# HG changeset patch
# User iuc
# Date 1490974549 14400
# Node ID 36681c1ad6d7b7ea6f27ca126f97bd9230995cfd
# Parent  7d1758a8688418066a96f382a81b76b1ab089b6b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7efdf3224552d113a01043ee5bf4517d770df933

diff -r 7d1758a86884 -r 36681c1ad6d7 README.rst
--- a/README.rst	Thu Mar 23 10:15:57 2017 -0400
+++ b/README.rst	Fri Mar 31 11:35:49 2017 -0400
@@ -6,13 +6,25 @@
 trinity requires a large amount of memory to perform the assembly: "roughly
 ~1G of RAM per 1M reads to be assembled"
 
-By default, this tool is configured to limit the memory consumption to 30G.
+By default, this tool is configured to limit the memory consumption to 1G.
 You might need to lower this limit if the machine(s) executing the jobs have less memory available.
 If you have a lot of reads to assemble and a machine with enough memory, you can increase it.
-In both cases, you can edit the TRINITY_MEM_OPTIONS in the file:
-
-<tool_dependency_dir>/environment_settings/TRINITY_MEM_OPTIONS/iuc/trinity/<hash_string>/env.sh
+In both cases, you can set the TRINITY_MAX_MEMORY environmental variable in the destination section of the job_conf.xml file:
 
-to lower the maximum memory usage to 2G for example:
+<?xml version="1.0"?>
+<!-- A sample job config that explicitly configures job running the way it is configured by default (if there is no explicit config). -->
+<job_conf>
+    <plugins>
+        <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/>
+    </plugins>
+    <handlers>
+        <handler id="main"/>
+    </handlers>
+    <destinations>
+        <destination id="local" runner="local">
+            <env id="TRINITY_MAX_MEMORY">1G</env>
+        </destination>
+    </destinations>
+</job_conf>
 
-TRINITY_MEM_OPTIONS='--max_memory 2G --bflyHeapSpaceMax 2G'
+
diff -r 7d1758a86884 -r 36681c1ad6d7 macros.xml
--- a/macros.xml	Thu Mar 23 10:15:57 2017 -0400
+++ b/macros.xml	Fri Mar 31 11:35:49 2017 -0400
@@ -2,18 +2,12 @@
 <macros>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="2.2.0">trinity</requirement>
+            <requirement type="package" version="2.4.0">trinity</requirement>
             <yield/>
         </requirements>
     </xml>
 
-    <token name="@WRAPPER_VERSION@">2.2.0</token>
-
-    <xml name="stdio">
-        <stdio>
-            <exit_code range="1:" level="fatal" description="Error in Trinity execution" />
-        </stdio>
-    </xml>
+    <token name="@WRAPPER_VERSION@">2.4.0</token>
 
     <xml name="citation">
         <citations>
diff -r 7d1758a86884 -r 36681c1ad6d7 samples_qccheck.xml
--- a/samples_qccheck.xml	Thu Mar 23 10:15:57 2017 -0400
+++ b/samples_qccheck.xml	Fri Mar 31 11:35:49 2017 -0400
@@ -1,16 +1,15 @@
-<tool id="trinity_samples_qccheck" name="RNASeq samples quality check" version="@WRAPPER_VERSION@.1">
+<tool id="trinity_samples_qccheck" name="RNASeq samples quality check" version="@WRAPPER_VERSION@.0">
     <description>for transcript quantification</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements">
-        <requirement type="package" version="2.30.0">bioconductor-biobase</requirement>
-        <requirement type="package" version="2.2.2">bioconductor-qvalue</requirement>
+        <requirement type="package" version="2.34.0">bioconductor-biobase</requirement>
+        <requirement type="package" version="2.6.0">bioconductor-qvalue</requirement>
     </expand>
-    <expand macro="stdio"/>
-    <command><![CDATA[
+    <command detect_errors="aggressive"><![CDATA[
 
-        ln -s "${matrix}" "input.matrix"
+        ln -f -s "${matrix}" "input.matrix"
 
         &&
 
diff -r 7d1758a86884 -r 36681c1ad6d7 test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results
--- a/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results	Thu Mar 23 10:15:57 2017 -0400
+++ b/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results	Fri Mar 31 11:35:49 2017 -0400
@@ -1,39 +1,38 @@
-id	baseMeanA	baseMeanB	baseMean	log2FoldChange	lfcSE	stat	pvalue	padj
-TR4277|c0_g1_i1	3852.97388871986	161.116814813422	2007.04535176664	-4.57259674791206	0.121601866332754	-37.6030145409076	0	0
-TR131|c0_g1_i1	26.1866396538608	1340.30918254958	683.247911101723	5.67372481552909	0.187406695960058	30.274931140872	2.45144211418965e-201	4.04487948841292e-200
-TR4761|c0_g1_i1	1645.20640957447	193.196157329029	919.201283451752	-3.08847487551254	0.143642016580712	-21.5011940728159	1.51733402752078e-102	1.66906743027286e-101
-TR3091|c0_g1_i1	16.7444693227929	328.569936894811	172.657203108802	4.29039998257063	0.240421038467916	17.8453599980735	3.14072644239509e-71	2.59109931497595e-70
-TR3638|c0_g1_i1	583.00358519031	183.754416330029	383.37900076017	-1.66018915730897	0.144484444213305	-11.4904352945982	1.47367477630653e-30	9.72625352362312e-30
-TR2487|c0_g1_i1	342.210853400436	920.407318992504	631.30908619647	1.42690938766606	0.124693202553469	11.4433614539188	2.5385551583546e-30	1.39620533709503e-29
-TR3788|c0_g1_i1	19.5075441237117	134.95369713876	77.2306206312357	2.77038513264018	0.262760026053246	10.5434040871909	5.44900939296595e-26	2.56881871382681e-25
-TR1479|c0_g1_i1	129.593534475689	371.064629188207	250.329081831948	1.51441163103673	0.145431922863633	10.4131995315551	2.1584296431011e-25	8.90352227779205e-25
-TR2107|c1_g1_i1	48.9228907410258	7.40521775805688	28.1640542495414	-2.6949883047084	0.431525668867458	-6.24525607429428	4.23106352657394e-10	1.55138995974378e-09
-TR3854|c0_g1_i1	1573.69549271337	2374.56159860719	1974.12854566028	0.593513416954248	0.111306645736399	5.33223701987958	9.70102011419466e-08	3.20133663768424e-07
-TR2122|c0_g2_i2	119.534640490118	199.143666337033	159.339153413576	0.738656537188098	0.168436715892782	4.38536534788702	1.15791268060543e-05	3.47373804181628e-05
-TR1449|c0_g1_i1	180.814952011467	104.755290736358	142.785121373912	-0.784194659361461	0.185749133486416	-4.2217944420118	2.42365089281258e-05	6.61949164163031e-05
-TR4163|c0_g1_i1	347.283468916919	232.772947466212	290.028208191566	-0.576744528291395	0.137147958253208	-4.20527243450891	2.60767852549073e-05	6.61949164163031e-05
-TR2672|c0_g1_i1	18.3155337236093	2.26581902751323	10.2906763755613	-2.88818323474529	0.724350842979802	-3.98727117216294	6.68376171815065e-05	0.000157545811927837
-TR127|c1_g1_i1	13.461799216177	1.21881296083961	7.34030608850831	-3.33218181130749	0.914685635912973	-3.64298036448506	0.000269499403689035	0.000576210779000196
-TR5055|c0_g2_i1	23.3590211688541	5.52768338415684	14.4433522765055	-2.04478780320925	0.562727305023446	-3.63370994255211	0.00027937492315161	0.000576210779000196
-TR2844|c0_g1_i1	158.206282615139	231.762548186068	194.984415400603	0.550641897280872	0.154759496937021	3.55804915484414	0.000373619406412113	0.000725261200682336
-TR5212|c0_g1_i1	65.7079302129484	107.875371765755	86.7916509893515	0.713884138135847	0.209708011296715	3.40418152707468	0.000663626354411326	0.00121664831642076
-TR1894|c2_g1_i1	13.3497721959996	2.96749216411516	8.15863218005739	-2.04982326482473	0.714661961266818	-2.8682417365424	0.00412760030232129	0.00716898999876856
-TR24|c0_g1_i1	69.9065207344592	41.2394742844514	55.5729975094553	-0.760369639593845	0.269117661787534	-2.8254170853868	0.00472191070589177	0.00779115266472142
-TR4669|c0_g2_i1	0	167.096667347181	83.5483336735905	4.37844609928899	2.00484514683835	2.18393231327309	0.0289672221614669	0.0455199205394479
-TR2779|c0_g1_i1	155.915506826481	205.619872596257	180.767689711369	0.402360429872658	0.188906223389576	2.12994798505331	0.0331759079102528	0.0497638618653791
-TR1492|c0_g1_i2	1640.89375005483	1435.64893261411	1538.27134133447	-0.192484740220531	0.101376439014472	-1.89871277874588	0.0576022504671541	0.0796285639028554
-TR3807|c0_g1_i1	3.48709246029019	0.350050334268211	1.9185713972792	-2.70461238638113	1.4262081182078	-1.89636586123194	0.0579116828384403	0.0796285639028554
-TR4084|c0_g1_i1	93.2264707954139	121.352438036668	107.289454416041	0.3802042378315	0.213056828958299	1.78452030704877	0.0743391580521785	0.0981276886288757
-TR1891|c0_g1_i1	107.628573623499	135.399287466928	121.513930545214	0.328806752550927	0.189034600977243	1.73939982866159	0.0819644583677276	0.104031812543654
-TR1837|c2_g1_i1	0.308903905435236	2.22601224010275	1.26745807276899	2.42365647560727	1.53486167088074	1.57907160077593	0.114319634794044	1
-TR5075|c0_g1_i1	15.8633018853512	9.23822794034992	12.5507649128506	-0.764079585128418	0.506894456921462	-1.50737411840904	0.131714788977897	0.158065100778825
-TR4859|c0_g1_i1	7.32690480813971	3.17910584569163	5.25300532691567	-1.18284590433612	0.789581441931072	-1.49806700299749	0.134115843085064	0.158065100778825
-TR939|c0_g1_i1	84.2568220960088	96.9171174594069	90.5869697777078	0.202696971338398	0.202184598546511	1.00253418309589	0.316085665578007	0.354180332604713
-TR2278|c0_g1_i1	486.5272515724	448.140178813055	467.333715192727	-0.118822731208233	0.119975347874694	-0.990392887481645	0.321982120549739	0.354180332604713
-TR2011|c5_g1_i1	5.60408627995835	7.88255079488408	6.74331853742122	0.488779860259128	0.689341019893534	0.70905378637502	0.478291099766969	0.509148590074515
-TR2182|c3_g2_i6	2.24974854180929	1.3031439398571	1.77644624083319	-0.780861388045469	1.28191780274725	-0.609135302101293	0.54243475986365	0.559385846109389
-TR3249|c0_g1_i1	1.12573841927462	2.128954842887	1.62734663108081	0.761533075632955	1.28978972955114	0.590431958159547	0.554901090261946	1
-TR1678|c0_g1_i1	0.595141051681226	0.700100668536423	0.647620860108824	0.247986780508542	1.73527723872539	0.142909026277954	0.886362029808798	1
-TR1122|c0_g1_i1	1.41370386226057	1.3031439398571	1.35842390105883	-0.16283641618004	1.43170451886811	-0.113736049606644	0.909447034479058	1
-TR1982|c2_g1_i1	5.73684100209948	5.71221669652109	5.72452884931028	0.0102126833240523	0.713573951255734	0.0143120181252136	0.988581051536513	0.988581051536513
-TR2090|c0_g1_i1	0	9.55638889228537	4.77819444614269	3.06235120305875	2.04796345977052	1.49531535264887	NA	1
+sampleA	sampleB	baseMeanA	baseMeanB	baseMean	log2FoldChange	lfcSE	stat	pvalue	padj
+TR4277|c0_g1_i1	wt_37	wt_GSNO	3852.97388871986	161.116814813422	2007.04535176664	4.57260002898197	0.121471586836965	37.6433711623376	0	0
+TR131|c0_g1_i1	wt_37	wt_GSNO	26.1866396538608	1340.30918254958	683.247911101723	-5.67373033438939	0.187375754459626	-30.2799599166492	2.10486694333775e-201	3.89400384517483e-200
+TR4761|c0_g1_i1	wt_37	wt_GSNO	1645.20640957447	193.196157329029	919.201283451752	3.08848040390227	0.143569117275296	21.5121501233448	1.19819880470067e-102	1.47777852579749e-101
+TR3091|c0_g1_i1	wt_37	wt_GSNO	16.7444693227929	328.569936894811	172.657203108802	-4.29037251456992	0.240582794801874	-17.8332474610379	3.90090325510546e-71	3.60833551097255e-70
+TR3638|c0_g1_i1	wt_37	wt_GSNO	583.00358519031	183.754416330029	383.37900076017	1.66018954854466	0.144513974558734	11.4880900176883	1.51422805973163e-30	1.12052876420141e-29
+TR2487|c0_g1_i1	wt_37	wt_GSNO	342.210853400436	920.407318992504	631.30908619647	-1.42691086642688	0.124648977132644	-11.4474334186348	2.42211055832184e-30	1.49363484429847e-29
+TR3788|c0_g1_i1	wt_37	wt_GSNO	19.5075441237117	134.95369713876	77.2306206312357	-2.77036684869735	0.263152237265066	-10.527620351967	6.4442989603998e-26	3.40627230763989e-25
+TR1479|c0_g1_i1	wt_37	wt_GSNO	129.593534475689	371.064629188207	250.329081831948	-1.51441062491813	0.145530800926874	-10.4061175728641	2.32511621828936e-25	1.07536625095883e-24
+TR2107|c1_g1_i1	wt_37	wt_GSNO	48.9228907410258	7.40521775805688	28.1640542495414	2.69488884014666	0.432209832999676	6.23514005094067	4.51374085119887e-10	1.85564901660398e-09
+TR3854|c0_g1_i1	wt_37	wt_GSNO	1573.69549271337	2374.56159860719	1974.12854566028	-0.593515573382884	0.111170659243154	-5.33877893163104	9.35746583039244e-08	3.4622623572452e-07
+TR2122|c0_g2_i2	wt_37	wt_GSNO	119.534640490118	199.143666337033	159.339153413576	-0.738644008220832	0.168659021315898	-4.37951081690053	1.18946017688789e-05	4.00091150407745e-05
+TR1449|c0_g1_i1	wt_37	wt_GSNO	180.814952011467	104.755290736358	142.785121373912	0.784193680180578	0.186004942516637	4.21598302480827	2.48692468039376e-05	7.49709472786912e-05
+TR4163|c0_g1_i1	wt_37	wt_GSNO	347.283468916919	232.772947466212	290.028208191566	0.576743600823335	0.13722219355458	4.20299068163444	2.63411436384591e-05	7.49709472786912e-05
+TR2672|c0_g1_i1	wt_37	wt_GSNO	18.3155337236093	2.26581902751323	10.2906763755613	2.88788179640237	0.725539563189254	3.98032298019437	6.88216980025882e-05	0.000181885916149697
+TR127|c1_g1_i1	wt_37	wt_GSNO	13.461799216177	1.21881296083961	7.34030608850831	3.33150202228086	0.915899815581865	3.63740877070095	0.000275394687501815	0.000667511143840185
+TR5055|c0_g2_i1	wt_37	wt_GSNO	23.3590211688541	5.52768338415684	14.4433522765055	2.04460941512382	0.563987307210913	3.62527558507482	0.000288653467606567	0.000667511143840185
+TR2844|c0_g1_i1	wt_37	wt_GSNO	158.206282615139	231.762548186068	194.984415400603	-0.550639207704626	0.154913717539885	-3.55448966333699	0.000378713397971402	0.000824258572055403
+TR5212|c0_g1_i1	wt_37	wt_GSNO	65.7079302129484	107.875371765755	86.7916509893515	-0.713874873222434	0.210087143945163	-3.39799408862815	0.000678818868686303	0.00139534989674407
+TR1894|c2_g1_i1	wt_37	wt_GSNO	13.3497721959996	2.96749216411516	8.15863218005739	2.04972102673103	0.716146945354672	2.86215146210796	0.00420775772107294	0.00819405450945783
+TR24|c0_g1_i1	wt_37	wt_GSNO	69.9065207344592	41.2394742844514	55.5729975094553	0.760351613917761	0.269735390145923	2.81887969356346	0.00481915767774413	0.00891544170382664
+TR2779|c0_g1_i1	wt_37	wt_GSNO	155.915506826481	205.619872596257	180.767689711369	-0.402350189521528	0.18910416680051	-2.12766432558821	0.0333649247395808	0.0587858197792614
+TR3807|c0_g1_i1	wt_37	wt_GSNO	3.48709246029019	0.350050334268211	1.9185713972792	2.6523001983829	1.38324824664578	1.91744338358239	0.055181627150862	0.092164962039527
+TR1492|c0_g1_i2	wt_37	wt_GSNO	1640.89375005483	1435.64893261411	1538.27134133447	0.192484568368337	0.101250195527162	1.90107848548993	0.057291733159706	0.092164962039527
+TR4084|c0_g1_i1	wt_37	wt_GSNO	93.2264707954139	121.352438036668	107.289454416041	-0.380198430346905	0.213412163689062	-1.78152183912463	0.0748272403991533	0.115358662282028
+TR1891|c0_g1_i1	wt_37	wt_GSNO	107.628573623499	135.399287466928	121.513930545214	-0.328810062058933	0.189329296532127	-1.73670989161013	0.0824383909023624	0.122008818535496
+TR4669|c0_g2_i1	wt_37	wt_GSNO	0	167.096667347181	83.5483336735905	-3.46077834317638	2.04233842282563	-1.69451757088734	0.0901669757000038	0.128314542342313
+TR1837|c2_g1_i1	wt_37	wt_GSNO	0.308903905435236	2.22601224010275	1.26745807276899	-2.41951712666755	1.51166579847997	-1.60056351681732	0.1094736282342	0.150019416469089
+TR5075|c0_g1_i1	wt_37	wt_GSNO	15.8633018853512	9.23822794034992	12.5507649128506	0.764028730403883	0.508108615055784	1.50367206491864	0.132665825459353	0.172493073735055
+TR4859|c0_g1_i1	wt_37	wt_GSNO	7.32690480813971	3.17910584569163	5.25300532691567	1.18248087647214	0.791530422232021	1.49391715499409	0.135197274008557	0.172493073735055
+TR939|c0_g1_i1	wt_37	wt_GSNO	84.2568220960088	96.9171174594069	90.5869697777078	-0.202690605185084	0.202556787736977	-1.00066064163834	0.316990901598642	0.384256032989688
+TR2278|c0_g1_i1	wt_37	wt_GSNO	486.5272515724	448.140178813055	467.333715192727	0.118822806572317	0.119966033346418	0.99047041281427	0.321944243856225	0.384256032989688
+TR2011|c5_g1_i1	wt_37	wt_GSNO	5.60408627995835	7.88255079488408	6.74331853742122	-0.48861876789566	0.691406970296359	-0.706702114510391	0.479751615248569	0.554712805131158
+TR2182|c3_g2_i6	wt_37	wt_GSNO	2.24974854180929	1.3031439398571	1.77644624083319	0.779605221657958	1.28583289420755	0.606303684693354	0.544313112275579	0.605163179078445
+TR3249|c0_g1_i1	wt_37	wt_GSNO	1.12573841927462	2.128954842887	1.62734663108081	-0.761341397480685	1.29336792501876	-0.58865028485196	0.556095894288301	0.605163179078445
+TR1678|c0_g1_i1	wt_37	wt_GSNO	0.595141051681226	0.700100668536423	0.647620860108824	-0.247288262290953	1.73789746083653	-0.14229162989393	0.886849657633351	0.935371730620685
+TR1122|c0_g1_i1	wt_37	wt_GSNO	1.41370386226057	1.3031439398571	1.35842390105883	0.162148276801819	1.43591594510694	0.112923237153511	0.910091413576882	0.935371730620685
+TR1982|c2_g1_i1	wt_37	wt_GSNO	5.73684100209948	5.71221669652109	5.72452884931028	-0.0101267142582557	0.715373046105777	-0.0141558510114153	0.988705642243408	0.988705642243408
diff -r 7d1758a86884 -r 36681c1ad6d7 test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.count_matrix
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.count_matrix	Fri Mar 31 11:35:49 2017 -0400
@@ -0,0 +1,38 @@
+wt_37_1	wt_37_2	wt_37_3	wt_GSNO_1	wt_GSNO_2	wt_GSNO_3
+TR24|c0_g1_i1	85	90	67	35	34	36
+TR2779|c0_g1_i1	217	186	137	186	197	147
+TR127|c1_g1_i1	16	9	23	0	1	2
+TR2107|c1_g1_i1	47	59	65	6	7	6
+TR2011|c5_g1_i1	4	11	4	5	7	8
+TR4163|c0_g1_i1	425	368	422	216	210	172
+TR5055|c0_g2_i1	27	36	17	7	3	4
+TR1449|c0_g1_i1	207	196	230	113	91	66
+TR1982|c2_g1_i1	6	7	7	3	8	4
+TR1492|c0_g1_i2	1921	1895	1906	1263	1319	1104
+TR1122|c0_g1_i1	0	2	3	0	0	3
+TR2278|c0_g1_i1	598	497	610	406	413	333
+TR4084|c0_g1_i1	86	95	148	111	127	77
+TR4761|c0_g1_i1	1875	2089	1746	174	165	155
+TR3638|c0_g1_i1	712	647	676	184	174	117
+TR3854|c0_g1_i1	1864	1878	1734	2173	2151	1775
+TR131|c0_g1_i1	31	32	28	1233	1208	1001
+TR5075|c0_g1_i1	21	13	22	8	10	6
+TR2182|c3_g2_i6	4	1	3	0	0	3
+TR3788|c0_g1_i1	22	17	30	132	125	91
+TR4859|c0_g1_i1	8	6	12	1	3	4
+TR2487|c0_g1_i1	424	386	383	866	806	689
+TR2122|c0_g2_i2	136	145	135	157	201	155
+TR4277|c0_g1_i1	4284	4466	4701	134	164	118
+TR4669|c0_g2_i1	0	0	0	0	218	209
+TR3091|c0_g1_i1	19	22	17	308	284	250
+TR3807|c0_g1_i1	2	6	4	0	1	0
+TR1894|c2_g1_i1	11	21	14	2	5	1
+TR5212|c0_g1_i1	78	64	89	98	108	73
+TR939|c0_g1_i1	99	96	99	89	88	72
+TR1891|c0_g1_i1	124	115	138	139	111	97
+TR2672|c0_g1_i1	22	14	29	4	2	0
+TR2844|c0_g1_i1	178	166	211	214	223	161
+TR1837|c2_g1_i1	0	1	0	1	4	1
+TR1678|c0_g1_i1	1	1	0	0	2	0
+TR3249|c0_g1_i1	1	1	2	1	0	4
+TR1479|c0_g1_i1	141	136	178	324	354	277
diff -r 7d1758a86884 -r 36681c1ad6d7 test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.edgeR.count_matrix
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.edgeR.count_matrix	Fri Mar 31 11:35:49 2017 -0400
@@ -0,0 +1,38 @@
+wt_37_1	wt_37_2	wt_37_3	wt_GSNO_1	wt_GSNO_2	wt_GSNO_3
+TR24|c0_g1_i1	85	90	67	35	34	36
+TR2779|c0_g1_i1	217	186	137	186	197	147
+TR127|c1_g1_i1	16	9	23	0	1	2
+TR2107|c1_g1_i1	47	59	65	6	7	6
+TR2011|c5_g1_i1	4	11	4	5	7	8
+TR4163|c0_g1_i1	425	368	422	216	210	172
+TR5055|c0_g2_i1	27	36	17	7	3	4
+TR1449|c0_g1_i1	207	196	230	113	91	66
+TR1982|c2_g1_i1	6	7	7	3	8	4
+TR1492|c0_g1_i2	1921	1895	1906	1263	1319	1104
+TR1122|c0_g1_i1	0	2	3	0	0	3
+TR2278|c0_g1_i1	598	497	610	406	413	333
+TR4084|c0_g1_i1	86	95	148	111	127	77
+TR4761|c0_g1_i1	1875	2089	1746	174	165	155
+TR3638|c0_g1_i1	712	647	676	184	174	117
+TR3854|c0_g1_i1	1864	1878	1734	2173	2151	1775
+TR131|c0_g1_i1	31	32	28	1233	1208	1001
+TR5075|c0_g1_i1	21	13	22	8	10	6
+TR2182|c3_g2_i6	4	1	3	0	0	3
+TR3788|c0_g1_i1	22	17	30	132	125	91
+TR4859|c0_g1_i1	8	6	12	1	3	4
+TR2487|c0_g1_i1	424	386	383	866	806	689
+TR2122|c0_g2_i2	136	145	135	157	201	155
+TR4277|c0_g1_i1	4284	4466	4701	134	164	118
+TR4669|c0_g2_i1	0	0	0	0	218	209
+TR3091|c0_g1_i1	19	22	17	308	284	250
+TR3807|c0_g1_i1	2	6	4	0	1	0
+TR1894|c2_g1_i1	11	21	14	2	5	1
+TR5212|c0_g1_i1	78	64	89	98	108	73
+TR939|c0_g1_i1	99	96	99	89	88	72
+TR1891|c0_g1_i1	124	115	138	139	111	97
+TR2672|c0_g1_i1	22	14	29	4	2	0
+TR2844|c0_g1_i1	178	166	211	214	223	161
+TR1837|c2_g1_i1	0	1	0	1	4	1
+TR1678|c0_g1_i1	1	1	0	0	2	0
+TR3249|c0_g1_i1	1	1	2	1	0	4
+TR1479|c0_g1_i1	141	136	178	324	354	277
diff -r 7d1758a86884 -r 36681c1ad6d7 test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.voom.count_matrix
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.voom.count_matrix	Fri Mar 31 11:35:49 2017 -0400
@@ -0,0 +1,38 @@
+wt_37_1	wt_37_2	wt_37_3	wt_GSNO_1	wt_GSNO_2	wt_GSNO_3
+TR24|c0_g1_i1	85	90	67	35	34	36
+TR2779|c0_g1_i1	217	186	137	186	197	147
+TR127|c1_g1_i1	16	9	23	0	1	2
+TR2107|c1_g1_i1	47	59	65	6	7	6
+TR2011|c5_g1_i1	4	11	4	5	7	8
+TR4163|c0_g1_i1	425	368	422	216	210	172
+TR5055|c0_g2_i1	27	36	17	7	3	4
+TR1449|c0_g1_i1	207	196	230	113	91	66
+TR1982|c2_g1_i1	6	7	7	3	8	4
+TR1492|c0_g1_i2	1921	1895	1906	1263	1319	1104
+TR1122|c0_g1_i1	0	2	3	0	0	3
+TR2278|c0_g1_i1	598	497	610	406	413	333
+TR4084|c0_g1_i1	86	95	148	111	127	77
+TR4761|c0_g1_i1	1875	2089	1746	174	165	155
+TR3638|c0_g1_i1	712	647	676	184	174	117
+TR3854|c0_g1_i1	1864	1878	1734	2173	2151	1775
+TR131|c0_g1_i1	31	32	28	1233	1208	1001
+TR5075|c0_g1_i1	21	13	22	8	10	6
+TR2182|c3_g2_i6	4	1	3	0	0	3
+TR3788|c0_g1_i1	22	17	30	132	125	91
+TR4859|c0_g1_i1	8	6	12	1	3	4
+TR2487|c0_g1_i1	424	386	383	866	806	689
+TR2122|c0_g2_i2	136	145	135	157	201	155
+TR4277|c0_g1_i1	4284	4466	4701	134	164	118
+TR4669|c0_g2_i1	0	0	0	0	218	209
+TR3091|c0_g1_i1	19	22	17	308	284	250
+TR3807|c0_g1_i1	2	6	4	0	1	0
+TR1894|c2_g1_i1	11	21	14	2	5	1
+TR5212|c0_g1_i1	78	64	89	98	108	73
+TR939|c0_g1_i1	99	96	99	89	88	72
+TR1891|c0_g1_i1	124	115	138	139	111	97
+TR2672|c0_g1_i1	22	14	29	4	2	0
+TR2844|c0_g1_i1	178	166	211	214	223	161
+TR1837|c2_g1_i1	0	1	0	1	4	1
+TR1678|c0_g1_i1	1	1	0	0	2	0
+TR3249|c0_g1_i1	1	1	2	1	0	4
+TR1479|c0_g1_i1	141	136	178	324	354	277
diff -r 7d1758a86884 -r 36681c1ad6d7 test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results
--- a/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results	Thu Mar 23 10:15:57 2017 -0400
+++ b/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results	Fri Mar 31 11:35:49 2017 -0400
@@ -1,39 +1,39 @@
-id	baseMeanA	baseMeanB	baseMean	log2FoldChange	lfcSE	stat	pvalue	padj
-TR4277|c0_g1_i1	4705.34614971641	162.902721493704	2434.12443560506	-4.84860951090545	0.124597307945428	-38.9142397284305	0	0
-TR131|c0_g1_i1	32.0461070493257	1436.30905989883	734.177583474076	5.48367743370229	0.196017912869615	27.9753893581648	3.23827538807456e-172	6.15272323734167e-171
-TR4761|c0_g1_i1	2012.6141923276	384.620292965437	1198.61724264652	-2.38450946693381	0.143863830576436	-16.5747669680385	1.06073316501088e-61	1.34359534234711e-60
-TR3091|c0_g1_i1	20.4914097091341	321.651020117047	171.071214913091	3.96886910507283	0.256323110469072	15.4838519937191	4.45952081812589e-54	4.2365447772196e-53
-TR2779|c0_g1_i1	191.51955185349	1058.15934185376	624.839446853626	2.46616535412611	0.177102083131526	13.9251064161374	4.4587691300744e-44	3.38866453885655e-43
-TR1492|c0_g1_i2	2006.11782336441	890.823502721036	1448.47066304272	-1.17029110983798	0.12207086547883	-9.58698134274255	9.06997941755552e-22	5.74432029778516e-21
-TR5075|c0_g1_i1	19.3833722195684	136.98672801182	78.1850501156942	2.80049241151413	0.293976352213923	9.52625063350759	1.63066468983638e-21	8.85217974482605e-21
-TR1891|c0_g1_i1	131.416087212132	376.595292171713	254.005689691923	1.51493508389526	0.17090866237033	8.86400409952692	7.71909159725621e-19	3.6665685086967e-18
-TR2487|c0_g1_i1	418.818667162757	965.862817209246	692.340742186001	1.20547893236143	0.136832960243688	8.80985787499278	1.25304626500959e-18	5.29063978559604e-18
-TR3638|c0_g1_i1	713.131183384274	326.063958913919	519.597571149096	-1.1281436752687	0.141731779309567	-7.95970868893582	1.72444792020844e-15	6.55290209679206e-15
-TR2107|c1_g1_i1	59.5986596731862	1.89840873462066	30.7485342039034	-4.81058600791914	0.641850436461167	-7.49487066557473	6.63637683134955e-14	2.29256654173894e-13
-TR2122|c0_g2_i2	146.135958637131	360.821667264163	253.478812950647	1.30334955915215	0.177300500792357	7.35107658087526	1.96616724778278e-13	6.22619628464548e-13
-TR1479|c0_g1_i1	158.005105094407	334.827472148091	246.416288621249	1.07882286721986	0.173458235018578	6.2194963940704	4.98753084614221e-10	1.45789363194926e-09
-TR24|c0_g1_i1	85.6614643869141	199.923709280262	142.792586833588	1.22623657127381	0.213504266341901	5.74338205172044	9.2804014146814e-09	2.51896609827067e-08
-TR4163|c0_g1_i1	424.593720981574	227.471218917767	326.03246994967	-0.900786056392834	0.160721595544993	-5.60463609969988	2.08692952426197e-08	5.28688812813031e-08
-TR2278|c0_g1_i1	594.657329919233	348.341653317169	471.499491618201	-0.772446091346236	0.159105007190944	-4.85494520244241	1.20420038267752e-06	2.79113819122931e-06
-TR1449|c0_g1_i1	220.782434528097	117.26089394399	169.021664236043	-0.913694497348233	0.188477876305836	-4.84775462911953	1.24866708554995e-06	2.79113819122931e-06
-TR127|c1_g1_i1	16.3791628279609	1.58772512712498	8.98344397754296	-3.19771077466237	0.834376974262452	-3.83245328346816	0.00012687169720824	0.000267840249661839
-TR1894|c2_g1_i1	16.2826445742552	1.67571344127509	8.97917900776516	-3.15659686337855	0.834779400611257	-3.7813545244015	0.00015597736029041	0.000307529893573321
-TR5055|c0_g2_i1	28.6665933385886	6.05959103586122	17.3630921872249	-2.17768048931004	0.577307428800381	-3.77213314894485	0.000161857838722801	0.000307529893573321
-TR4084|c0_g1_i1	113.2594381118	173.837287636503	143.548362874151	0.609755827935052	0.219803235717165	2.7740985065373	0.00553549140639085	0.00984268771318224
-TR2090|c0_g1_i1	0	5.87877087384675	2.93938543692337	4.81114433617716	1.74023660764341	2.76464953963491	0.00569839814973709	0.00984268771318224
-TR1678|c0_g1_i1	0.738899982352077	7.85275634721875	4.29582816478541	3.12892233414853	1.14660116223239	2.72886722708063	0.00635522860739327	0.0104999429165628
-TR4859|c0_g1_i1	8.91205730249659	1.28188505334354	5.09697117792006	-2.61274053843141	0.973661400721484	-2.68341801009608	0.00728738414676855	0.0115383582323835
-TR2672|c0_g1_i1	22.3129914439134	7.89947501226409	15.1062332280887	-1.45907440559266	0.562189545530202	-2.59534247335852	0.0094496708578661	0.0143634997039565
-TR3807|c0_g1_i1	4.23896204531587	0.352255997713617	2.29560902151474	-3.05008419968594	1.43726100452922	-2.12215052803511	0.0338250994349076	0.0494366837894803
-TR3249|c0_g1_i1	1.36481976577862	4.37661229401476	2.87071602989669	1.51948727816201	1.15409756308282	1.31660210260141	0.187972033660362	0.255148785128113
-TR1859|c3_g1_i1	0.361569353912422	2.25550826604853	1.30853880998047	2.09887277242766	1.59427549709957	1.31650569568817	0.188004367989136	0.255148785128113
-TR1982|c2_g1_i1	7.00144976454503	11.520013112092	9.26073143831853	0.70490953188932	0.647715898283926	1.0883004937148	0.276462472665158	0.362261171078483
-TR3854|c0_g1_i1	1925.26464813324	2107.16376011081	2016.21420412203	0.130534071096341	0.124633726123269	1.04734147936199	0.29494211171073	0.373593341500258
-TR5212|c0_g1_i1	80.2050001877881	94.8352723753388	87.5201362815635	0.236773654582184	0.240888724170321	0.982917134862537	0.325648223857982	0.399181693761397
-TR1837|c2_g1_i1	0.377330628439655	1.67813520813222	1.02773291828594	1.63744709452968	1.70484764845029	0.960465350682869	0.336821061516539	0.39997501055089
-TR2844|c0_g1_i1	193.030766468894	213.82243412349	203.426600296192	0.144163413939115	0.182129405153131	0.791543868591151	0.428626687374099	0.493570124855023
-TR1122|c0_g1_i1	1.69354093201913	0.660517838352177	1.17702938518565	-1.10951489814723	1.57444243758247	-0.704703374135971	0.48099485111646	0.537582480659573
-TR2011|c5_g1_i1	6.84875389533898	4.81927837273561	5.8340161340373	-0.467994718304978	0.83497566164615	-0.560489053516039	0.575145904101733	0.62444412445331
-TR2182|c3_g2_i6	2.76248771922916	1.94482465855284	2.353656188891	-0.463555959442342	1.17585679724627	-0.394228243207794	0.69341253558072	0.731935454224094
-TR3788|c0_g1_i1	23.7579432209456	26.0024682525169	24.8802057367313	0.125242792795277	0.407913046833573	0.307033064442226	0.75881820512208	0.779326805260514
-TR939|c0_g1_i1	103.002135647151	102.820214322362	102.911174984756	-0.00127076378479059	0.216917077821033	-0.00585829293643274	0.995325785249569	0.995325785249569
+sampleA	sampleB	baseMeanA	baseMeanB	baseMean	log2FoldChange	lfcSE	stat	pvalue	padj
+TR4277|c0_g1_i1	wt_37	wt_ph8	4705.34614971641	162.902721493704	2434.12443560506	4.84804012036106	0.130783542648097	37.0691909868646	8.81406568413535e-301	3.34934495997143e-299
+TR131|c0_g1_i1	wt_37	wt_ph8	32.0461070493257	1436.30905989883	734.177583474076	-5.48335951236111	0.197548955320184	-27.7569653733364	1.43583336471356e-169	2.72808339295576e-168
+TR3091|c0_g1_i1	wt_37	wt_ph8	20.4914097091341	321.651020117047	171.071214913091	-3.97084930318667	0.245881056057371	-16.1494722971263	1.14537343838751e-58	1.45080635529084e-57
+TR4761|c0_g1_i1	wt_37	wt_ph8	2012.6141923276	384.620292965437	1198.61724264652	2.38432084623308	0.148099583891604	16.0994432501458	2.57410332221217e-58	2.44539815610156e-57
+TR5075|c0_g1_i1	wt_37	wt_ph8	19.3833722195684	136.98672801182	78.1850501156942	-2.80247674171473	0.269715041166808	-10.3905096637956	2.73885623424733e-25	2.08153073802797e-24
+TR2779|c0_g1_i1	wt_37	wt_ph8	191.51955185349	1058.15934185376	624.839446853626	-2.45909834872711	0.247058756007882	-9.95349603658112	2.43476309780354e-23	1.54201662860891e-22
+TR1891|c0_g1_i1	wt_37	wt_ph8	131.416087212132	376.595292171713	254.005689691923	-1.51504907455703	0.163541333568612	-9.26401320997792	1.96889433896152e-20	1.06882835543625e-19
+TR1492|c0_g1_i2	wt_37	wt_ph8	2006.11782336441	890.823502721036	1448.47066304272	1.17018000582475	0.127273970398445	9.19418167093695	3.77859650812701e-20	1.79483334136033e-19
+TR2487|c0_g1_i1	wt_37	wt_ph8	418.818667162757	965.862817209246	692.340742186001	-1.2054117169244	0.138501088570193	-8.70326529104133	3.22468912161225e-18	1.36153540690295e-17
+TR3638|c0_g1_i1	wt_37	wt_ph8	713.131183384274	326.063958913919	519.597571149096	1.12815426477841	0.141332330235517	7.98228022490288	1.43654437320665e-15	5.45886861818526e-15
+TR2107|c1_g1_i1	wt_37	wt_ph8	59.5986596731862	1.89840873462066	30.7485342039034	4.82151434610286	0.613172060454942	7.86323229164347	3.74345886500564e-15	1.29319488063831e-14
+TR2122|c0_g2_i2	wt_37	wt_ph8	146.135958637131	360.821667264163	253.478812950647	-1.30371385707787	0.169650604759161	-7.68469914344628	1.53356953387865e-14	4.85630352394907e-14
+TR1479|c0_g1_i1	wt_37	wt_ph8	158.005105094407	334.827472148091	246.416288621249	-1.0787542477693	0.165556938369539	-6.51591083039607	7.22498877976404e-11	2.1119197971618e-10
+TR24|c0_g1_i1	wt_37	wt_ph8	85.6614643869141	199.923709280262	142.792586833588	-1.2279226670979	0.196562275775691	-6.24699048814003	4.18436531652641e-10	1.13575630020003e-09
+TR4163|c0_g1_i1	wt_37	wt_ph8	424.593720981574	227.471218917767	326.03246994967	0.900981410818221	0.155876696706134	5.78009048085484	7.46604610022994e-09	1.89139834539158e-08
+TR1449|c0_g1_i1	wt_37	wt_ph8	220.782434528097	117.26089394399	169.021664236043	0.914395516820343	0.174920034977504	5.22750591113215	1.71811907274331e-07	4.08053279776536e-07
+TR2278|c0_g1_i1	wt_37	wt_ph8	594.657329919233	348.341653317169	471.499491618201	0.772496794598277	0.157892732036131	4.89254182023719	9.95419556957436e-07	2.2250554802578e-06
+TR5055|c0_g2_i1	wt_37	wt_ph8	28.6665933385886	6.05959103586122	17.3630921872249	2.18372312866756	0.505600668447204	4.31906693354301	1.5669025864333e-05	3.30790546024808e-05
+TR127|c1_g1_i1	wt_37	wt_ph8	16.3791628279609	1.58772512712498	8.98344397754296	3.22742307122337	0.758365755070441	4.25576056097574	2.08339575851481e-05	4.16679151702962e-05
+TR1894|c2_g1_i1	wt_37	wt_ph8	16.2826445742552	1.67571344127509	8.97917900776516	3.18830464179373	0.7590595028564	4.20033558607184	2.66519649541344e-05	5.06387334128554e-05
+TR2672|c0_g1_i1	wt_37	wt_ph8	22.3129914439134	7.89947501226409	15.1062332280887	1.46563545973546	0.482353842293509	3.0385068620302	0.00237753690029721	0.00429545997952877
+TR4859|c0_g1_i1	wt_37	wt_ph8	8.91205730249659	1.28188505334354	5.09697117792006	2.65126611500267	0.876469721997014	3.02493748325022	0.00248684525130613	0.00429545997952877
+TR1678|c0_g1_i1	wt_37	wt_ph8	0.738899982352077	7.85275634721875	4.29582816478541	-3.18849648433777	1.0594001628342	-3.00971870327794	0.00261489744098202	0.00432026533727463
+TR4084|c0_g1_i1	wt_37	wt_ph8	113.2594381118	173.837287636503	143.548362874151	-0.608939120027998	0.203268581921877	-2.99573654851409	0.00273782859610482	0.00433489527716597
+TR3807|c0_g1_i1	wt_37	wt_ph8	4.23896204531587	0.352255997713617	2.29560902151474	3.15525660545126	1.31164110647326	2.4055792319098	0.0161468501576278	0.0245432122395943
+TR3249|c0_g1_i1	wt_37	wt_ph8	1.36481976577862	4.37661229401476	2.87071602989669	-1.55893212196469	1.01682768784581	-1.53313303777885	0.125243078950272	0.176625758092245
+TR1859|c3_g1_i1	wt_37	wt_ph8	0.361569353912422	2.25550826604853	1.30853880998047	-2.19284922770108	1.43126836745787	-1.53210206943641	0.125497249170806	0.176625758092245
+TR2090|c0_g1_i1	wt_37	wt_ph8	0	5.87877087384675	2.93938543692337	-2.86225136793822	1.9729684338102	-1.45073348305458	0.146854088052773	0.19930197664305
+TR1982|c2_g1_i1	wt_37	wt_ph8	7.00144976454503	11.520013112092	9.26073143831853	-0.712688609925078	0.555640746749963	-1.28264281209345	0.199617243880331	0.261567423015607
+TR1837|c2_g1_i1	wt_37	wt_ph8	0.377330628439655	1.67813520813222	1.02773291828594	-1.7572235261621	1.52690431775837	-1.15084062945205	0.249797806431129	0.316410554812763
+TR5212|c0_g1_i1	wt_37	wt_ph8	80.2050001877881	94.8352723753388	87.5201362815635	-0.23592411895009	0.215502649097795	-1.09476203628025	0.273620902411289	0.335406267471903
+TR3854|c0_g1_i1	wt_37	wt_ph8	1925.26464813324	2107.16376011081	2016.21420412203	-0.130483054839334	0.130739272627028	-0.998040238540833	0.318259846991125	0.377933568301961
+TR1122|c0_g1_i1	wt_37	wt_ph8	1.69354093201913	0.660517838352177	1.17702938518565	1.18649040337028	1.40558655511286	0.84412475279761	0.398599697111289	0.448776409473292
+TR2844|c0_g1_i1	wt_37	wt_ph8	193.030766468894	213.82243412349	203.426600296192	-0.143791883173722	0.17140940841448	-0.838879758723761	0.401536787423471	0.448776409473292
+TR2011|c5_g1_i1	wt_37	wt_ph8	6.84875389533898	4.81927837273561	5.8340161340373	0.467659672901774	0.714270969980296	0.654737057162879	0.512637061952329	0.556577381548243
+TR2182|c3_g2_i6	wt_37	wt_ph8	2.76248771922916	1.94482465855284	2.353656188891	0.479324872360299	1.02378035563408	0.468191120998245	0.639647921157653	0.675183916777523
+TR3788|c0_g1_i1	wt_37	wt_ph8	23.7579432209456	26.0024682525169	24.8802057367313	-0.124358222905796	0.350105186670918	-0.355202458119214	0.72243792333433	0.741963272613636
+TR939|c0_g1_i1	wt_37	wt_ph8	103.002135647151	102.820214322362	102.911174984756	0.000971215955472081	0.195414642848595	0.00497002651037041	0.996034508905975	0.996034508905975
diff -r 7d1758a86884 -r 36681c1ad6d7 test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.count_matrix
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.count_matrix	Fri Mar 31 11:35:49 2017 -0400
@@ -0,0 +1,39 @@
+wt_37_1	wt_37_2	wt_37_3	wt_ph8_1	wt_ph8_2	wt_ph8_3
+TR24|c0_g1_i1	85	90	67	196	201	222
+TR2779|c0_g1_i1	217	186	137	1094	1086	1088
+TR127|c1_g1_i1	16	9	23	1	1	3
+TR2107|c1_g1_i1	47	59	65	1	2	3
+TR2011|c5_g1_i1	4	11	4	4	8	3
+TR4163|c0_g1_i1	425	368	422	254	212	234
+TR5055|c0_g2_i1	27	36	17	4	11	4
+TR1449|c0_g1_i1	207	196	230	130	107	124
+TR1982|c2_g1_i1	6	7	7	9	11	16
+TR1859|c3_g1_i1	1	0	0	2	4	1
+TR1492|c0_g1_i2	1921	1895	1906	929	922	899
+TR1122|c0_g1_i1	0	2	3	1	0	1
+TR2278|c0_g1_i1	598	497	610	409	337	323
+TR4084|c0_g1_i1	86	95	148	201	158	175
+TR4761|c0_g1_i1	1875	2089	1746	389	406	394
+TR3638|c0_g1_i1	712	647	676	344	338	324
+TR2090|c0_g1_i1	0	0	0	0	9	10
+TR3854|c0_g1_i1	1864	1878	1734	2142	2155	2216
+TR131|c0_g1_i1	31	32	28	1492	1457	1486
+TR5075|c0_g1_i1	21	13	22	121	142	163
+TR2182|c3_g2_i6	4	1	3	2	3	1
+TR3788|c0_g1_i1	22	17	30	22	27	32
+TR4859|c0_g1_i1	8	6	12	1	2	1
+TR2487|c0_g1_i1	424	386	383	989	1032	963
+TR2122|c0_g2_i2	136	145	135	398	344	369
+TR4277|c0_g1_i1	4284	4466	4701	162	170	172
+TR3091|c0_g1_i1	19	22	17	343	316	333
+TR3807|c0_g1_i1	2	6	4	1	0	0
+TR1894|c2_g1_i1	11	21	14	3	1	1
+TR5212|c0_g1_i1	78	64	89	105	84	103
+TR939|c0_g1_i1	99	96	99	103	108	107
+TR1891|c0_g1_i1	124	115	138	411	384	365
+TR2672|c0_g1_i1	22	14	29	4	7	14
+TR2844|c0_g1_i1	178	166	211	245	213	199
+TR1837|c2_g1_i1	0	1	0	3	2	0
+TR1678|c0_g1_i1	1	1	0	10	6	8
+TR3249|c0_g1_i1	1	1	2	1	7	6
+TR1479|c0_g1_i1	141	136	178	363	302	367
diff -r 7d1758a86884 -r 36681c1ad6d7 test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.edgeR.count_matrix
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.edgeR.count_matrix	Fri Mar 31 11:35:49 2017 -0400
@@ -0,0 +1,39 @@
+wt_37_1	wt_37_2	wt_37_3	wt_ph8_1	wt_ph8_2	wt_ph8_3
+TR24|c0_g1_i1	85	90	67	196	201	222
+TR2779|c0_g1_i1	217	186	137	1094	1086	1088
+TR127|c1_g1_i1	16	9	23	1	1	3
+TR2107|c1_g1_i1	47	59	65	1	2	3
+TR2011|c5_g1_i1	4	11	4	4	8	3
+TR4163|c0_g1_i1	425	368	422	254	212	234
+TR5055|c0_g2_i1	27	36	17	4	11	4
+TR1449|c0_g1_i1	207	196	230	130	107	124
+TR1982|c2_g1_i1	6	7	7	9	11	16
+TR1859|c3_g1_i1	1	0	0	2	4	1
+TR1492|c0_g1_i2	1921	1895	1906	929	922	899
+TR1122|c0_g1_i1	0	2	3	1	0	1
+TR2278|c0_g1_i1	598	497	610	409	337	323
+TR4084|c0_g1_i1	86	95	148	201	158	175
+TR4761|c0_g1_i1	1875	2089	1746	389	406	394
+TR3638|c0_g1_i1	712	647	676	344	338	324
+TR2090|c0_g1_i1	0	0	0	0	9	10
+TR3854|c0_g1_i1	1864	1878	1734	2142	2155	2216
+TR131|c0_g1_i1	31	32	28	1492	1457	1486
+TR5075|c0_g1_i1	21	13	22	121	142	163
+TR2182|c3_g2_i6	4	1	3	2	3	1
+TR3788|c0_g1_i1	22	17	30	22	27	32
+TR4859|c0_g1_i1	8	6	12	1	2	1
+TR2487|c0_g1_i1	424	386	383	989	1032	963
+TR2122|c0_g2_i2	136	145	135	398	344	369
+TR4277|c0_g1_i1	4284	4466	4701	162	170	172
+TR3091|c0_g1_i1	19	22	17	343	316	333
+TR3807|c0_g1_i1	2	6	4	1	0	0
+TR1894|c2_g1_i1	11	21	14	3	1	1
+TR5212|c0_g1_i1	78	64	89	105	84	103
+TR939|c0_g1_i1	99	96	99	103	108	107
+TR1891|c0_g1_i1	124	115	138	411	384	365
+TR2672|c0_g1_i1	22	14	29	4	7	14
+TR2844|c0_g1_i1	178	166	211	245	213	199
+TR1837|c2_g1_i1	0	1	0	3	2	0
+TR1678|c0_g1_i1	1	1	0	10	6	8
+TR3249|c0_g1_i1	1	1	2	1	7	6
+TR1479|c0_g1_i1	141	136	178	363	302	367
diff -r 7d1758a86884 -r 36681c1ad6d7 test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.voom.count_matrix
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.voom.count_matrix	Fri Mar 31 11:35:49 2017 -0400
@@ -0,0 +1,39 @@
+wt_37_1	wt_37_2	wt_37_3	wt_ph8_1	wt_ph8_2	wt_ph8_3
+TR24|c0_g1_i1	85	90	67	196	201	222
+TR2779|c0_g1_i1	217	186	137	1094	1086	1088
+TR127|c1_g1_i1	16	9	23	1	1	3
+TR2107|c1_g1_i1	47	59	65	1	2	3
+TR2011|c5_g1_i1	4	11	4	4	8	3
+TR4163|c0_g1_i1	425	368	422	254	212	234
+TR5055|c0_g2_i1	27	36	17	4	11	4
+TR1449|c0_g1_i1	207	196	230	130	107	124
+TR1982|c2_g1_i1	6	7	7	9	11	16
+TR1859|c3_g1_i1	1	0	0	2	4	1
+TR1492|c0_g1_i2	1921	1895	1906	929	922	899
+TR1122|c0_g1_i1	0	2	3	1	0	1
+TR2278|c0_g1_i1	598	497	610	409	337	323
+TR4084|c0_g1_i1	86	95	148	201	158	175
+TR4761|c0_g1_i1	1875	2089	1746	389	406	394
+TR3638|c0_g1_i1	712	647	676	344	338	324
+TR2090|c0_g1_i1	0	0	0	0	9	10
+TR3854|c0_g1_i1	1864	1878	1734	2142	2155	2216
+TR131|c0_g1_i1	31	32	28	1492	1457	1486
+TR5075|c0_g1_i1	21	13	22	121	142	163
+TR2182|c3_g2_i6	4	1	3	2	3	1
+TR3788|c0_g1_i1	22	17	30	22	27	32
+TR4859|c0_g1_i1	8	6	12	1	2	1
+TR2487|c0_g1_i1	424	386	383	989	1032	963
+TR2122|c0_g2_i2	136	145	135	398	344	369
+TR4277|c0_g1_i1	4284	4466	4701	162	170	172
+TR3091|c0_g1_i1	19	22	17	343	316	333
+TR3807|c0_g1_i1	2	6	4	1	0	0
+TR1894|c2_g1_i1	11	21	14	3	1	1
+TR5212|c0_g1_i1	78	64	89	105	84	103
+TR939|c0_g1_i1	99	96	99	103	108	107
+TR1891|c0_g1_i1	124	115	138	411	384	365
+TR2672|c0_g1_i1	22	14	29	4	7	14
+TR2844|c0_g1_i1	178	166	211	245	213	199
+TR1837|c2_g1_i1	0	1	0	3	2	0
+TR1678|c0_g1_i1	1	1	0	10	6	8
+TR3249|c0_g1_i1	1	1	2	1	7	6
+TR1479|c0_g1_i1	141	136	178	363	302	367
diff -r 7d1758a86884 -r 36681c1ad6d7 test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results
--- a/test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results	Thu Mar 23 10:15:57 2017 -0400
+++ b/test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results	Fri Mar 31 11:35:49 2017 -0400
@@ -1,40 +1,40 @@
-id	baseMeanA	baseMeanB	baseMean	log2FoldChange	lfcSE	stat	pvalue	padj
-TR2779|c0_g1_i1	195.849684476753	966.924129135581	581.386906806167	2.25621220756415	0.156114979193812	14.4522467940961	2.42639762934434e-47	5.82335431042642e-46
-TR1891|c0_g1_i1	128.246229498835	343.028289972482	235.637259735659	1.40479466067472	0.104376051709838	13.4589749052781	2.72672776456232e-41	3.27207331747478e-40
-TR4761|c0_g1_i1	184.029205648389	351.782300021135	267.905752834762	0.934185686537064	0.0945413616088594	9.88123791152932	5.0208774429335e-23	4.0167019543468e-22
-TR24|c0_g1_i1	39.3724575919554	183.288101009647	111.330279300801	2.11680322693425	0.240338854880295	8.80757806717753	1.27878744153922e-18	7.67272464923531e-18
-TR3638|c0_g1_i1	174.266398355818	297.555274221606	235.910836288712	0.75598517202537	0.0975355931355663	7.75086455848598	9.12689947000201e-15	3.81892706573808e-14
-TR2122|c0_g2_i2	190.673533226329	328.707071692642	259.690302459485	0.782528370953275	0.101034702024136	7.74514454218254	9.54731766434521e-15	3.81892706573808e-14
-TR2278|c0_g1_i1	426.804298570637	315.99710709695	371.400702833793	-0.429046906426044	0.106511998284025	-4.02815563822158	5.62161256784655e-05	0.000192741002326167
-TR4084|c0_g1_i1	115.544575735664	157.970364768418	136.757470252041	0.435378746345168	0.157905703989027	2.75720721510747	0.00582973950434901	0.017489218513047
-TR3788|c0_g1_i1	128.115824993653	24.010679388938	76.0632521912957	-1.20076602288383	0.555078500739638	-2.16323640941564	0.0305230012251409	0.0813946699337092
-TR1678|c0_g1_i1	0.695005959508731	7.10082184137838	3.89791390044355	1.13542782611345	0.54389306361848	2.08759387104432	0.0368344853417399	1
-TR1859|c3_g1_i1	0	2.05957798928713	1.02978899464357	1.08547672488113	0.52169423531112	2.08067609609255	0.0374635634690378	1
-TR1479|c0_g1_i1	353.92669362375	305.546165789569	329.736429706659	-0.210273055725041	0.101401657889395	-2.07366487000044	0.0381104459877385	0.0914650703705724
-TR1492|c0_g1_i2	1368.89238848897	813.514514376559	1091.20345143276	-0.673957173112486	0.33643480733027	-2.00323259790084	0.0451523282811554	0.0985141707952481
-TR2844|c0_g1_i1	220.566338218013	194.214843050373	207.390590634193	-0.1851823349888	0.101213323108161	-1.8296240979155	0.0673061677634479	0.134612335526896
-TR5075|c0_g1_i1	8.81552188359314	126.23137395943	67.5234479215117	0.86620707327725	0.498591364017662	1.73730861741634	0.0823327113057556	0.151998851641395
-TR2107|c1_g1_i1	7.08292121571621	1.78415791317121	4.43353956444371	-0.87765751535477	0.553196716703176	-1.58651974759584	0.112621456124343	1
-TR2672|c0_g1_i1	2.07518941673641	7.44710458698621	4.76114700186131	0.652733502871168	0.537764458916032	1.21379070715621	0.224827655823799	1
-TR4859|c0_g1_i1	3.10763825129944	1.1806627783491	2.14415051482427	-0.587630876626665	0.551071114588281	-1.06634309269812	0.28626857627862	1
-TR3091|c0_g1_i1	312.47018793986	293.531643106953	303.000915523406	-0.0879738435317154	0.0902971665647824	-0.97427025540829	0.329922369379669	0.501282895914669
-TR4163|c0_g1_i1	221.469120691076	207.118822998308	214.293971844692	-0.0959599050588562	0.0987561344325879	-0.97168551209707	0.331207026506115	0.501282895914669
-TR4669|c0_g2_i1	165.630009730314	0	82.8150048651569	-0.322459466822447	0.333908718519009	-0.965711432311973	0.334188597276446	0.501282895914669
-TR1894|c2_g1_i1	2.85762748931802	1.47338219762144	2.16550484346973	-0.426208431542948	0.551264679640795	-0.773146634064541	0.439435604855973	1
-TR3249|c0_g1_i1	2.06512931203634	4.15451161800812	3.10982046502223	0.3941103325595	0.539435464341514	0.730597742661558	0.465024891244583	1
-TR5212|c0_g1_i1	102.736339436612	86.4452993262187	94.5908193814151	-0.222704356323449	0.346653224187607	-0.642441324021618	0.520586675617895	0.734945894989969
-TR1122|c0_g1_i1	1.29006258579706	0.5946183773076	0.942340481552333	-0.302591524122929	0.512417527863229	-0.590517512905403	0.554843748171664	1
-TR2011|c5_g1_i1	7.597917075274	4.42090354598533	6.00941031062966	-0.246737820349972	0.517913150509813	-0.476407714511773	0.633783939711306	1
-TR1837|c2_g1_i1	2.16507864525674	1.46465683073113	1.81486773799393	-0.235474161889615	0.546181064177423	-0.431128388246582	0.666375020163124	1
-TR2182|c3_g2_i6	1.29006258579706	1.76655578876639	1.52830918728173	0.209843639881372	0.537581597903129	0.390347513195914	0.696279593847798	1
-TR1449|c0_g1_i1	98.9943307118646	106.843279101242	102.918804906553	0.100194141469895	0.276715374273995	0.362083753867198	0.717289443676285	0.9108498942696
-TR4277|c0_g1_i1	153.969096204861	149.159426886469	151.564261545665	-0.0459267760105497	0.128823197370029	-0.356510139075578	0.721458560376159	0.9108498942696
-TR1982|c2_g1_i1	5.5352448786851	10.687042573374	8.11114372602957	0.110416157924497	0.359967068804195	0.306739608962835	0.759041578558	0.9108498942696
-TR127|c1_g1_i1	1.20754470361908	1.49113571265046	1.34934020813477	0.142968860758062	0.541343527667515	0.26410006484066	0.791702813929264	1
-TR3854|c0_g1_i1	2260.55060252051	1927.46472630351	2094.00766441201	-0.135348942475858	0.546438760787258	-0.247692792291784	0.804372109047297	0.919282410339768
-TR2090|c0_g1_i1	9.46045896251181	5.6546754787973	7.55756722065455	-0.0586395744056909	0.302337767579782	-0.193953851267414	0.846212017000596	1
-TR3807|c0_g1_i1	0.347502979754365	0.292870809896544	0.320186894825454	-0.0640837282416973	0.445995787050203	-0.143686846608001	0.885747758296628	1
-TR131|c0_g1_i1	1275.67603302799	1312.2934796972	1293.9847563626	0.0343724958045096	0.405262489992082	0.0848153891695754	0.932408158838271	0.963782835492881
-TR5055|c0_g2_i1	5.17791343714095	5.60171771495863	5.38981557604979	0.043552763660028	0.53975688204026	0.0806895939805349	0.935688812631814	1
-TR939|c0_g1_i1	92.2508462008296	94.0990807885678	93.1749634946987	0.0253693962827489	0.353966153466169	0.0716718139130601	0.942863087697354	0.963782835492881
-TR2487|c0_g1_i1	875.181494043204	882.631049341941	878.906271692572	0.0115839334384507	0.255112918612705	0.0454070828770402	0.963782835492881	0.963782835492881
+sampleA	sampleB	baseMeanA	baseMeanB	baseMean	log2FoldChange	lfcSE	stat	pvalue	padj
+TR2779|c0_g1_i1	wt_GSNO	wt_ph8	195.849684476753	966.924129135581	581.386906806167	-2.26327524632747	0.139880929176731	-16.1800129556472	6.97797522934818e-59	2.3027318256849e-57
+TR1891|c0_g1_i1	wt_GSNO	wt_ph8	128.246229498835	343.028289972482	235.637259735659	-1.40437008666625	0.103208263182426	-13.6071477550587	3.63141533276091e-42	5.99183529905551e-41
+TR4761|c0_g1_i1	wt_GSNO	wt_ph8	184.029205648389	351.782300021135	267.905752834762	-0.934295661860181	0.0925945355062913	-10.0901814210915	6.10565695161207e-24	6.71622264677328e-23
+TR24|c0_g1_i1	wt_GSNO	wt_ph8	39.3724575919554	183.288101009647	111.330279300801	-2.12198385961523	0.229366226812664	-9.25150964508988	2.21344016014191e-20	1.82608813211707e-19
+TR3638|c0_g1_i1	wt_GSNO	wt_ph8	174.266398355818	297.555274221606	235.910836288712	-0.755625651268871	0.0961172743232099	-7.86149687024996	3.79569918101421e-15	2.50516145946938e-14
+TR2122|c0_g2_i2	wt_GSNO	wt_ph8	190.673533226329	328.707071692642	259.690302459485	-0.781951344246178	0.102125767694546	-7.65674875105918	1.90699193392882e-14	1.04884556366085e-13
+TR2278|c0_g1_i1	wt_GSNO	wt_ph8	426.804298570637	315.99710709695	371.400702833793	0.428907012124225	0.105320470989525	4.07239929801383	4.65313200258197e-05	0.000219361937264579
+TR4084|c0_g1_i1	wt_GSNO	wt_ph8	115.544575735664	157.970364768418	136.757470252041	-0.434913653199297	0.157209464946713	-2.76645972522529	0.00566685842046991	0.0233757909844384
+TR3788|c0_g1_i1	wt_GSNO	wt_ph8	128.115824993653	24.010679388938	76.0632521912957	1.36551096405932	0.534260069919225	2.55589186043003	0.0105916029199559	0.0388358773731717
+TR1492|c0_g1_i2	wt_GSNO	wt_ph8	1368.89238848897	813.514514376559	1091.20345143276	0.692062260203308	0.290167592747528	2.38504325603812	0.0170771132686324	0.0563544737864868
+TR1678|c0_g1_i1	wt_GSNO	wt_ph8	0.695005959508731	7.10082184137838	3.89791390044355	-1.19229893380239	0.533516728634619	-2.23479203145837	0.0254310052417055	0.0762930157251164
+TR5075|c0_g1_i1	wt_GSNO	wt_ph8	8.81552188359314	126.23137395943	67.5234479215117	-1.10768013972448	0.513345367512952	-2.15776786900981	0.0309458842036983	0.0851011815601704
+TR1479|c0_g1_i1	wt_GSNO	wt_ph8	353.92669362375	305.546165789569	329.736429706659	0.210154850632672	0.101920088147959	2.06195711219939	0.0392118193266939	0.0995376952139152
+TR1859|c3_g1_i1	wt_GSNO	wt_ph8	0	2.05957798928713	1.02978899464357	-1.01742987508067	0.500302018271162	-2.03363136250477	0.0419887772494581	1
+TR2844|c0_g1_i1	wt_GSNO	wt_ph8	220.566338218013	194.214843050373	207.390590634193	0.185176880395552	0.100284765132021	1.84651058564851	0.0648181037840442	0.152785530348104
+TR2107|c1_g1_i1	wt_GSNO	wt_ph8	7.08292121571621	1.78415791317121	4.43353956444371	0.951944042839851	0.540599552522162	1.76090423752399	0.0782546125949942	0.170760316089935
+TR4669|c0_g2_i1	wt_GSNO	wt_ph8	165.630009730314	0	82.8150048651569	0.762969565911357	0.439826422982926	1.73470607049221	0.0827928805284532	0.170760316089935
+TR2672|c0_g1_i1	wt_GSNO	wt_ph8	2.07518941673641	7.44710458698621	4.76114700186131	-0.686459125319668	0.52860452101472	-1.29862514986048	0.194072602638997	0.376729169828641
+TR4859|c0_g1_i1	wt_GSNO	wt_ph8	3.10763825129944	1.1806627783491	2.14415051482427	0.593225714064679	0.537217960853533	1.10425517628294	0.269482460872864	0.494051178266917
+TR3091|c0_g1_i1	wt_GSNO	wt_ph8	312.47018793986	293.531643106953	303.000915523406	0.0878939148373507	0.0878811164283744	1.00014563320878	0.317240035048796	0.536180698490786
+TR4163|c0_g1_i1	wt_GSNO	wt_ph8	221.469120691076	207.118822998308	214.293971844692	0.0959413488001967	0.0974696330347526	0.984320406397642	0.324957999085325	0.536180698490786
+TR1894|c2_g1_i1	wt_GSNO	wt_ph8	2.85762748931802	1.47338219762144	2.16550484346973	0.431530486406946	0.537372709941065	0.803037590900872	0.421953007665329	0.663069012045517
+TR3249|c0_g1_i1	wt_GSNO	wt_ph8	2.06512931203634	4.15451161800812	3.10982046502223	-0.38612563978518	0.523142120053183	-0.738089373774619	0.460460140618999	0.675718500003336
+TR5212|c0_g1_i1	wt_GSNO	wt_ph8	102.736339436612	86.4452993262187	94.5908193814151	0.226915890105892	0.314756340859895	0.720925556212693	0.470955318184143	0.675718500003336
+TR1122|c0_g1_i1	wt_GSNO	wt_ph8	1.29006258579706	0.5946183773076	0.942340481552333	0.279366026492593	0.486443515520964	0.57430311552905	0.565762701275693	1
+TR2011|c5_g1_i1	wt_GSNO	wt_ph8	7.597917075274	4.42090354598533	6.00941031062966	0.293830308686626	0.525066976727929	0.559605386950241	0.575748629670957	0.791654365797565
+TR1837|c2_g1_i1	wt_GSNO	wt_ph8	2.16507864525674	1.46465683073113	1.81486773799393	0.232644077202222	0.530765383353658	0.438318105322267	0.661155703054792	1
+TR1982|c2_g1_i1	wt_GSNO	wt_ph8	5.5352448786851	10.687042573374	8.11114372602957	-0.163617497783336	0.41190705551325	-0.397219459082736	0.691205633846634	0.874699343226649
+TR1449|c0_g1_i1	wt_GSNO	wt_ph8	98.9943307118646	106.843279101242	102.918804906553	-0.100378154615576	0.259464578599584	-0.38686650469729	0.69885503944156	0.874699343226649
+TR2182|c3_g2_i6	wt_GSNO	wt_ph8	1.29006258579706	1.76655578876639	1.52830918728173	-0.199699696686908	0.518464312092113	-0.385175395932417	0.700107470922461	1
+TR4277|c0_g1_i1	wt_GSNO	wt_ph8	153.969096204861	149.159426886469	151.564261545665	0.0459499001744168	0.126145529370448	0.364261027748966	0.715663099003622	0.874699343226649
+TR3854|c0_g1_i1	wt_GSNO	wt_ph8	2260.55060252051	1927.46472630351	2094.00766441201	0.149461409336011	0.515737174792397	0.289801504799756	0.771968096584582	0.909819542403257
+TR127|c1_g1_i1	wt_GSNO	wt_ph8	1.20754470361908	1.49113571265046	1.34934020813477	-0.140499936513031	0.525109891787989	-0.267562921038549	0.789035775295455	1
+TR2090|c0_g1_i1	wt_GSNO	wt_ph8	9.46045896251181	5.6546754787973	7.55756722065455	0.0558182109444541	0.287850208274631	0.193914089133468	0.846243151562143	0.956832805790417
+TR3807|c0_g1_i1	wt_GSNO	wt_ph8	0.347502979754365	0.292870809896544	0.320186894825454	0.0816135421729034	0.465942705668376	0.175157892118586	0.860955569985101	1
+TR131|c0_g1_i1	wt_GSNO	wt_ph8	1275.67603302799	1312.2934796972	1293.9847563626	-0.035805337908038	0.355352253126282	-0.100760126305753	0.919740880292126	0.956832805790417
+TR5055|c0_g2_i1	wt_GSNO	wt_ph8	5.17791343714095	5.60171771495863	5.38981557604979	-0.0489219520111245	0.535247232645477	-0.091400663146498	0.927174234841818	0.956832805790417
+TR939|c0_g1_i1	wt_GSNO	wt_ph8	92.2508462008296	94.0990807885678	93.1749634946987	-0.0260132924520656	0.31360944301959	-0.0829480522065804	0.933892845523313	0.956832805790417
+TR2487|c0_g1_i1	wt_GSNO	wt_ph8	875.181494043204	882.631049341941	878.906271692572	-0.0117684251443531	0.217416529127567	-0.0541284749212796	0.956832805790417	0.956832805790417
diff -r 7d1758a86884 -r 36681c1ad6d7 test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.count_matrix
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.count_matrix	Fri Mar 31 11:35:49 2017 -0400
@@ -0,0 +1,40 @@
+wt_GSNO_1	wt_GSNO_2	wt_GSNO_3	wt_ph8_1	wt_ph8_2	wt_ph8_3
+TR24|c0_g1_i1	35	34	36	196	201	222
+TR2779|c0_g1_i1	186	197	147	1094	1086	1088
+TR127|c1_g1_i1	0	1	2	1	1	3
+TR2107|c1_g1_i1	6	7	6	1	2	3
+TR2011|c5_g1_i1	5	7	8	4	8	3
+TR4163|c0_g1_i1	216	210	172	254	212	234
+TR5055|c0_g2_i1	7	3	4	4	11	4
+TR1449|c0_g1_i1	113	91	66	130	107	124
+TR1982|c2_g1_i1	3	8	4	9	11	16
+TR1859|c3_g1_i1	0	0	0	2	4	1
+TR1492|c0_g1_i2	1263	1319	1104	929	922	899
+TR1122|c0_g1_i1	0	0	3	1	0	1
+TR2278|c0_g1_i1	406	413	333	409	337	323
+TR4084|c0_g1_i1	111	127	77	201	158	175
+TR4761|c0_g1_i1	174	165	155	389	406	394
+TR3638|c0_g1_i1	184	174	117	344	338	324
+TR2090|c0_g1_i1	0	0	22	0	9	10
+TR3854|c0_g1_i1	2173	2151	1775	2142	2155	2216
+TR131|c0_g1_i1	1233	1208	1001	1492	1457	1486
+TR5075|c0_g1_i1	8	10	6	121	142	163
+TR2182|c3_g2_i6	0	0	3	2	3	1
+TR3788|c0_g1_i1	132	125	91	22	27	32
+TR4859|c0_g1_i1	1	3	4	1	2	1
+TR2487|c0_g1_i1	866	806	689	989	1032	963
+TR2122|c0_g2_i2	157	201	155	398	344	369
+TR4277|c0_g1_i1	134	164	118	162	170	172
+TR4669|c0_g2_i1	0	218	209	0	0	0
+TR3091|c0_g1_i1	308	284	250	343	316	333
+TR3807|c0_g1_i1	0	1	0	1	0	0
+TR1894|c2_g1_i1	2	5	1	3	1	1
+TR5212|c0_g1_i1	98	108	73	105	84	103
+TR939|c0_g1_i1	89	88	72	103	108	107
+TR1891|c0_g1_i1	139	111	97	411	384	365
+TR2672|c0_g1_i1	4	2	0	4	7	14
+TR2844|c0_g1_i1	214	223	161	245	213	199
+TR1837|c2_g1_i1	1	4	1	3	2	0
+TR1678|c0_g1_i1	0	2	0	10	6	8
+TR3249|c0_g1_i1	1	0	4	1	7	6
+TR1479|c0_g1_i1	324	354	277	363	302	367
diff -r 7d1758a86884 -r 36681c1ad6d7 test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.edgeR.count_matrix
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.edgeR.count_matrix	Fri Mar 31 11:35:49 2017 -0400
@@ -0,0 +1,40 @@
+wt_GSNO_1	wt_GSNO_2	wt_GSNO_3	wt_ph8_1	wt_ph8_2	wt_ph8_3
+TR24|c0_g1_i1	35	34	36	196	201	222
+TR2779|c0_g1_i1	186	197	147	1094	1086	1088
+TR127|c1_g1_i1	0	1	2	1	1	3
+TR2107|c1_g1_i1	6	7	6	1	2	3
+TR2011|c5_g1_i1	5	7	8	4	8	3
+TR4163|c0_g1_i1	216	210	172	254	212	234
+TR5055|c0_g2_i1	7	3	4	4	11	4
+TR1449|c0_g1_i1	113	91	66	130	107	124
+TR1982|c2_g1_i1	3	8	4	9	11	16
+TR1859|c3_g1_i1	0	0	0	2	4	1
+TR1492|c0_g1_i2	1263	1319	1104	929	922	899
+TR1122|c0_g1_i1	0	0	3	1	0	1
+TR2278|c0_g1_i1	406	413	333	409	337	323
+TR4084|c0_g1_i1	111	127	77	201	158	175
+TR4761|c0_g1_i1	174	165	155	389	406	394
+TR3638|c0_g1_i1	184	174	117	344	338	324
+TR2090|c0_g1_i1	0	0	22	0	9	10
+TR3854|c0_g1_i1	2173	2151	1775	2142	2155	2216
+TR131|c0_g1_i1	1233	1208	1001	1492	1457	1486
+TR5075|c0_g1_i1	8	10	6	121	142	163
+TR2182|c3_g2_i6	0	0	3	2	3	1
+TR3788|c0_g1_i1	132	125	91	22	27	32
+TR4859|c0_g1_i1	1	3	4	1	2	1
+TR2487|c0_g1_i1	866	806	689	989	1032	963
+TR2122|c0_g2_i2	157	201	155	398	344	369
+TR4277|c0_g1_i1	134	164	118	162	170	172
+TR4669|c0_g2_i1	0	218	209	0	0	0
+TR3091|c0_g1_i1	308	284	250	343	316	333
+TR3807|c0_g1_i1	0	1	0	1	0	0
+TR1894|c2_g1_i1	2	5	1	3	1	1
+TR5212|c0_g1_i1	98	108	73	105	84	103
+TR939|c0_g1_i1	89	88	72	103	108	107
+TR1891|c0_g1_i1	139	111	97	411	384	365
+TR2672|c0_g1_i1	4	2	0	4	7	14
+TR2844|c0_g1_i1	214	223	161	245	213	199
+TR1837|c2_g1_i1	1	4	1	3	2	0
+TR1678|c0_g1_i1	0	2	0	10	6	8
+TR3249|c0_g1_i1	1	0	4	1	7	6
+TR1479|c0_g1_i1	324	354	277	363	302	367
diff -r 7d1758a86884 -r 36681c1ad6d7 test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.voom.count_matrix
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.voom.count_matrix	Fri Mar 31 11:35:49 2017 -0400
@@ -0,0 +1,40 @@
+wt_GSNO_1	wt_GSNO_2	wt_GSNO_3	wt_ph8_1	wt_ph8_2	wt_ph8_3
+TR24|c0_g1_i1	35	34	36	196	201	222
+TR2779|c0_g1_i1	186	197	147	1094	1086	1088
+TR127|c1_g1_i1	0	1	2	1	1	3
+TR2107|c1_g1_i1	6	7	6	1	2	3
+TR2011|c5_g1_i1	5	7	8	4	8	3
+TR4163|c0_g1_i1	216	210	172	254	212	234
+TR5055|c0_g2_i1	7	3	4	4	11	4
+TR1449|c0_g1_i1	113	91	66	130	107	124
+TR1982|c2_g1_i1	3	8	4	9	11	16
+TR1859|c3_g1_i1	0	0	0	2	4	1
+TR1492|c0_g1_i2	1263	1319	1104	929	922	899
+TR1122|c0_g1_i1	0	0	3	1	0	1
+TR2278|c0_g1_i1	406	413	333	409	337	323
+TR4084|c0_g1_i1	111	127	77	201	158	175
+TR4761|c0_g1_i1	174	165	155	389	406	394
+TR3638|c0_g1_i1	184	174	117	344	338	324
+TR2090|c0_g1_i1	0	0	22	0	9	10
+TR3854|c0_g1_i1	2173	2151	1775	2142	2155	2216
+TR131|c0_g1_i1	1233	1208	1001	1492	1457	1486
+TR5075|c0_g1_i1	8	10	6	121	142	163
+TR2182|c3_g2_i6	0	0	3	2	3	1
+TR3788|c0_g1_i1	132	125	91	22	27	32
+TR4859|c0_g1_i1	1	3	4	1	2	1
+TR2487|c0_g1_i1	866	806	689	989	1032	963
+TR2122|c0_g2_i2	157	201	155	398	344	369
+TR4277|c0_g1_i1	134	164	118	162	170	172
+TR4669|c0_g2_i1	0	218	209	0	0	0
+TR3091|c0_g1_i1	308	284	250	343	316	333
+TR3807|c0_g1_i1	0	1	0	1	0	0
+TR1894|c2_g1_i1	2	5	1	3	1	1
+TR5212|c0_g1_i1	98	108	73	105	84	103
+TR939|c0_g1_i1	89	88	72	103	108	107
+TR1891|c0_g1_i1	139	111	97	411	384	365
+TR2672|c0_g1_i1	4	2	0	4	7	14
+TR2844|c0_g1_i1	214	223	161	245	213	199
+TR1837|c2_g1_i1	1	4	1	3	2	0
+TR1678|c0_g1_i1	0	2	0	10	6	8
+TR3249|c0_g1_i1	1	0	4	1	7	6
+TR1479|c0_g1_i1	324	354	277	363	302	367
diff -r 7d1758a86884 -r 36681c1ad6d7 test-data/count/trinotate/genes.lengths.txt
--- a/test-data/count/trinotate/genes.lengths.txt	Thu Mar 23 10:15:57 2017 -0400
+++ b/test-data/count/trinotate/genes.lengths.txt	Fri Mar 31 11:35:49 2017 -0400
@@ -38,3 +38,4 @@
 TR1678|c0_g1_i1	221.00
 TR3249|c0_g1_i1	221.00
 TR1479|c0_g1_i1	136.00
+TR4669|c0_g2_i1 136.00
diff -r 7d1758a86884 -r 36681c1ad6d7 test-data/filtered/Trinity_filtered_exp.fasta
--- a/test-data/filtered/Trinity_filtered_exp.fasta	Thu Mar 23 10:15:57 2017 -0400
+++ b/test-data/filtered/Trinity_filtered_exp.fasta	Fri Mar 31 11:35:49 2017 -0400
@@ -1,4 +1,4 @@
->TRINITY_DN1_c0_g1_i1 len=380 path=[358:0-379] [-1, 358, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100
+>TRINITY_DN1_c0_g1_i1 len=380 path=[358:0-379] [-1, 358, -2] top_iso:0 pct_iso_expr=NA pct_dom_iso_expr=NA
 CCAAGGTAGAAAACATCCCTGCTGACAAGACCTACCTGTGACATACTCACTCTCTTAGGG
 CTTTTAAAGACAAGCCATTAAAATAGATGACCTTTCACAGACTGAAACTTGAATCACTGC
 AAAATGAATCTAGGTTGCTGTCACTTTTTCTTTTGGGTGGCGGGGCTTGATGTAGATTTT
@@ -6,12 +6,12 @@
 GGAGGTTAGATTTACTGGAAATGTATTCATACTGTGAACTGTGCTCTGATGGTTAGAATG
 AAAAGCTTATCAAGCATTCCATATAACAGTGGATGTAGAAAATGTTTTCAGGTGGATATG
 TATATGGTACAGATGTAAAG
->TRINITY_DN0_c0_g1_i1 len=229 path=[207:0-228] [-1, 207, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100
+>TRINITY_DN0_c0_g1_i1 len=229 path=[207:0-228] [-1, 207, -2] top_iso:0 pct_iso_expr=NA pct_dom_iso_expr=NA
 AAATATCACAACCACCTGAACAGGAACTTGGGATAAACAGGCAATGATGAGAGCCGATGT
 TTTTCTGTTGGTGTTTACATTGCTCTGCTCTGTGAAAGGATCCTGCAGCAGAGGCTTCCT
 ACCTGAAAAATGTTTCTCTCAATTGTAGTGTGTGAGTTACTGGTAAGACGCTTACACCTA
 TAACTCAAGGTCGGAATAGTCCCTCCAGTCCCTTTAGTAACCCAGTGGC
->TRINITY_DN2_c1_g1_i1 len=541 path=[519:0-540] [-1, 519, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100
+>TRINITY_DN2_c1_g1_i1 len=541 path=[519:0-540] [-1, 519, -2] top_iso:0 pct_iso_expr=NA pct_dom_iso_expr=NA
 GTCTGAATTCGCATGTAATGCAGCTTTCCCAGACACAAGTATGGAAGCAATCCGACTTAT
 TCGCCATTGTGCAAAATATGTGTCTGATAGACCGCAGGCTTTCAAGGAGTACACAAGTGA
 TGACATGAGCGTGGCACCTGAAGACAGGGTGTGGGTGAGAGGGTGGTTCCCGATCCTCTT
@@ -22,12 +22,12 @@
 CCAGTATTTAGAAGTTCTCAGCGATGTACTTTTGGATGATATTTTTGCCCAGCTTTACTG
 GTGTGTACAACAAGACAATGAGCAGTTAGCACGATCTGGTACAAACTGCTTAGAAAACGT
 G
->TRINITY_DN2_c3_g1_i1 len=202 path=[180:0-201] [-1, 180, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100
+>TRINITY_DN2_c3_g1_i1 len=202 path=[180:0-201] [-1, 180, -2] top_iso:0 pct_iso_expr=NA pct_dom_iso_expr=NA
 GGTGAAAAGTTTACTCTTGAAATCTGGGATAAAACGTGTAACTGCACCCTGGATATCTTC
 AAAACCACAATTCCTCACGCGCTTCTGACTTGGCGTCCCACCTCTGGCGAGGCCGAACCC
 CCATCTCCATCAGCTGTGAGTGAAAAGCCGTTGGATGCAATATCACAAAAATCTGTAGAC
 ATACATGATTCTATTCAACCAA
->TRINITY_DN3_c0_g1_i1 len=216 path=[194:0-215] [-1, 194, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100
+>TRINITY_DN3_c0_g1_i1 len=216 path=[194:0-215] [-1, 194, -2] top_iso:0 pct_iso_expr=NA pct_dom_iso_expr=NA
 ATTGATTTATTTAATAAGAAACCAAAGAGAGGAATACAATACCTCCAAGAACAAGGGATG
 CTTGGCACCACACCCGAAGATATAGCTCAGTTCTTACATCAAGAAGAAAGATTAGACTCT
 ACTCAGGTGGGTGAGTTCCTGGGAGATAATGATAAATTCAATAAAGAAGTCATGTATGCA
diff -r 7d1758a86884 -r 36681c1ad6d7 test-data/filtered/Trinity_filtered_hi_iso.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/filtered/Trinity_filtered_hi_iso.fasta	Fri Mar 31 11:35:49 2017 -0400
@@ -0,0 +1,45 @@
+>TRINITY_DN1_c0_g1_i1 len=380 path=[358:0-379] [-1, 358, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100
+CCAAGGTAGAAAACATCCCTGCTGACAAGACCTACCTGTGACATACTCACTCTCTTAGGG
+CTTTTAAAGACAAGCCATTAAAATAGATGACCTTTCACAGACTGAAACTTGAATCACTGC
+AAAATGAATCTAGGTTGCTGTCACTTTTTCTTTTGGGTGGCGGGGCTTGATGTAGATTTT
+ATTCTATGTACAGAATTTAATGTTGAATATATTAAAAATAACAAACCTGGCATGGTTTTG
+GGAGGTTAGATTTACTGGAAATGTATTCATACTGTGAACTGTGCTCTGATGGTTAGAATG
+AAAAGCTTATCAAGCATTCCATATAACAGTGGATGTAGAAAATGTTTTCAGGTGGATATG
+TATATGGTACAGATGTAAAG
+>TRINITY_DN0_c0_g1_i1 len=229 path=[207:0-228] [-1, 207, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100
+AAATATCACAACCACCTGAACAGGAACTTGGGATAAACAGGCAATGATGAGAGCCGATGT
+TTTTCTGTTGGTGTTTACATTGCTCTGCTCTGTGAAAGGATCCTGCAGCAGAGGCTTCCT
+ACCTGAAAAATGTTTCTCTCAATTGTAGTGTGTGAGTTACTGGTAAGACGCTTACACCTA
+TAACTCAAGGTCGGAATAGTCCCTCCAGTCCCTTTAGTAACCCAGTGGC
+>TRINITY_DN2_c0_g1_i1 len=279 path=[257:0-278] [-1, 257, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100
+TCCAGACCATCGACAACATTGTCTTCTTCCCAGCCACAAGCAAGAAGGAGGATGCAGAGA
+ACTTAGCTGCAGCCCAGAGAGATGCAGTAGACTTCGATGTTCGAGTTGATACTCAAGACC
+AAGGAATGTACCGCTTTTTAACATCACAACAACTGTTCAAGCTACTGGACTGCTTATTAG
+AGTCGCATAGATTTGCAAAAGCATTTAATTCCAACAATGAACAGAGGACTGCTCTGTGGA
+AAGCAGGCTTCAAAGGCAAGTCCAAGCCCAATCTTCTAA
+>TRINITY_DN2_c1_g1_i1 len=541 path=[519:0-540] [-1, 519, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100
+GTCTGAATTCGCATGTAATGCAGCTTTCCCAGACACAAGTATGGAAGCAATCCGACTTAT
+TCGCCATTGTGCAAAATATGTGTCTGATAGACCGCAGGCTTTCAAGGAGTACACAAGTGA
+TGACATGAGCGTGGCACCTGAAGACAGGGTGTGGGTGAGAGGGTGGTTCCCGATCCTCTT
+TGAGTTGTCTTGTATCATCAATAGATGCAAATTAGATGTAAGAACCAGGGGCTTAACAGT
+AATGTTTGAAATAATGAAAACATATGGCCACACTTATGAAAAACATTGGTGGCAGGACTT
+ATTCAGAATTGTTTTCAGAATCTTTGACAACATGAAATTGCCAGAACAGCAGACAGAGAA
+AGCTGAATGGATGACAACAACTTGTAACCATGTCCTTTATGCAATATGTGATGTATTCAC
+CCAGTATTTAGAAGTTCTCAGCGATGTACTTTTGGATGATATTTTTGCCCAGCTTTACTG
+GTGTGTACAACAAGACAATGAGCAGTTAGCACGATCTGGTACAAACTGCTTAGAAAACGT
+G
+>TRINITY_DN2_c2_g1_i1 len=240 path=[218:0-239] [-1, 218, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100
+ACAAGCAGCCTGGCGTGTGGGCTGCGCATTCTCTTCCGGATGTACATGGACGAGAGCAGA
+GTCAGTGCCTGGGAAGAAGTCCAGCAGAGGCTTTTAAACGTCTGCAGGGAAGCGCTGAGC
+TACTTCCTCACTCTAACATCCGAAAGTCACCGGGAAGCCTGGACTAACTTACTGTTACTG
+TTCCTCACTAAAGTTCTGAAGATCAGTGACAGCAGGTTTAAAGCTCACGCATCATTCTAC
+>TRINITY_DN2_c3_g1_i1 len=202 path=[180:0-201] [-1, 180, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100
+GGTGAAAAGTTTACTCTTGAAATCTGGGATAAAACGTGTAACTGCACCCTGGATATCTTC
+AAAACCACAATTCCTCACGCGCTTCTGACTTGGCGTCCCACCTCTGGCGAGGCCGAACCC
+CCATCTCCATCAGCTGTGAGTGAAAAGCCGTTGGATGCAATATCACAAAAATCTGTAGAC
+ATACATGATTCTATTCAACCAA
+>TRINITY_DN3_c0_g1_i1 len=216 path=[194:0-215] [-1, 194, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100
+ATTGATTTATTTAATAAGAAACCAAAGAGAGGAATACAATACCTCCAAGAACAAGGGATG
+CTTGGCACCACACCCGAAGATATAGCTCAGTTCTTACATCAAGAAGAAAGATTAGACTCT
+ACTCAGGTGGGTGAGTTCCTGGGAGATAATGATAAATTCAATAAAGAAGTCATGTATGCA
+TATGTAGACCAACATGACTTTTCAGGAAAAGACTTT
diff -r 7d1758a86884 -r 36681c1ad6d7 tool_dependencies.xml
--- a/tool_dependencies.xml	Thu Mar 23 10:15:57 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,30 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="trinity" version="2.2.0">
-        <repository changeset_revision="76d63b5c571a" name="package_trinity_2_2_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="bowtie" version="1.1.2">
-        <repository changeset_revision="a1c1a92e13a6" name="package_bowtie_1_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="bowtie2" version="2.2.6">
-        <repository changeset_revision="0d9cd7487cc9" name="package_bowtie_2_2_6" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="bioconductor-edger" version="3.14.0">
-        <repository changeset_revision="5f4abad5b2c1" name="package_bioconductor_edger_3_14_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="rsem" version="1.2.28">
-        <repository changeset_revision="4567331d510a" name="package_rsem_1_2_28" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="eXpress" version="1.5.1">
-        <repository changeset_revision="93017e8743e5" name="package_express_1_5_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="bioconductor-limma" version="3.28.10">
-        <repository changeset_revision="b313488c66bd" name="package_bioconductor_limma_3_28_10" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="deseq2" version="1.10.0">
-       <repository changeset_revision="e4a11a7d33d6" name="package_deseq2_1_10_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
-    <set_environment version="1.0">
-        <environment_variable action="set_to" name="TRINITY_MEM_OPTIONS">'--max_memory 30G --bflyHeapSpaceMax 30G'</environment_variable>
-    </set_environment>
-</tool_dependency>