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Changeset 5:2be382e6918a (2017-03-31)

Previous changeset 4:36b2700b604d (2017-03-23) Next changeset 6:f7db3f7c7bf3 (2017-08-28)

Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7efdf3224552d113a01043ee5bf4517d770df933

modified:
README.rst
macros.xml
run_de_analysis.xml
test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results
test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results
test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results
test-data/count/trinotate/genes.lengths.txt
test-data/filtered/Trinity_filtered_exp.fasta

removed:
tool_dependencies.xml

diff -r 36b2700b604d -r 2be382e6918a README.rst
--- a/README.rst Thu Mar 23 10:16:19 2017 -0400
+++ b/README.rst Fri Mar 31 11:36:02 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"?>
+
+<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 36b2700b604d -r 2be382e6918a macros.xml
--- a/macros.xml Thu Mar 23 10:16:19 2017 -0400
+++ b/macros.xml Fri Mar 31 11:36:02 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 36b2700b604d -r 2be382e6918a run_de_analysis.xml
--- a/run_de_analysis.xml Thu Mar 23 10:16:19 2017 -0400
+++ b/run_de_analysis.xml Fri Mar 31 11:36:02 2017 -0400

[

@@ -1,18 +1,16 @@
-<tool id="trinity_run_de_analysis" name="Differential expression analysis" version="@WRAPPER_VERSION@.1">
+<tool id="trinity_run_de_analysis" name="Differential expression analysis" version="@WRAPPER_VERSION@.0">
     <description>using a Trinity assembly</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements">
-        
-        <requirement type="package" version="3.14.0">bioconductor-edger</requirement>
-        <requirement type="package" version="3.28.10">bioconductor-limma</requirement>
-        <requirement type="package" version="1.10.0">bioconductor-deseq2</requirement>
+        <requirement type="package" version="3.16.5">bioconductor-edger</requirement>
+        <requirement type="package" version="3.30.13">bioconductor-limma</requirement>
+        <requirement type="package" version="1.14.1">bioconductor-deseq2</requirement>
     </expand>
-    <expand macro="stdio"/>
-    <command><![CDATA[
+    <command detect_errors="aggressive"><![CDATA[

-        ln -s "${matrix}" "input.matrix"
+        ln -f -s "${matrix}" "input.matrix"

         &&

@@ -33,7 +31,7 @@
             --ROTS_K ${method_choice.rots_k}
         #end if

-        --min_rowSum_counts ${additional_params.min_rowSum_counts}
+        --min_reps_min_cpm ${additional_params.min_reps},${additional_params.min_cpm}

         #if $additional_params.reference_sample:
             --reference_sample ${additional_params.reference_sample}
@@ -71,7 +69,8 @@
         </conditional>

         <section name="additional_params" title="Additional Options" expanded="False">
-            <param name="min_rowSum_counts" argument="--min_rowSum_counts" type="integer" value="2" label="Minimum count" help="Only those rows of matrix meeting requirement will be tested"/>
+            <param name="min_cpm" type="integer" value="1" label="Minimum count per replicate" help="Only those rows of matrix meeting requirement will be tested"/>
+            <param name="min_reps" type="integer" value="2" label="Minimum number of replicates meeting minimum count per replicate" help="Only those rows of matrix meeting requirement will be tested"/>
             <param name="reference_sample" argument="--reference_sample" type="text" optional="true" value="" label="Name of a sample to which all other samples should be compared" help="default is doing all pairwise-comparisons among samples"/>
             <param format="tabular" name="contrasts" argument="--contrasts" optional="true" type="data" label="Pairs of sample comparisons to perform" help="A 2-column tabular with lists of pairs of samples to compare"/>
         </section>
@@ -80,6 +79,9 @@
         <collection name="DE_results" type="list" label="Differential expression results on ${on_string}">
             <discover_datasets pattern="(?P<name>.+)\.DE_results$" ext="tabular" directory="results" />
         </collection>
+        <collection name="count_matrices" type="list" label="Count matrices generated for differential expression on ${on_string}">
+            <discover_datasets pattern="(?P<name>.+)\.count_matrix$" ext="tabular" directory="results" />
+        </collection>
         <collection name="PDF_results" type="list" label="Differential expression plots on ${on_string}">
             <discover_datasets pattern="(?P<name>.+)\.pdf$" ext="pdf" directory="results" />
         </collection>
@@ -94,6 +96,11 @@
                 <element name="input.matrix.wt_37_vs_wt_ph8.DESeq2" compare="sim_size" file="count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results"/>
                 <element name="input.matrix.wt_GSNO_vs_wt_ph8.DESeq2" compare="sim_size" file="count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results"/>
             </output_collection>
+            <output_collection name="count_matrices">
+                <element name="input.matrix.wt_37_vs_wt_GSNO.DESeq2" compare="sim_size" file="count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.count_matrix"/>
+                <element name="input.matrix.wt_37_vs_wt_ph8.DESeq2" compare="sim_size" file="count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.count_matrix"/>
+                <element name="input.matrix.wt_GSNO_vs_wt_ph8.DESeq2" compare="sim_size" file="count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.count_matrix"/>
+            </output_collection>
             <output_collection name="PDF_results">
                 <element name="input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.MA_n_Volcano" compare="sim_size" delta="100" file="count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.MA_n_Volcano.pdf"/>
                 <element name="input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.MA_n_Volcano" compare="sim_size" delta="100" file="count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.MA_n_Volcano.pdf"/>
@@ -109,6 +116,11 @@
                 <element name="input.matrix.wt_37_vs_wt_ph8.edgeR" compare="sim_size" file="count/exp_diff/input.matrix.wt_37_vs_wt_ph8.edgeR.DE_results"/>
                 <element name="input.matrix.wt_GSNO_vs_wt_ph8.edgeR" compare="sim_size" file="count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.edgeR.DE_results"/>
             </output_collection>
+            <output_collection name="count_matrices">
+                <element name="input.matrix.wt_37_vs_wt_GSNO.edgeR" compare="sim_size" file="count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.edgeR.count_matrix"/>
+                <element name="input.matrix.wt_37_vs_wt_ph8.edgeR" compare="sim_size" file="count/exp_diff/input.matrix.wt_37_vs_wt_ph8.edgeR.count_matrix"/>
+                <element name="input.matrix.wt_GSNO_vs_wt_ph8.edgeR" compare="sim_size" file="count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.edgeR.count_matrix"/>
+            </output_collection>
             <output_collection name="PDF_results">
                 <element name="input.matrix.wt_37_vs_wt_GSNO.edgeR.DE_results.MA_n_Volcano" compare="sim_size" delta="100" file="count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.edgeR.DE_results.MA_n_Volcano.pdf"/>
                 <element name="input.matrix.wt_37_vs_wt_ph8.edgeR.DE_results.MA_n_Volcano" compare="sim_size" delta="100" file="count/exp_diff/input.matrix.wt_37_vs_wt_ph8.edgeR.DE_results.MA_n_Volcano.pdf"/>
@@ -124,6 +136,11 @@
                 <element name="input.matrix.wt_37_vs_wt_ph8.voom" compare="sim_size" file="count/exp_diff/input.matrix.wt_37_vs_wt_ph8.voom.DE_results"/>
                 <element name="input.matrix.wt_GSNO_vs_wt_ph8.voom" compare="sim_size" file="count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.voom.DE_results"/>
             </output_collection>
+            <output_collection name="count_matrices">
+                <element name="input.matrix.wt_37_vs_wt_GSNO.voom" compare="sim_size" file="count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.voom.count_matrix"/>
+                <element name="input.matrix.wt_37_vs_wt_ph8.voom" compare="sim_size" file="count/exp_diff/input.matrix.wt_37_vs_wt_ph8.voom.count_matrix"/>
+                <element name="input.matrix.wt_GSNO_vs_wt_ph8.voom" compare="sim_size" file="count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.voom.count_matrix"/>
+            </output_collection>
             <output_collection name="PDF_results">
                 <element name="input.matrix.wt_37_vs_wt_GSNO.voom.DE_results.MA_n_Volcano" compare="sim_size" delta="100" file="count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.voom.DE_results.MA_n_Volcano.pdf"/>
                 <element name="input.matrix.wt_37_vs_wt_ph8.voom.DE_results.MA_n_Volcano" compare="sim_size" delta="100" file="count/exp_diff/input.matrix.wt_37_vs_wt_ph8.voom.DE_results.MA_n_Volcano.pdf"/>

diff -r 36b2700b604d -r 2be382e6918a 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 10:16:19 2017 -0400
+++ b/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results Fri Mar 31 11:36:02 2017 -0400

b'@@ -1,39 +1,38 @@\n-id\tbaseMeanA\tbaseMeanB\tbaseMean\tlog2FoldChange\tlfcSE\tstat\tpvalue\tpadj\n-TR4277|c0_g1_i1\t3852.97388871986\t161.116814813422\t2007.04535176664\t-4.57259674791206\t0.121601866332754\t-37.6030145409076\t0\t0\n-TR131|c0_g1_i1\t26.1866396538608\t1340.30918254958\t683.247911101723\t5.67372481552909\t0.187406695960058\t30.274931140872\t2.45144211418965e-201\t4.04487948841292e-200\n-TR4761|c0_g1_i1\t1645.20640957447\t193.196157329029\t919.201283451752\t-3.08847487551254\t0.143642016580712\t-21.5011940728159\t1.51733402752078e-102\t1.66906743027286e-101\n-TR3091|c0_g1_i1\t16.7444693227929\t328.569936894811\t172.657203108802\t4.29039998257063\t0.240421038467916\t17.8453599980735\t3.14072644239509e-71\t2.59109931497595e-70\n-TR3638|c0_g1_i1\t583.00358519031\t183.754416330029\t383.37900076017\t-1.66018915730897\t0.144484444213305\t-11.4904352945982\t1.47367477630653e-30\t9.72625352362312e-30\n-TR2487|c0_g1_i1\t342.210853400436\t920.407318992504\t631.30908619647\t1.42690938766606\t0.124693202553469\t11.4433614539188\t2.5385551583546e-30\t1.39620533709503e-29\n-TR3788|c0_g1_i1\t19.5075441237117\t134.95369713876\t77.2306206312357\t2.77038513264018\t0.262760026053246\t10.5434040871909\t5.44900939296595e-26\t2.56881871382681e-25\n-TR1479|c0_g1_i1\t129.593534475689\t371.064629188207\t250.329081831948\t1.51441163103673\t0.145431922863633\t10.4131995315551\t2.1584296431011e-25\t8.90352227779205e-25\n-TR2107|c1_g1_i1\t48.9228907410258\t7.40521775805688\t28.1640542495414\t-2.6949883047084\t0.431525668867458\t-6.24525607429428\t4.23106352657394e-10\t1.55138995974378e-09\n-TR3854|c0_g1_i1\t1573.69549271337\t2374.56159860719\t1974.12854566028\t0.593513416954248\t0.111306645736399\t5.33223701987958\t9.70102011419466e-08\t3.20133663768424e-07\n-TR2122|c0_g2_i2\t119.534640490118\t199.143666337033\t159.339153413576\t0.738656537188098\t0.168436715892782\t4.38536534788702\t1.15791268060543e-05\t3.47373804181628e-05\n-TR1449|c0_g1_i1\t180.814952011467\t104.755290736358\t142.785121373912\t-0.784194659361461\t0.185749133486416\t-4.2217944420118\t2.42365089281258e-05\t6.61949164163031e-05\n-TR4163|c0_g1_i1\t347.283468916919\t232.772947466212\t290.028208191566\t-0.576744528291395\t0.137147958253208\t-4.20527243450891\t2.60767852549073e-05\t6.61949164163031e-05\n-TR2672|c0_g1_i1\t18.3155337236093\t2.26581902751323\t10.2906763755613\t-2.88818323474529\t0.724350842979802\t-3.98727117216294\t6.68376171815065e-05\t0.000157545811927837\n-TR127|c1_g1_i1\t13.461799216177\t1.21881296083961\t7.34030608850831\t-3.33218181130749\t0.914685635912973\t-3.64298036448506\t0.000269499403689035\t0.000576210779000196\n-TR5055|c0_g2_i1\t23.3590211688541\t5.52768338415684\t14.4433522765055\t-2.04478780320925\t0.562727305023446\t-3.63370994255211\t0.00027937492315161\t0.000576210779000196\n-TR2844|c0_g1_i1\t158.206282615139\t231.762548186068\t194.984415400603\t0.550641897280872\t0.154759496937021\t3.55804915484414\t0.000373619406412113\t0.000725261200682336\n-TR5212|c0_g1_i1\t65.7079302129484\t107.875371765755\t86.7916509893515\t0.713884138135847\t0.209708011296715\t3.40418152707468\t0.000663626354411326\t0.00121664831642076\n-TR1894|c2_g1_i1\t13.3497721959996\t2.96749216411516\t8.15863218005739\t-2.04982326482473\t0.714661961266818\t-2.8682417365424\t0.00412760030232129\t0.00716898999876856\n-TR24|c0_g1_i1\t69.9065207344592\t41.2394742844514\t55.5729975094553\t-0.760369639593845\t0.269117661787534\t-2.8254170853868\t0.00472191070589177\t0.00779115266472142\n-TR4669|c0_g2_i1\t0\t167.096667347181\t83.5483336735905\t4.37844609928899\t2.00484514683835\t2.18393231327309\t0.0289672221614669\t0.0455199205394479\n-TR2779|c0_g1_i1\t155.915506826481\t205.619872596257\t180.767689711369\t0.402360429872658\t0.188906223389576\t2.12994798505331\t0.0331759079102528\t0.0497638618653791\n-TR1492|c0_g1_i2\t1640.89375005483\t1435.64893261411\t1538.27134133447\t-0.192484740220531\t0.101376439014472\t-1.89871277874588\t0.0576022504671541\t0.0796285639028554\n-TR3807|c0_g1_i1\t3.48709246029019\t0.350050334268211\t1.9185713972792\t-2.70461238638113\t1.4262081182078\t-1.89636586123194\t0.0579116828384403\t0.0796285639028554\n-TR4084|c0_g1_i1\t93.2264707954139\t121.352438036668\t107.289454416041\t0.3802042'..b'.88216980025882e-05\t0.000181885916149697\n+TR127|c1_g1_i1\twt_37\twt_GSNO\t13.461799216177\t1.21881296083961\t7.34030608850831\t3.33150202228086\t0.915899815581865\t3.63740877070095\t0.000275394687501815\t0.000667511143840185\n+TR5055|c0_g2_i1\twt_37\twt_GSNO\t23.3590211688541\t5.52768338415684\t14.4433522765055\t2.04460941512382\t0.563987307210913\t3.62527558507482\t0.000288653467606567\t0.000667511143840185\n+TR2844|c0_g1_i1\twt_37\twt_GSNO\t158.206282615139\t231.762548186068\t194.984415400603\t-0.550639207704626\t0.154913717539885\t-3.55448966333699\t0.000378713397971402\t0.000824258572055403\n+TR5212|c0_g1_i1\twt_37\twt_GSNO\t65.7079302129484\t107.875371765755\t86.7916509893515\t-0.713874873222434\t0.210087143945163\t-3.39799408862815\t0.000678818868686303\t0.00139534989674407\n+TR1894|c2_g1_i1\twt_37\twt_GSNO\t13.3497721959996\t2.96749216411516\t8.15863218005739\t2.04972102673103\t0.716146945354672\t2.86215146210796\t0.00420775772107294\t0.00819405450945783\n+TR24|c0_g1_i1\twt_37\twt_GSNO\t69.9065207344592\t41.2394742844514\t55.5729975094553\t0.760351613917761\t0.269735390145923\t2.81887969356346\t0.00481915767774413\t0.00891544170382664\n+TR2779|c0_g1_i1\twt_37\twt_GSNO\t155.915506826481\t205.619872596257\t180.767689711369\t-0.402350189521528\t0.18910416680051\t-2.12766432558821\t0.0333649247395808\t0.0587858197792614\n+TR3807|c0_g1_i1\twt_37\twt_GSNO\t3.48709246029019\t0.350050334268211\t1.9185713972792\t2.6523001983829\t1.38324824664578\t1.91744338358239\t0.055181627150862\t0.092164962039527\n+TR1492|c0_g1_i2\twt_37\twt_GSNO\t1640.89375005483\t1435.64893261411\t1538.27134133447\t0.192484568368337\t0.101250195527162\t1.90107848548993\t0.057291733159706\t0.092164962039527\n+TR4084|c0_g1_i1\twt_37\twt_GSNO\t93.2264707954139\t121.352438036668\t107.289454416041\t-0.380198430346905\t0.213412163689062\t-1.78152183912463\t0.0748272403991533\t0.115358662282028\n+TR1891|c0_g1_i1\twt_37\twt_GSNO\t107.628573623499\t135.399287466928\t121.513930545214\t-0.328810062058933\t0.189329296532127\t-1.73670989161013\t0.0824383909023624\t0.122008818535496\n+TR4669|c0_g2_i1\twt_37\twt_GSNO\t0\t167.096667347181\t83.5483336735905\t-3.46077834317638\t2.04233842282563\t-1.69451757088734\t0.0901669757000038\t0.128314542342313\n+TR1837|c2_g1_i1\twt_37\twt_GSNO\t0.308903905435236\t2.22601224010275\t1.26745807276899\t-2.41951712666755\t1.51166579847997\t-1.60056351681732\t0.1094736282342\t0.150019416469089\n+TR5075|c0_g1_i1\twt_37\twt_GSNO\t15.8633018853512\t9.23822794034992\t12.5507649128506\t0.764028730403883\t0.508108615055784\t1.50367206491864\t0.132665825459353\t0.172493073735055\n+TR4859|c0_g1_i1\twt_37\twt_GSNO\t7.32690480813971\t3.17910584569163\t5.25300532691567\t1.18248087647214\t0.791530422232021\t1.49391715499409\t0.135197274008557\t0.172493073735055\n+TR939|c0_g1_i1\twt_37\twt_GSNO\t84.2568220960088\t96.9171174594069\t90.5869697777078\t-0.202690605185084\t0.202556787736977\t-1.00066064163834\t0.316990901598642\t0.384256032989688\n+TR2278|c0_g1_i1\twt_37\twt_GSNO\t486.5272515724\t448.140178813055\t467.333715192727\t0.118822806572317\t0.119966033346418\t0.99047041281427\t0.321944243856225\t0.384256032989688\n+TR2011|c5_g1_i1\twt_37\twt_GSNO\t5.60408627995835\t7.88255079488408\t6.74331853742122\t-0.48861876789566\t0.691406970296359\t-0.706702114510391\t0.479751615248569\t0.554712805131158\n+TR2182|c3_g2_i6\twt_37\twt_GSNO\t2.24974854180929\t1.3031439398571\t1.77644624083319\t0.779605221657958\t1.28583289420755\t0.606303684693354\t0.544313112275579\t0.605163179078445\n+TR3249|c0_g1_i1\twt_37\twt_GSNO\t1.12573841927462\t2.128954842887\t1.62734663108081\t-0.761341397480685\t1.29336792501876\t-0.58865028485196\t0.556095894288301\t0.605163179078445\n+TR1678|c0_g1_i1\twt_37\twt_GSNO\t0.595141051681226\t0.700100668536423\t0.647620860108824\t-0.247288262290953\t1.73789746083653\t-0.14229162989393\t0.886849657633351\t0.935371730620685\n+TR1122|c0_g1_i1\twt_37\twt_GSNO\t1.41370386226057\t1.3031439398571\t1.35842390105883\t0.162148276801819\t1.43591594510694\t0.112923237153511\t0.910091413576882\t0.935371730620685\n+TR1982|c2_g1_i1\twt_37\twt_GSNO\t5.73684100209948\t5.71221669652109\t5.72452884931028\t-0.0101267142582557\t0.715373046105777\t-0.0141558510114153\t0.988705642243408\t0.988705642243408\n'

diff -r 36b2700b604d -r 2be382e6918a 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 11:36:02 2017 -0400

diff -r 36b2700b604d -r 2be382e6918a 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 11:36:02 2017 -0400

diff -r 36b2700b604d -r 2be382e6918a 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 11:36:02 2017 -0400

diff -r 36b2700b604d -r 2be382e6918a 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 10:16:19 2017 -0400
+++ b/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results Fri Mar 31 11:36:02 2017 -0400

b'@@ -1,39 +1,39 @@\n-id\tbaseMeanA\tbaseMeanB\tbaseMean\tlog2FoldChange\tlfcSE\tstat\tpvalue\tpadj\n-TR4277|c0_g1_i1\t4705.34614971641\t162.902721493704\t2434.12443560506\t-4.84860951090545\t0.124597307945428\t-38.9142397284305\t0\t0\n-TR131|c0_g1_i1\t32.0461070493257\t1436.30905989883\t734.177583474076\t5.48367743370229\t0.196017912869615\t27.9753893581648\t3.23827538807456e-172\t6.15272323734167e-171\n-TR4761|c0_g1_i1\t2012.6141923276\t384.620292965437\t1198.61724264652\t-2.38450946693381\t0.143863830576436\t-16.5747669680385\t1.06073316501088e-61\t1.34359534234711e-60\n-TR3091|c0_g1_i1\t20.4914097091341\t321.651020117047\t171.071214913091\t3.96886910507283\t0.256323110469072\t15.4838519937191\t4.45952081812589e-54\t4.2365447772196e-53\n-TR2779|c0_g1_i1\t191.51955185349\t1058.15934185376\t624.839446853626\t2.46616535412611\t0.177102083131526\t13.9251064161374\t4.4587691300744e-44\t3.38866453885655e-43\n-TR1492|c0_g1_i2\t2006.11782336441\t890.823502721036\t1448.47066304272\t-1.17029110983798\t0.12207086547883\t-9.58698134274255\t9.06997941755552e-22\t5.74432029778516e-21\n-TR5075|c0_g1_i1\t19.3833722195684\t136.98672801182\t78.1850501156942\t2.80049241151413\t0.293976352213923\t9.52625063350759\t1.63066468983638e-21\t8.85217974482605e-21\n-TR1891|c0_g1_i1\t131.416087212132\t376.595292171713\t254.005689691923\t1.51493508389526\t0.17090866237033\t8.86400409952692\t7.71909159725621e-19\t3.6665685086967e-18\n-TR2487|c0_g1_i1\t418.818667162757\t965.862817209246\t692.340742186001\t1.20547893236143\t0.136832960243688\t8.80985787499278\t1.25304626500959e-18\t5.29063978559604e-18\n-TR3638|c0_g1_i1\t713.131183384274\t326.063958913919\t519.597571149096\t-1.1281436752687\t0.141731779309567\t-7.95970868893582\t1.72444792020844e-15\t6.55290209679206e-15\n-TR2107|c1_g1_i1\t59.5986596731862\t1.89840873462066\t30.7485342039034\t-4.81058600791914\t0.641850436461167\t-7.49487066557473\t6.63637683134955e-14\t2.29256654173894e-13\n-TR2122|c0_g2_i2\t146.135958637131\t360.821667264163\t253.478812950647\t1.30334955915215\t0.177300500792357\t7.35107658087526\t1.96616724778278e-13\t6.22619628464548e-13\n-TR1479|c0_g1_i1\t158.005105094407\t334.827472148091\t246.416288621249\t1.07882286721986\t0.173458235018578\t6.2194963940704\t4.98753084614221e-10\t1.45789363194926e-09\n-TR24|c0_g1_i1\t85.6614643869141\t199.923709280262\t142.792586833588\t1.22623657127381\t0.213504266341901\t5.74338205172044\t9.2804014146814e-09\t2.51896609827067e-08\n-TR4163|c0_g1_i1\t424.593720981574\t227.471218917767\t326.03246994967\t-0.900786056392834\t0.160721595544993\t-5.60463609969988\t2.08692952426197e-08\t5.28688812813031e-08\n-TR2278|c0_g1_i1\t594.657329919233\t348.341653317169\t471.499491618201\t-0.772446091346236\t0.159105007190944\t-4.85494520244241\t1.20420038267752e-06\t2.79113819122931e-06\n-TR1449|c0_g1_i1\t220.782434528097\t117.26089394399\t169.021664236043\t-0.913694497348233\t0.188477876305836\t-4.84775462911953\t1.24866708554995e-06\t2.79113819122931e-06\n-TR127|c1_g1_i1\t16.3791628279609\t1.58772512712498\t8.98344397754296\t-3.19771077466237\t0.834376974262452\t-3.83245328346816\t0.00012687169720824\t0.000267840249661839\n-TR1894|c2_g1_i1\t16.2826445742552\t1.67571344127509\t8.97917900776516\t-3.15659686337855\t0.834779400611257\t-3.7813545244015\t0.00015597736029041\t0.000307529893573321\n-TR5055|c0_g2_i1\t28.6665933385886\t6.05959103586122\t17.3630921872249\t-2.17768048931004\t0.577307428800381\t-3.77213314894485\t0.000161857838722801\t0.000307529893573321\n-TR4084|c0_g1_i1\t113.2594381118\t173.837287636503\t143.548362874151\t0.609755827935052\t0.219803235717165\t2.7740985065373\t0.00553549140639085\t0.00984268771318224\n-TR2090|c0_g1_i1\t0\t5.87877087384675\t2.93938543692337\t4.81114433617716\t1.74023660764341\t2.76464953963491\t0.00569839814973709\t0.00984268771318224\n-TR1678|c0_g1_i1\t0.738899982352077\t7.85275634721875\t4.29582816478541\t3.12892233414853\t1.14660116223239\t2.72886722708063\t0.00635522860739327\t0.0104999429165628\n-TR4859|c0_g1_i1\t8.91205730249659\t1.28188505334354\t5.09697117792006\t-2.61274053843141\t0.973661400721484\t-2.68341801009608\t0.00728738414676855\t0.0115383582323835\n-TR2672|c0_g1_i1\t22.3129914439134\t7.89947501226409\t15.1062332280887\t-1.45907440'..b'4\t5.78009048085484\t7.46604610022994e-09\t1.89139834539158e-08\n+TR1449|c0_g1_i1\twt_37\twt_ph8\t220.782434528097\t117.26089394399\t169.021664236043\t0.914395516820343\t0.174920034977504\t5.22750591113215\t1.71811907274331e-07\t4.08053279776536e-07\n+TR2278|c0_g1_i1\twt_37\twt_ph8\t594.657329919233\t348.341653317169\t471.499491618201\t0.772496794598277\t0.157892732036131\t4.89254182023719\t9.95419556957436e-07\t2.2250554802578e-06\n+TR5055|c0_g2_i1\twt_37\twt_ph8\t28.6665933385886\t6.05959103586122\t17.3630921872249\t2.18372312866756\t0.505600668447204\t4.31906693354301\t1.5669025864333e-05\t3.30790546024808e-05\n+TR127|c1_g1_i1\twt_37\twt_ph8\t16.3791628279609\t1.58772512712498\t8.98344397754296\t3.22742307122337\t0.758365755070441\t4.25576056097574\t2.08339575851481e-05\t4.16679151702962e-05\n+TR1894|c2_g1_i1\twt_37\twt_ph8\t16.2826445742552\t1.67571344127509\t8.97917900776516\t3.18830464179373\t0.7590595028564\t4.20033558607184\t2.66519649541344e-05\t5.06387334128554e-05\n+TR2672|c0_g1_i1\twt_37\twt_ph8\t22.3129914439134\t7.89947501226409\t15.1062332280887\t1.46563545973546\t0.482353842293509\t3.0385068620302\t0.00237753690029721\t0.00429545997952877\n+TR4859|c0_g1_i1\twt_37\twt_ph8\t8.91205730249659\t1.28188505334354\t5.09697117792006\t2.65126611500267\t0.876469721997014\t3.02493748325022\t0.00248684525130613\t0.00429545997952877\n+TR1678|c0_g1_i1\twt_37\twt_ph8\t0.738899982352077\t7.85275634721875\t4.29582816478541\t-3.18849648433777\t1.0594001628342\t-3.00971870327794\t0.00261489744098202\t0.00432026533727463\n+TR4084|c0_g1_i1\twt_37\twt_ph8\t113.2594381118\t173.837287636503\t143.548362874151\t-0.608939120027998\t0.203268581921877\t-2.99573654851409\t0.00273782859610482\t0.00433489527716597\n+TR3807|c0_g1_i1\twt_37\twt_ph8\t4.23896204531587\t0.352255997713617\t2.29560902151474\t3.15525660545126\t1.31164110647326\t2.4055792319098\t0.0161468501576278\t0.0245432122395943\n+TR3249|c0_g1_i1\twt_37\twt_ph8\t1.36481976577862\t4.37661229401476\t2.87071602989669\t-1.55893212196469\t1.01682768784581\t-1.53313303777885\t0.125243078950272\t0.176625758092245\n+TR1859|c3_g1_i1\twt_37\twt_ph8\t0.361569353912422\t2.25550826604853\t1.30853880998047\t-2.19284922770108\t1.43126836745787\t-1.53210206943641\t0.125497249170806\t0.176625758092245\n+TR2090|c0_g1_i1\twt_37\twt_ph8\t0\t5.87877087384675\t2.93938543692337\t-2.86225136793822\t1.9729684338102\t-1.45073348305458\t0.146854088052773\t0.19930197664305\n+TR1982|c2_g1_i1\twt_37\twt_ph8\t7.00144976454503\t11.520013112092\t9.26073143831853\t-0.712688609925078\t0.555640746749963\t-1.28264281209345\t0.199617243880331\t0.261567423015607\n+TR1837|c2_g1_i1\twt_37\twt_ph8\t0.377330628439655\t1.67813520813222\t1.02773291828594\t-1.7572235261621\t1.52690431775837\t-1.15084062945205\t0.249797806431129\t0.316410554812763\n+TR5212|c0_g1_i1\twt_37\twt_ph8\t80.2050001877881\t94.8352723753388\t87.5201362815635\t-0.23592411895009\t0.215502649097795\t-1.09476203628025\t0.273620902411289\t0.335406267471903\n+TR3854|c0_g1_i1\twt_37\twt_ph8\t1925.26464813324\t2107.16376011081\t2016.21420412203\t-0.130483054839334\t0.130739272627028\t-0.998040238540833\t0.318259846991125\t0.377933568301961\n+TR1122|c0_g1_i1\twt_37\twt_ph8\t1.69354093201913\t0.660517838352177\t1.17702938518565\t1.18649040337028\t1.40558655511286\t0.84412475279761\t0.398599697111289\t0.448776409473292\n+TR2844|c0_g1_i1\twt_37\twt_ph8\t193.030766468894\t213.82243412349\t203.426600296192\t-0.143791883173722\t0.17140940841448\t-0.838879758723761\t0.401536787423471\t0.448776409473292\n+TR2011|c5_g1_i1\twt_37\twt_ph8\t6.84875389533898\t4.81927837273561\t5.8340161340373\t0.467659672901774\t0.714270969980296\t0.654737057162879\t0.512637061952329\t0.556577381548243\n+TR2182|c3_g2_i6\twt_37\twt_ph8\t2.76248771922916\t1.94482465855284\t2.353656188891\t0.479324872360299\t1.02378035563408\t0.468191120998245\t0.639647921157653\t0.675183916777523\n+TR3788|c0_g1_i1\twt_37\twt_ph8\t23.7579432209456\t26.0024682525169\t24.8802057367313\t-0.124358222905796\t0.350105186670918\t-0.355202458119214\t0.72243792333433\t0.741963272613636\n+TR939|c0_g1_i1\twt_37\twt_ph8\t103.002135647151\t102.820214322362\t102.911174984756\t0.000971215955472081\t0.195414642848595\t0.00497002651037041\t0.996034508905975\t0.996034508905975\n'

diff -r 36b2700b604d -r 2be382e6918a 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 11:36:02 2017 -0400

diff -r 36b2700b604d -r 2be382e6918a 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 11:36:02 2017 -0400

diff -r 36b2700b604d -r 2be382e6918a 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 11:36:02 2017 -0400

diff -r 36b2700b604d -r 2be382e6918a 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 10:16:19 2017 -0400
+++ b/test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results Fri Mar 31 11:36:02 2017 -0400

b'@@ -1,40 +1,40 @@\n-id\tbaseMeanA\tbaseMeanB\tbaseMean\tlog2FoldChange\tlfcSE\tstat\tpvalue\tpadj\n-TR2779|c0_g1_i1\t195.849684476753\t966.924129135581\t581.386906806167\t2.25621220756415\t0.156114979193812\t14.4522467940961\t2.42639762934434e-47\t5.82335431042642e-46\n-TR1891|c0_g1_i1\t128.246229498835\t343.028289972482\t235.637259735659\t1.40479466067472\t0.104376051709838\t13.4589749052781\t2.72672776456232e-41\t3.27207331747478e-40\n-TR4761|c0_g1_i1\t184.029205648389\t351.782300021135\t267.905752834762\t0.934185686537064\t0.0945413616088594\t9.88123791152932\t5.0208774429335e-23\t4.0167019543468e-22\n-TR24|c0_g1_i1\t39.3724575919554\t183.288101009647\t111.330279300801\t2.11680322693425\t0.240338854880295\t8.80757806717753\t1.27878744153922e-18\t7.67272464923531e-18\n-TR3638|c0_g1_i1\t174.266398355818\t297.555274221606\t235.910836288712\t0.75598517202537\t0.0975355931355663\t7.75086455848598\t9.12689947000201e-15\t3.81892706573808e-14\n-TR2122|c0_g2_i2\t190.673533226329\t328.707071692642\t259.690302459485\t0.782528370953275\t0.101034702024136\t7.74514454218254\t9.54731766434521e-15\t3.81892706573808e-14\n-TR2278|c0_g1_i1\t426.804298570637\t315.99710709695\t371.400702833793\t-0.429046906426044\t0.106511998284025\t-4.02815563822158\t5.62161256784655e-05\t0.000192741002326167\n-TR4084|c0_g1_i1\t115.544575735664\t157.970364768418\t136.757470252041\t0.435378746345168\t0.157905703989027\t2.75720721510747\t0.00582973950434901\t0.017489218513047\n-TR3788|c0_g1_i1\t128.115824993653\t24.010679388938\t76.0632521912957\t-1.20076602288383\t0.555078500739638\t-2.16323640941564\t0.0305230012251409\t0.0813946699337092\n-TR1678|c0_g1_i1\t0.695005959508731\t7.10082184137838\t3.89791390044355\t1.13542782611345\t0.54389306361848\t2.08759387104432\t0.0368344853417399\t1\n-TR1859|c3_g1_i1\t0\t2.05957798928713\t1.02978899464357\t1.08547672488113\t0.52169423531112\t2.08067609609255\t0.0374635634690378\t1\n-TR1479|c0_g1_i1\t353.92669362375\t305.546165789569\t329.736429706659\t-0.210273055725041\t0.101401657889395\t-2.07366487000044\t0.0381104459877385\t0.0914650703705724\n-TR1492|c0_g1_i2\t1368.89238848897\t813.514514376559\t1091.20345143276\t-0.673957173112486\t0.33643480733027\t-2.00323259790084\t0.0451523282811554\t0.0985141707952481\n-TR2844|c0_g1_i1\t220.566338218013\t194.214843050373\t207.390590634193\t-0.1851823349888\t0.101213323108161\t-1.8296240979155\t0.0673061677634479\t0.134612335526896\n-TR5075|c0_g1_i1\t8.81552188359314\t126.23137395943\t67.5234479215117\t0.86620707327725\t0.498591364017662\t1.73730861741634\t0.0823327113057556\t0.151998851641395\n-TR2107|c1_g1_i1\t7.08292121571621\t1.78415791317121\t4.43353956444371\t-0.87765751535477\t0.553196716703176\t-1.58651974759584\t0.112621456124343\t1\n-TR2672|c0_g1_i1\t2.07518941673641\t7.44710458698621\t4.76114700186131\t0.652733502871168\t0.537764458916032\t1.21379070715621\t0.224827655823799\t1\n-TR4859|c0_g1_i1\t3.10763825129944\t1.1806627783491\t2.14415051482427\t-0.587630876626665\t0.551071114588281\t-1.06634309269812\t0.28626857627862\t1\n-TR3091|c0_g1_i1\t312.47018793986\t293.531643106953\t303.000915523406\t-0.0879738435317154\t0.0902971665647824\t-0.97427025540829\t0.329922369379669\t0.501282895914669\n-TR4163|c0_g1_i1\t221.469120691076\t207.118822998308\t214.293971844692\t-0.0959599050588562\t0.0987561344325879\t-0.97168551209707\t0.331207026506115\t0.501282895914669\n-TR4669|c0_g2_i1\t165.630009730314\t0\t82.8150048651569\t-0.322459466822447\t0.333908718519009\t-0.965711432311973\t0.334188597276446\t0.501282895914669\n-TR1894|c2_g1_i1\t2.85762748931802\t1.47338219762144\t2.16550484346973\t-0.426208431542948\t0.551264679640795\t-0.773146634064541\t0.439435604855973\t1\n-TR3249|c0_g1_i1\t2.06512931203634\t4.15451161800812\t3.10982046502223\t0.3941103325595\t0.539435464341514\t0.730597742661558\t0.465024891244583\t1\n-TR5212|c0_g1_i1\t102.736339436612\t86.4452993262187\t94.5908193814151\t-0.222704356323449\t0.346653224187607\t-0.642441324021618\t0.520586675617895\t0.734945894989969\n-TR1122|c0_g1_i1\t1.29006258579706\t0.5946183773076\t0.942340481552333\t-0.302591524122929\t0.512417527863229\t-0.590517512905403\t0.554843748171664\t1\n-TR2011|c5_g1_i1\t7.597917075274\t4.42090354598533\t6.00941031062966\t-0.2467378203'..b'53956444371\t0.951944042839851\t0.540599552522162\t1.76090423752399\t0.0782546125949942\t0.170760316089935\n+TR4669|c0_g2_i1\twt_GSNO\twt_ph8\t165.630009730314\t0\t82.8150048651569\t0.762969565911357\t0.439826422982926\t1.73470607049221\t0.0827928805284532\t0.170760316089935\n+TR2672|c0_g1_i1\twt_GSNO\twt_ph8\t2.07518941673641\t7.44710458698621\t4.76114700186131\t-0.686459125319668\t0.52860452101472\t-1.29862514986048\t0.194072602638997\t0.376729169828641\n+TR4859|c0_g1_i1\twt_GSNO\twt_ph8\t3.10763825129944\t1.1806627783491\t2.14415051482427\t0.593225714064679\t0.537217960853533\t1.10425517628294\t0.269482460872864\t0.494051178266917\n+TR3091|c0_g1_i1\twt_GSNO\twt_ph8\t312.47018793986\t293.531643106953\t303.000915523406\t0.0878939148373507\t0.0878811164283744\t1.00014563320878\t0.317240035048796\t0.536180698490786\n+TR4163|c0_g1_i1\twt_GSNO\twt_ph8\t221.469120691076\t207.118822998308\t214.293971844692\t0.0959413488001967\t0.0974696330347526\t0.984320406397642\t0.324957999085325\t0.536180698490786\n+TR1894|c2_g1_i1\twt_GSNO\twt_ph8\t2.85762748931802\t1.47338219762144\t2.16550484346973\t0.431530486406946\t0.537372709941065\t0.803037590900872\t0.421953007665329\t0.663069012045517\n+TR3249|c0_g1_i1\twt_GSNO\twt_ph8\t2.06512931203634\t4.15451161800812\t3.10982046502223\t-0.38612563978518\t0.523142120053183\t-0.738089373774619\t0.460460140618999\t0.675718500003336\n+TR5212|c0_g1_i1\twt_GSNO\twt_ph8\t102.736339436612\t86.4452993262187\t94.5908193814151\t0.226915890105892\t0.314756340859895\t0.720925556212693\t0.470955318184143\t0.675718500003336\n+TR1122|c0_g1_i1\twt_GSNO\twt_ph8\t1.29006258579706\t0.5946183773076\t0.942340481552333\t0.279366026492593\t0.486443515520964\t0.57430311552905\t0.565762701275693\t1\n+TR2011|c5_g1_i1\twt_GSNO\twt_ph8\t7.597917075274\t4.42090354598533\t6.00941031062966\t0.293830308686626\t0.525066976727929\t0.559605386950241\t0.575748629670957\t0.791654365797565\n+TR1837|c2_g1_i1\twt_GSNO\twt_ph8\t2.16507864525674\t1.46465683073113\t1.81486773799393\t0.232644077202222\t0.530765383353658\t0.438318105322267\t0.661155703054792\t1\n+TR1982|c2_g1_i1\twt_GSNO\twt_ph8\t5.5352448786851\t10.687042573374\t8.11114372602957\t-0.163617497783336\t0.41190705551325\t-0.397219459082736\t0.691205633846634\t0.874699343226649\n+TR1449|c0_g1_i1\twt_GSNO\twt_ph8\t98.9943307118646\t106.843279101242\t102.918804906553\t-0.100378154615576\t0.259464578599584\t-0.38686650469729\t0.69885503944156\t0.874699343226649\n+TR2182|c3_g2_i6\twt_GSNO\twt_ph8\t1.29006258579706\t1.76655578876639\t1.52830918728173\t-0.199699696686908\t0.518464312092113\t-0.385175395932417\t0.700107470922461\t1\n+TR4277|c0_g1_i1\twt_GSNO\twt_ph8\t153.969096204861\t149.159426886469\t151.564261545665\t0.0459499001744168\t0.126145529370448\t0.364261027748966\t0.715663099003622\t0.874699343226649\n+TR3854|c0_g1_i1\twt_GSNO\twt_ph8\t2260.55060252051\t1927.46472630351\t2094.00766441201\t0.149461409336011\t0.515737174792397\t0.289801504799756\t0.771968096584582\t0.909819542403257\n+TR127|c1_g1_i1\twt_GSNO\twt_ph8\t1.20754470361908\t1.49113571265046\t1.34934020813477\t-0.140499936513031\t0.525109891787989\t-0.267562921038549\t0.789035775295455\t1\n+TR2090|c0_g1_i1\twt_GSNO\twt_ph8\t9.46045896251181\t5.6546754787973\t7.55756722065455\t0.0558182109444541\t0.287850208274631\t0.193914089133468\t0.846243151562143\t0.956832805790417\n+TR3807|c0_g1_i1\twt_GSNO\twt_ph8\t0.347502979754365\t0.292870809896544\t0.320186894825454\t0.0816135421729034\t0.465942705668376\t0.175157892118586\t0.860955569985101\t1\n+TR131|c0_g1_i1\twt_GSNO\twt_ph8\t1275.67603302799\t1312.2934796972\t1293.9847563626\t-0.035805337908038\t0.355352253126282\t-0.100760126305753\t0.919740880292126\t0.956832805790417\n+TR5055|c0_g2_i1\twt_GSNO\twt_ph8\t5.17791343714095\t5.60171771495863\t5.38981557604979\t-0.0489219520111245\t0.535247232645477\t-0.091400663146498\t0.927174234841818\t0.956832805790417\n+TR939|c0_g1_i1\twt_GSNO\twt_ph8\t92.2508462008296\t94.0990807885678\t93.1749634946987\t-0.0260132924520656\t0.31360944301959\t-0.0829480522065804\t0.933892845523313\t0.956832805790417\n+TR2487|c0_g1_i1\twt_GSNO\twt_ph8\t875.181494043204\t882.631049341941\t878.906271692572\t-0.0117684251443531\t0.217416529127567\t-0.0541284749212796\t0.956832805790417\t0.956832805790417\n'

diff -r 36b2700b604d -r 2be382e6918a 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 11:36:02 2017 -0400

diff -r 36b2700b604d -r 2be382e6918a 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 11:36:02 2017 -0400

diff -r 36b2700b604d -r 2be382e6918a 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 11:36:02 2017 -0400

diff -r 36b2700b604d -r 2be382e6918a test-data/count/trinotate/genes.lengths.txt
--- a/test-data/count/trinotate/genes.lengths.txt Thu Mar 23 10:16:19 2017 -0400
+++ b/test-data/count/trinotate/genes.lengths.txt Fri Mar 31 11:36:02 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 36b2700b604d -r 2be382e6918a test-data/filtered/Trinity_filtered_exp.fasta
--- a/test-data/filtered/Trinity_filtered_exp.fasta Thu Mar 23 10:16:19 2017 -0400
+++ b/test-data/filtered/Trinity_filtered_exp.fasta Fri Mar 31 11:36:02 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 36b2700b604d -r 2be382e6918a 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 11:36:02 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 36b2700b604d -r 2be382e6918a tool_dependencies.xml
--- a/tool_dependencies.xml Thu Mar 23 10:16:19 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>