.36	2456.4	2540.2	3367.98	2179.99	1475.83	2299.58	2163.25	2417.45	552.18	1869.28	2155.91	1924.65	1709.17	1633.53	3130.02	2070.43	550.12	1852.97	935.78	2010.54	1819.26	2184.75	2451.9	1909.68	5332.67	2312.19	1296.17
-V95	24091.97	15443.29	15942.72	17970	12145.72	10870.02	14682.71	15930	15884.55	4008.56	13247.25	15454.42	13712.53	11623.37	9969.61	19752.29	13959.91	3398.12	9621.47	5782.84	11913.08	12015.65	12566.22	17116.78	13006.74	34928.36	14618.89	8804.83
-V96	60793.4	33382.53	33715.73	32764.43	24127.78	25432.17	29776.84	35260.09	34406.62	11394.51	28888.49	34024.7	31279.19	25136.41	21490.99	42646.24	30577.67	7389.9	16961.84	12299.55	24074.2	26183.98	25604.38	38438.79	28979.32	78126.8	31333.61	20446.85
-V97	17570.51	9240.64	9721.88	10284.94	6788.15	7088.16	9220.42	9323.72	9904.8	3334.56	7668.14	9513.44	7976.91	7000.53	6579.27	12453.69	8532	2170.52	4915.75	3693.18	6545.25	7271.72	7741.63	11272.66	8234.6	21625.05	8912.48	5612.76
-V98	0	149.15	135.65	144.37	124.09	117.76	110.31	127.3	113.58	47.7	128.4	127.61	126.27	136.02	105.67	160.41	130.73	17.73	118.88	107.55	121.9	120.41	133.07	129.53	119.35	0	106.34	43.64
-V99	314.71	233.89	257.32	290.71	136.54	131.91	212.71	151.12	216.11	70.67	144.84	161.98	199.1	177.26	109.83	276.15	178.19	56.71	136.06	92.56	133.57	240.27	196.46	181.17	175.41	0	144.44	73.62
-V100	1063.57	888.31	802.4	899.21	524.53	465.73	990.79	508.3	767.86	235.42	425.38	531.11	631.35	755.31	380.35	795.06	586.43	170.6	399.27	323.3	426.24	771.87	698.1	557.47	570.57	1826.56	696.67	480.86
-V101	2587.9	1673.54	1654.1	1984.41	1404.72	1474.72	2767.56	1490.35	1879.66	525.82	725.28	1591.13	1128.98	1962.5	1210.7	1571.45	1365.01	433.48	897.88	885.71	1024.88	1264.44	2472.8	1515.25	1349.88	4852	1782.85	1340.9
-V102	3565.72	1975.42	2013.22	2140.6	1668.46	2455.07	3602.33	2361.46	2472.79	726.93	769.9	2420.79	1099.54	1908.1	1814.65	1765.41	1629.73	596.03	990.98	1185.95	1435.53	1123.37	4179.54	2564.22	1660.72	6490.51	2453.85	1944.54
-V103	0	48.29	0	0	0	0	70.19	0	14.81	28.04	0	0	0	0	0	0	0	0	0	123.9	0	0	0	0	0	5.93	16.23	43.56
-V104	0	123.49	65.51	80.81	98.52	68.99	195.36	83.25	89.49	55.5	97.05	128.29	99.81	113.05	120.62	0	93.14	47.16	119.68	367.75	78.17	59.42	81.7	79.25	121.63	0	113.45	109.53
-V105	0	85.23	0	0	0	0	168.05	0	31.66	62.66	0	0	0	0	0	0	0	0	0	233.87	0	0	0	0	0	0	29.23	82.69
-V106	0	183.94	76.89	113	125.6	0	370.73	0	108.77	125.97	150.38	121.92	135.84	186.45	103.87	0	116.41	63.52	154.21	496.94	107.83	94.48	106.85	0	141.87	0	137.77	156.29
-V107	423.7	0	164.21	507.86	578.77	522.85	0	346.55	317.99	234.19	0	299.3	343.68	661.93	499.17	759.59	427.28	274.44	363.88	432.47	486.04	383.04	381.67	0	497.37	0	318.06	202.18
-V108	4.6	2.76	2.42	3.59	3.85	3.27	5.32	4.47	3.79	0.98	4.96	3.56	3.84	4.62	5.72	5.58	4.72	0.89	3.99	4.66	4.99	4.79	4.25	2.82	3.33	4.09	4.11	0.74
-V109	1.46	1.14	1.27	1.13	1.52	1.57	1.35	1.14	1.32	0.18	1.18	1.28	1.13	1.2	1.14	1.63	1.26	0.19	1.32	0.9	1.14	1.6	1.07	1.42	1.87	0.91	1.28	0.34
-V110	0.52	0.55	0	0.49	0	0	0	0.51	0.26	0.28	0.35	0.38	0.56	0.44	0	0.55	0.38	0.2	0.32	0.37	0.35	0.52	0	0.44	0.44	0.28	0.34	0.16
-V111	0.4	0	0	0.43	0.32	0	0	0.39	0.19	0.21	0.3	0.37	0	0.4	0	0.42	0.25	0.2	0	0.36	0.25	0.47	0	0.39	0.38	0	0.23	0.2
-V112	0.76	0.49	0.43	0.64	0.49	0.48	0.23	0.71	0.53	0.17	0.47	0.52	0.59	0.62	0.38	0.65	0.54	0.1	0.32	0.49	0.38	0.55	0.49	0.6	0.64	0.47	0.49	0.11
-V113	0.61	0.58	0.53	0.53	0.45	0.31	0.15	0.51	0.46	0.15	0.36	0.51	0.44	0.45	0.48	0.66	0.48	0.1	0.33	0.53	0.37	0.61	0.36	0.51	0.67	0.33	0.46	0.13
-V114	0	0	0	0	0.09	0	0	0.12	0.03	0.05	0	0.1	0	0	0	0	0.02	0.04	0	0	0.1	0	0.12	0.11	0	0	0.04	0.06
-V115	0	0	0	0	0	0	0	0.13	0.02	0.04	0	0.11	0	0	0	0	0.02	0.05	0	0	0	0	0.15	0.12	0	0	0.03	0.06
-V116	1.76	1.89	1.43	1.19	1.34	1.64	0	2.33	1.44	0.68	1.16	2.16	0	1.74	2.23	1.12	1.4	0.83	0	1.47	1.37	1.34	2.27	1.83	1.51	1.43	1.4	0.65
--- a/tests/exa2/sampleMetadata.tsv	Tue Aug 02 06:26:41 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,29 +0,0 @@
-sampleMetadata	meta1
-S1	A
-S2	A
-S3	A
-S4	A
-S5	A
-S6	A
-S7	A
-S8	A
-S9	B
-S10	B
-S11	B
-S12	B
-S13	B
-S14	B
-S15	B
-S16	C
-S17	C
-S18	C
-S19	C
-S20	C
-S21	C
-S22	C
-S23	C
-S24	C
-S25	BC
-S26	AB
-S27	BC
-S28	AC
--- a/tests/exa2/variableMetadata.tsv	Tue Aug 02 06:26:41 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,117 +0,0 @@
-variableMetadata	meta2
-V1	ER
-V2	GGG
-V3	GGG
-V4	GGG
-V5	GGG
-V6	CE
-V7	CE
-V8	CE
-V9	TG
-V10	TG
-V11	TG
-V12	TG
-V13	TG
-V14	AM
-V15	AM
-V16	AM
-V17	AM
-V18	AM
-V19	AM
-V20	AM
-V21	AM
-V22	AM
-V23	AM
-V24	AM
-V25	AM
-V26	AM
-V27	AM
-V28	AM
-V29	AM
-V30	AM
-V31	AM
-V32	ER
-V33	ER
-V34	ER
-V35	ER
-V36	ER
-V37	CER
-V38	CER
-V39	CER
-V40	CER
-V41	CER
-V42	CER
-V43	CER
-V44	CER
-V45	CER
-V46	CER
-V47	PP
-V48	PP
-V49	PP
-V50	PP
-V51	PP
-V52	PP
-V53	PP
-V54	PP
-V55	PP
-V56	PP
-V57	PP
-V58	PP
-V59	PP
-V60	PP
-V61	PP
-V62	PP
-V63	PP
-V64	CC
-V65	CC
-V66	CC
-V67	CC
-V68	CC
-V69	CC
-V70	CC
-V71	CC
-V72	CC
-V73	CC
-V74	CC
-V75	CC
-V76	CC
-V77	CC
-V78	CC
-V79	CC
-V80	CC
-V81	CC
-V82	CC
-V83	CC
-V84	CC
-V85	SM
-V86	SM
-V87	SM
-V88	SM
-V89	SM
-V90	SM
-V91	SM
-V92	SM
-V93	SM
-V94	SM
-V95	SM
-V96	PI
-V97	PI
-V98	PI
-V99	PI
-V100	PI
-V101	PI
-V102	PI
-V103	PI
-V104	PI
-V105	PI
-V106	PI
-V107	NG
-V108	NG
-V109	NG
-V110	SO
-V111	SO
-V112	SO
-V113	SO
-V114	SO
-V115	SO
-V116	SO
--- a/tests/heatmap_runtests.R	Tue Aug 02 06:26:41 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,105 +0,0 @@
-#!/usr/bin/env Rscript
-
-## Package
-##--------
-
-library(RUnit)
-
-## Constants
-##----------
-
-testOutDirC <- "output"
-argVc <- commandArgs(trailingOnly = FALSE)
-scriptPathC <- sub("--file=", "", argVc[grep("--file=", argVc)])
-
-
-## Functions
-##-----------
-
-## Reading tables (matrix or data frame)
-readTableF <- function(fileC, typeC = c("matrix", "dataframe")[1]) {
-
-    	file.exists(fileC) || stop(paste0("No output file \"", fileC ,"\"."))
-
-        switch(typeC,
-               matrix = return(t(as.matrix(read.table(file = fileC,
-                   header = TRUE,
-                   row.names = 1,
-                   sep = "\t",
-                   stringsAsFactors = FALSE)))),
-               dataframe = return(read.table(file = fileC,
-                   header = TRUE,
-                   row.names = 1,
-                   sep = "\t",
-                   stringsAsFactors = FALSE)))
-
-}
-
-## Call wrapper
-wrapperCallF <- function(paramLs) {
-
-	## Set program path
-    	wrapperPathC <- file.path(dirname(scriptPathC), "..", "heatmap_wrapper.R")
-
-	## Set arguments
-	argLs <- NULL
-	for (parC in names(paramLs))
-		argLs <- c(argLs, parC, paramLs[[parC]])
-
-	## Call
-	wrapperCallC <- paste(c(wrapperPathC, argLs), collapse = " ")
-
-        if(.Platform$OS.type == "windows")
-            wrapperCallC <- paste("Rscript", wrapperCallC)
-
-	wrapperCodeN <- system(wrapperCallC)
-
-	if (wrapperCodeN != 0)
-		stop("Error when running heatmap_wrapper.R.")
-
-	## Get output
-	outLs <- list()
-	if ("dataMatrix_out" %in% names(paramLs))
-            outLs[["datMN"]] <- readTableF(paramLs[["dataMatrix_out"]], "matrix")
-	if ("sampleMetadata_out" %in% names(paramLs))
-            outLs[["samDF"]] <- readTableF(paramLs[["sampleMetadata_out"]], "dataframe")
-	if ("variableMetadata_out" %in% names(paramLs))
-            outLs[["varDF"]] <- readTableF(paramLs[["variableMetadata_out"]], "dataframe")
-        if("information" %in% names(paramLs))
-            outLs[["infVc"]] <- readLines(paramLs[["information"]])
-
-	return(outLs)
-}
-
-## Setting default parameters
-defaultArgF <- function(testInDirC) {
-
-    defaultArgLs <- list()
-    if(file.exists(file.path(dirname(scriptPathC), testInDirC, "dataMatrix.tsv")))
-        defaultArgLs[["dataMatrix_in"]] <- file.path(dirname(scriptPathC), testInDirC, "dataMatrix.tsv")
-    if(file.exists(file.path(dirname(scriptPathC), testInDirC, "sampleMetadata.tsv")))
-        defaultArgLs[["sampleMetadata_in"]] <- file.path(dirname(scriptPathC), testInDirC, "sampleMetadata.tsv")
-    if(file.exists(file.path(dirname(scriptPathC), testInDirC, "variableMetadata.tsv")))
-        defaultArgLs[["variableMetadata_in"]] <- file.path(dirname(scriptPathC), testInDirC, "variableMetadata.tsv")
-
-    defaultArgLs[["dataMatrix_out"]] <- file.path(dirname(scriptPathC), testOutDirC, "dataMatrix.tsv")
-    defaultArgLs[["sampleMetadata_out"]] <- file.path(dirname(scriptPathC), testOutDirC, "sampleMetadata.tsv")
-    defaultArgLs[["variableMetadata_out"]] <- file.path(dirname(scriptPathC), testOutDirC, "variableMetadata.tsv")
-    defaultArgLs[["figure"]] <- file.path(dirname(scriptPathC), testOutDirC, "figure.pdf")
-    defaultArgLs[["information"]] <- file.path(dirname(scriptPathC), testOutDirC, "information.txt")
-
-    defaultArgLs
-
-}
-
-## Main
-##-----
-
-## Create output folder
-file.exists(testOutDirC) || dir.create(testOutDirC)
-
-## Run tests
-test.suite <- defineTestSuite('tests', dirname(scriptPathC), testFileRegexp = paste0('^.*_tests\\.R$'), testFuncRegexp = '^.*$')
-isValidTestSuite(test.suite)
-test.results <- runTestSuite(test.suite)
-print(test.results)
--- a/tests/heatmap_tests.R	Tue Aug 02 06:26:41 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,57 +0,0 @@
-test_input_cut4 <- function() {
-
-    testDirC <- "input"
-    argLs <- list(disC = "1-cor",
-                  cutSamN = "4",
-                  cutVarN = "3",
-                  corMetC = "spearman",
-                  aggMetC = "ward",
-                  colC = "blueOrangeRed",
-                  scaL = "TRUE",
-                  cexN = "0.8")
-
-    argLs <- c(defaultArgF(testDirC), argLs)
-    outLs <- wrapperCallF(argLs)
-
-    checkEqualsNumeric(outLs[['samDF']][13, 'heat_clust'], 4)
-
-}
-
-test_exa1_cut3 <- function() {
-
-    testDirC <- "exa1"
-    argLs <- list(disC = "1-cor",
-                  cutSamN = "3",
-                  cutVarN = "4",
-                  corMetC = "spearman",
-                  aggMetC = "ward",
-                  colC = "blueOrangeRed",
-                  scaL = "TRUE",
-                  cexN = "1")
-
-    argLs <- c(defaultArgF(testDirC), argLs)
-    outLs <- wrapperCallF(argLs)
-
-    checkEqualsNumeric(outLs[['varDF']]['V24', 'heat_clust'], 4)
-
-}
-
-test_exa2_cut4 <- function() {
-
-    testDirC <- "exa2"
-    argLs <- list(disC = "1-cor",
-                  cutSamN = "1",
-                  cutVarN = "1",
-                  corMetC = "spearman",
-                  aggMetC = "ward",
-                  colC = "blueOrangeRed",
-                  scaL = "TRUE",
-                  cexN = "1")
-
-    argLs <- c(defaultArgF(testDirC), argLs)
-    outLs <- wrapperCallF(argLs)
-
-    checkEquals(outLs[['varDF']]['V31', 'meta2'], 'AM')
-
-}
-
--- a/tests/input/dataMatrix.tsv	Tue Aug 02 06:26:41 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,16 +0,0 @@
-dataMatrix	HU_017	HU_028	HU_034	HU_051	HU_060	HU_078	HU_091	HU_093	HU_099	HU_110	HU_130	HU_134	HU_138	HU_149	HU_152	HU_175	HU_178	HU_185	HU_204	HU_208
-HMDB03193	76043	412165	44943	27242	436566	173175	242549	57066	559869	3732	339188	471368	262271	127285	451270	212500	79673	NA	891129	43907
-HMDB01101	30689	6877586	52217	3158	10789748	229568	4763576	3878773	976436	831937	608298	1605075	72021	442510	1107705	1464339	31250	2724553	72900	32742
-HMDB10348	47259	544877	60885	34582	529874	168264	176500	76457	610110	16262	279156	524468	451573	591487	433529	161069	214392	13781	1580343	39315
-HMDB59717	357351	1030464	301983	67604	306862	1028110	1530493	270027	1378535	289677	808334	1132813	871209	895435	715190	1563158	784738	146195	994336	239030
-HMDB00822	483755	579287	1132413	157113	1577570	1469735	1085454	477909	814755	245417	610681	763706	2406336	827531	992508	569605	355321	150259	1334200	271010
-HMDB13189	2644620	727587	1661412	619181	136278	2755434	593863	837865	3526136	2003278	1608814	3446611	1941527	113937	3132404	2893445	2092753	1034666	1517319	841661
-HMDB00299	250551	1046138	456162	159386	1013302	808657	614370	250403	768004	242085	504108	1014041	1362408	1057660	1110050	566050	411886	142233	1992420	284775
-HMDB00191	560002	771533	575790	392284	888498	785428	645785	591569	960658	910201	639437	1092885	1409045	2292023	1246459	1945577	710519	773384	1061418	622898
-HMDB00518	34236	58249	85944	NA	342102	129886	175800	13154	230242	NA	440223	315368	10657	419508	48673	28361	514579	23108	867108	73831
-HMDB00715	1252089	2547452	905408	371059	4983588	5140022	2658555	814523	2558923	859466	4184204	3865723	3236644	2615560	3820724	3577833	2295288	625924	7517724	1341900
-HMDB01032	2569205	26023086	1604999	430453	8103558	26222916	257139	675754	59906109	263055	31151730	18648127	14989438	1554658	20249262	5588731	871010	15920	9120781	44276
-HMDB00208	747080	13420742	595872	1172376	7172632	3143654	4059767	1433702	5593888	5402629	2477288	3346077	4230072	7621236	8960828	10335722	7037373	1574738	3359238	2540044
-HMDB04824	374028	1144386	539206	178517	1046190	959381	605191	310260	1253319	477259	477995	825691	1157093	1089284	1411802	1020206	782673	346761	1824553	387811
-HMDB00512	53304	319783	280560	85009	1333877	556003	590779	209285	342532	198512	569970	525240	246282	1140422	542345	1171008	827723	222953	438839	85554
-HMDB00251	368600	616555	94936	622468	180988	293988	352855	767894	268331	167246	310918	1248919	577184	10985	335711	403815	80614	63393	454489	616061
--- a/tests/input/sampleMetadata.tsv	Tue Aug 02 06:26:41 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,21 +0,0 @@
-sampleMetadata	injectionOrder	mode	age	bmi	gender
-HU_017	2	pos	41	23.03	M
-HU_028	7	pos	41	23.92	F
-HU_034	9	pos	52	23.37	M
-HU_051	20	pos	24	23.23	F
-HU_060	24	pos	55	28.72	F
-HU_078	34	pos	46	25.18	M
-HU_091	42	pos	61	26.12	M
-HU_093	43	pos	53	21.71	M
-HU_099	46	pos	23	21.3	M
-HU_110	53	pos	50	20.9	F
-HU_130	63	pos	33	26.06	M
-HU_134	67	pos	48	22.89	M
-HU_138	68	pos	42	21.88	M
-HU_149	72	pos	35	19.49	F
-HU_152	75	pos	26	17.58	F
-HU_175	87	pos	35	21.26	F
-HU_178	88	pos	60	32.87	F
-HU_185	95	pos	42	21.09	F
-HU_204	104	pos	31	29.06	M
-HU_208	106	pos	27	18.61	F
--- a/tests/input/variableMetadata.tsv	Tue Aug 02 06:26:41 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,16 +0,0 @@
-variableMetadata	name
-HMDB03193	Testosterone_glucuronide
-HMDB01101	p-Anisic_acid
-HMDB10348	Dehydroepiandrosterone_3-glucuronide
-HMDB59717	Glu-Val
-HMDB00822	p-Hydroxymandelic_acid
-HMDB13189	3-Indole_carboxylic_acid_glucuronide
-HMDB00299	Xanthosine
-HMDB00191	L-Aspartic_acid
-HMDB00518	Chenodeoxycholic_acid
-HMDB00715	Kynurenic_acid
-HMDB01032	Dehydroepiandrosterone_sulfate
-HMDB00208	Oxoglutaric_acid
-HMDB04824	N2,N2-Dimethylguanosine
-HMDB00512	N-Acetyl-L-phenylalanine
-HMDB00251	Taurine
--- a/tests/output/dataMatrix.tsv	Tue Aug 02 06:26:41 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,16 +0,0 @@
-dataMatrix	HU_051	HU_208	HU_178	HU_130	HU_175	HU_099	HU_152	HU_204	HU_017	HU_138	HU_034	HU_078	HU_060	HU_149	HU_028	HU_093	HU_134	HU_091	HU_110	HU_185
-HMDB13189	619181	841661	2092753	1608814	2893445	3526136	3132404	1517319	2644620	1941527	1661412	2755434	136278	113937	727587	837865	3446611	593863	2003278	1034666
-HMDB00251	622468	616061	80614	310918	403815	268331	335711	454489	368600	577184	94936	293988	180988	10985	616555	767894	1248919	352855	167246	63393
-HMDB01101	3158	32742	31250	608298	1464339	976436	1107705	72900	30689	72021	52217	229568	10789748	442510	6877586	3878773	1605075	4763576	831937	2724553
-HMDB00191	392284	622898	710519	639437	1945577	960658	1246459	1061418	560002	1409045	575790	785428	888498	2292023	771533	591569	1092885	645785	910201	773384
-HMDB00208	1172376	2540044	7037373	2477288	10335722	5593888	8960828	3359238	747080	4230072	595872	3143654	7172632	7621236	13420742	1433702	3346077	4059767	5402629	1574738
-HMDB59717	67604	239030	784738	808334	1563158	1378535	715190	994336	357351	871209	301983	1028110	306862	895435	1030464	270027	1132813	1530493	289677	146195
-HMDB00512	85009	85554	827723	569970	1171008	342532	542345	438839	53304	246282	280560	556003	1333877	1140422	319783	209285	525240	590779	198512	222953
-HMDB00518	NA	73831	514579	440223	28361	230242	48673	867108	34236	10657	85944	129886	342102	419508	58249	13154	315368	175800	NA	23108
-HMDB00822	157113	271010	355321	610681	569605	814755	992508	1334200	483755	2406336	1132413	1469735	1577570	827531	579287	477909	763706	1085454	245417	150259
-HMDB00715	371059	1341900	2295288	4184204	3577833	2558923	3820724	7517724	1252089	3236644	905408	5140022	4983588	2615560	2547452	814523	3865723	2658555	859466	625924
-HMDB01032	430453	44276	871010	31151730	5588731	59906109	20249262	9120781	2569205	14989438	1604999	26222916	8103558	1554658	26023086	675754	18648127	257139	263055	15920
-HMDB00299	159386	284775	411886	504108	566050	768004	1110050	1992420	250551	1362408	456162	808657	1013302	1057660	1046138	250403	1014041	614370	242085	142233
-HMDB04824	178517	387811	782673	477995	1020206	1253319	1411802	1824553	374028	1157093	539206	959381	1046190	1089284	1144386	310260	825691	605191	477259	346761
-HMDB03193	27242	43907	79673	339188	212500	559869	451270	891129	76043	262271	44943	173175	436566	127285	412165	57066	471368	242549	3732	NA
-HMDB10348	34582	39315	214392	279156	161069	610110	433529	1580343	47259	451573	60885	168264	529874	591487	544877	76457	524468	176500	16262	13781
--- a/tests/output/essai.tsv	Tue Aug 02 06:26:41 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,21 +0,0 @@
-sampleMetadata	injectionOrder	mode	age	bmi	gender	heat_clust
-HU_017	2	pos	41	23.03	M	1
-HU_034	9	pos	52	23.37	M	1
-HU_204	104	pos	31	29.06	M	2
-HU_134	67	pos	48	22.89	M	2
-HU_099	46	pos	23	21.3	M	2
-HU_078	34	pos	46	25.18	M	2
-HU_130	63	pos	33	26.06	M	2
-HU_028	7	pos	41	23.92	F	2
-HU_138	68	pos	42	21.88	M	2
-HU_152	75	pos	26	17.58	F	2
-HU_051	20	pos	24	23.23	F	3
-HU_208	106	pos	27	18.61	F	3
-HU_110	53	pos	50	20.9	F	3
-HU_178	88	pos	60	32.87	F	3
-HU_149	72	pos	35	19.49	F	3
-HU_175	87	pos	35	21.26	F	3
-HU_060	24	pos	55	28.72	F	4
-HU_091	42	pos	61	26.12	M	4
-HU_093	43	pos	53	21.71	M	4
-HU_185	95	pos	42	21.09	F	4
Binary file tests/output/figure.pdf has changed
--- a/tests/output/information.txt	Tue Aug 02 06:26:41 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,24 +0,0 @@
-
-Start of the 'Heatmap' module: Tue 02 Aug 2016 11:48:22 AM
-
-Arguments used:
-
-                     value
-dataMatrix_in        "tests/input/dataMatrix.tsv"
-sampleMetadata_in    "tests/input/sampleMetadata.tsv"
-variableMetadata_in  "tests/input/variableMetadata.tsv"
-dataMatrix_out       "tests/output/dataMatrix.tsv"
-sampleMetadata_out   "tests/output/sampleMetadata.tsv"
-variableMetadata_out "tests/output/variableMetadata.tsv"
-figure               "tests/output/figure.pdf"
-information          "tests/output/information.txt"
-disC                 "1-cor"
-cutSamN              "4"
-cutVarN              "3"
-corMetC              "spearman"
-aggMetC              "ward"
-colC                 "blueOrangeRed"
-scaL                 "TRUE"
-cexN                 "0.8"
-
-End of the 'Heatmap' Galaxy module call: Tue 02 Aug 2016 11:48:22 AM
--- a/tests/output/sampleMetadata.tsv	Tue Aug 02 06:26:41 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,21 +0,0 @@
-sampleMetadata	injectionOrder	mode	age	bmi	gender	heat_clust
-HU_051	20	pos	24	23.23	F	3
-HU_208	106	pos	27	18.61	F	3
-HU_178	88	pos	60	32.87	F	1
-HU_130	63	pos	33	26.06	M	1
-HU_175	87	pos	35	21.26	F	1
-HU_099	46	pos	23	21.3	M	1
-HU_152	75	pos	26	17.58	F	1
-HU_204	104	pos	31	29.06	M	1
-HU_017	2	pos	41	23.03	M	1
-HU_138	68	pos	42	21.88	M	1
-HU_034	9	pos	52	23.37	M	1
-HU_078	34	pos	46	25.18	M	1
-HU_060	24	pos	55	28.72	F	4
-HU_149	72	pos	35	19.49	F	4
-HU_028	7	pos	41	23.92	F	2
-HU_093	43	pos	53	21.71	M	2
-HU_134	67	pos	48	22.89	M	2
-HU_091	42	pos	61	26.12	M	2
-HU_110	53	pos	50	20.9	F	2
-HU_185	95	pos	42	21.09	F	2
--- a/tests/output/variableMetadata.tsv	Tue Aug 02 06:26:41 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,16 +0,0 @@
-variableMetadata	name	heat_clust
-HMDB13189	3-Indole_carboxylic_acid_glucuronide	3
-HMDB00251	Taurine	3
-HMDB01101	p-Anisic_acid	2
-HMDB00191	L-Aspartic_acid	2
-HMDB00208	Oxoglutaric_acid	2
-HMDB59717	Glu-Val	2
-HMDB00512	N-Acetyl-L-phenylalanine	2
-HMDB00518	Chenodeoxycholic_acid	1
-HMDB00822	p-Hydroxymandelic_acid	1
-HMDB00715	Kynurenic_acid	1
-HMDB01032	Dehydroepiandrosterone_sulfate	1
-HMDB00299	Xanthosine	1
-HMDB04824	N2,N2-Dimethylguanosine	1
-HMDB03193	Testosterone_glucuronide	1
-HMDB10348	Dehydroepiandrosterone_3-glucuronide	1