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Changeset 5:d38fd393402e (2016-09-22)

Previous changeset 4:8702e49e68b6 (2016-05-31) Next changeset 6:4939397c4706 (2016-11-09)

Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit da90fed6a52526d14b5e58fc3c5e7e8448d783d7

modified:
deseq2.xml
test-data/deseq2_out.tab
test-data/deseq2_out_filtered.tab

removed:
tool_dependencies.xml

diff -r 8702e49e68b6 -r d38fd393402e deseq2.xml
--- a/deseq2.xml Tue May 31 06:23:49 2016 -0400
+++ b/deseq2.xml Thu Sep 22 05:49:52 2016 -0400

[

@@ -1,8 +1,11 @@
-<tool id="deseq2" name="DESeq2" version="2.1.8.3">
+<tool id="deseq2" name="DESeq2" version="2.1.8.4">
     <description>Determines differentially expressed features from count tables</description>
     <requirements>
         
-        <requirement type="package" version="1.8.2">deseq2</requirement>
+        <requirement type="package" version="1.20.0">r-getopt</requirement>
+        <requirement type="package" version="2.17.0">r-gplots</requirement>
+        <requirement type="package" version="0.2.15">r-rjson</requirement>
+        <requirement type="package" version="1.10.1">bioconductor-deseq2</requirement>
     </requirements>
     <stdio>
         <regex match="Execution halted"
@@ -25,8 +28,10 @@
     </version_command>
     <command>
     <![CDATA[
+        R -e 'library(DESeq2); sink("DESEQ2_ROOT_PATH"); cat(file.path(find.package("DESeq2"),"script","deseq2.R"))' &&
+
         #import json
-        Rscript \$DESEQ2_ROOT_PATH/DESeq2/script/deseq2.R
+        Rscript \$(cat DESEQ2_ROOT_PATH)
             -o "$deseq_out"
             #if $pdf:
                 -p "$plots"
@@ -128,8 +133,8 @@
                 </repeat>
             </repeat>
             <param name="pdf" value="no"/>
-            <output name="deseq_out" file="deseq2_out.tab"/>
-            <output name="deseq_out_filtered" file="deseq2_out_filtered.tab"/>
+            <output name="deseq_out" file="deseq2_out.tab" compare="sim_size" delta="1000"/>
+            <output name="deseq_out_filtered" file="deseq2_out_filtered.tab" compare="sim_size" delta="1000"/>
         </test>
     </tests>
     <help>

diff -r 8702e49e68b6 -r d38fd393402e test-data/deseq2_out.tab
--- a/test-data/deseq2_out.tab Tue May 31 06:23:49 2016 -0400
+++ b/test-data/deseq2_out.tab Thu Sep 22 05:49:52 2016 -0400

b'@@ -1,3062 +1,3179 @@\n-FBgn0003360\t1933.95040021558\t2.83931228953808\t0.131427107601069\t21.6037036906911\t1.65776552489818e-103\t4.55056636584551e-100\n-FBgn0029167\t1648.81894046778\t2.12846963025105\t0.111026271791993\t19.1708646602015\t6.48223943041875e-82\t8.89687361824973e-79\n-FBgn0025111\t655.359768612902\t-2.5644293647992\t0.137667338019513\t-18.6277253682041\t1.91491281446672e-77\t1.75214522523705e-74\n-FBgn0029896\t211.4755450268\t2.08777269052165\t0.146415563061924\t14.2592265935463\t3.92783372063478e-46\t2.69547589078562e-43\n-FBgn0000071\t151.249383869297\t-2.07788825355436\t0.168180795911583\t-12.3550863360568\t4.57264975460857e-35\t2.5103847152801e-32\n-FBgn0027279\t1317.42349329018\t1.15789519295162\t0.0979487508070972\t11.8214391037208\t3.02458387385013e-32\t1.38374712228644e-29\n-FBgn0023479\t1361.36610109448\t1.42278095029403\t0.123382436293769\t11.5314707103565\t9.15659568231105e-31\t3.5906935925634e-28\n-FBgn0026562\t20055.4860668702\t1.89651463997866\t0.165538622297845\t11.4566293572648\t2.17828075409044e-30\t7.47422583747282e-28\n-FBgn0003501\t116.651152955291\t-1.80587016893758\t0.166034670798513\t-10.8764642965989\t1.49239989450017e-27\t4.55181967822551e-25\n-FBgn0001224\t272.471006012668\t-1.32281611833978\t0.13449523456877\t-9.83541255257933\t7.92421546640366e-23\t2.1751971455278e-20\n-FBgn0001226\t617.110611842554\t-1.45833380782402\t0.148670312494837\t-9.80917967650513\t1.02800841891188e-22\t2.5653482817392e-20\n-FBgn0011260\t80.9068053807535\t-1.72804173022181\t0.182772485944649\t-9.45460538707742\t3.2424265783911e-21\t7.41705079806965e-19\n-FBgn0001137\t215.314997012827\t1.29233947976019\t0.145480314070422\t8.88326017178248\t6.49288697031156e-19\t1.37099805642348e-16\n-FBgn0003137\t2007.00068863624\t-0.889614620490297\t0.104287928237073\t-8.53037005844027\t1.45880308282982e-17\t2.86029604454847e-15\n-FBgn0002527\t17292.4505923723\t0.737415379640642\t0.0906423951487406\t8.13543572442643\t4.10459365024519e-16\t7.51140637994869e-14\n-FBgn0003748\t480.807341866837\t-1.01051141976726\t0.130425341380685\t-7.7478150263589\t9.34871863829898e-15\t1.60388954138317e-12\n-FBgn0001258\t671.110480695285\t-0.895361042779412\t0.116548076280965\t-7.68233223018579\t1.56218059874144e-14\t2.52246220208544e-12\n-FBgn0001225\t193.977269091929\t-1.19104460534125\t0.161805987942363\t-7.36094269740816\t1.82615951375933e-13\t2.78489325848298e-11\n-FBgn0024288\t23.7733297010346\t1.57498531672731\t0.214878983535953\t7.32963871482473\t2.30774005599494e-13\t3.33407708089795e-11\n-FBgn0029002\t744.250236684945\t-1.17108787806286\t0.160714199450745\t-7.28677293023985\t3.17467299061412e-13\t4.35723867961788e-11\n-FBgn0030237\t915.313685217584\t0.850733969265291\t0.11842999352386\t7.1834333850056\t6.79821671113147e-13\t8.88624041526471e-11\n-FBgn0002868\t45.7700929054867\t1.52440227024969\t0.214738507124158\t7.09887709784769\t1.25774594124038e-12\t1.51229394007314e-10\n-FBgn0016715\t64.2462306620967\t1.42223212224615\t0.200375077399117\t7.09784939677539\t1.26713153448751e-12\t1.51229394007314e-10\n-FBgn0000116\t279.97574453728\t-1.11632217950968\t0.158425271367774\t-7.04636431973161\t1.83653028455796e-12\t2.10053151296316e-10\n-FBgn0000406\t120.154935949727\t1.37174702008268\t0.200388901602343\t6.84542411837165\t7.62496286681008e-12\t8.37220922775747e-10\n-FBgn0003502\t503.917225808725\t-0.801327666958021\t0.118268612161584\t-6.77548888341742\t1.23986276403457e-11\t1.30900895664419e-09\n-FBgn0024315\t31.3113542635758\t1.37632105256107\t0.2096323176551\t6.56540493353453\t5.18916511976397e-11\t5.27565120509337e-09\n-FBgn0027949\t652.544029710057\t-0.646429669860794\t0.10380165660846\t-6.22754675582033\t4.73795369351325e-10\t4.6448867459621e-08\n-FBgn0003076\t687.758986559078\t-0.667050306578347\t0.107718461514052\t-6.19253466121337\t5.92043246650118e-10\t5.60399555880887e-08\n-FBgn0029801\t670.98347311978\t0.754988076373586\t0.123107615557018\t6.13274875772335\t8.6373499128666e-10\t7.90317517027294e-08\n-FBgn0010591\t719.537870853329\t0.678169973258045\t0.111477789355044\t6.08345372815164\t1.17620874211439e-09\t1.04151387003355e-07\n-FBgn0028327\t1677.74174348924\t-0.623125756663358\t0.103267517769997\t-6.03409252124385\t1.59858460067849e-09\t1.3'..b'FBgn0030540\t0\tNA\tNA\tNA\tNA\tNA\n FBgn0030541\t0\tNA\tNA\tNA\tNA\tNA\n-FBgn0030542\t0.24813606918961\t-0.0328712287308722\t0.0428867931971805\t-0.766465064891662\t0.443399631082694\tNA\n+FBgn0030542\t0.24813606918961\t0.0328712249937809\t0.0428867883455157\t0.766465064461231\t0.443399631338715\tNA\n FBgn0030543\t0\tNA\tNA\tNA\tNA\tNA\n FBgn0030544\t0\tNA\tNA\tNA\tNA\tNA\n-FBgn0030551\t0.700889780748892\t-0.00208405049984523\t0.0848780638948201\t-0.0245534641603956\t0.980411138316637\tNA\n-FBgn0030558\t0.100529782041548\t0.020990392528342\t0.0404598205673976\t0.518795986585666\t0.603903016965853\tNA\n-FBgn0030559\t2.04818968352668\t0.0576383130266952\t0.132392299446769\t0.435360011628696\t0.663301131361537\tNA\n+FBgn0030551\t0.700889780748892\t0.0020840503355373\t0.0848780550042263\t0.0245534647964486\t0.980411137809293\tNA\n+FBgn0030558\t0.100529782041548\t-0.0209903901435717\t0.0404598159839989\t-0.518795986414596\t0.60390301708516\tNA\n FBgn0030563\t0\tNA\tNA\tNA\tNA\tNA\n FBgn0030566\t0\tNA\tNA\tNA\tNA\tNA\n-FBgn0030569\t0.953050839550445\t-0.0285435804729683\t0.0975885229416711\t-0.292489112577601\t0.769912683026423\tNA\n+FBgn0030569\t0.953050839550445\t0.0285435775697864\t0.0975885126736503\t0.292489113603361\t0.769912682242256\tNA\n FBgn0030570\t0\tNA\tNA\tNA\tNA\tNA\n-FBgn0030577\t0.269423611141796\t0.0265926273358347\t0.0432208169475914\t0.615273593002195\t0.538374053776731\tNA\n+FBgn0030577\t0.269423611141796\t-0.0265926243080571\t0.0432208120596076\t-0.615273592531813\t0.53837405408732\tNA\n FBgn0030578\t0\tNA\tNA\tNA\tNA\tNA\n-FBgn0030586\t1.74466208965234\t0.0132230825972386\t0.125336596329752\t0.105500571935507\t0.915978616184216\tNA\n-FBgn0030587\t2.59645602215874\t-0.0832823059817658\t0.149985601574232\t-0.55526867317692\t0.578710902887619\tNA\n-FBgn0030589\t1.42239350972207\t-0.0168631230081951\t0.106668225133595\t-0.158089468415502\t0.87438629924199\tNA\n-FBgn0030591\t1.68572973453371\t0.132147029708161\t0.124797060316463\t1.05889537280013\t0.289647431838965\tNA\n-FBgn0030595\t0.90385617240921\t-0.0140835800882291\t0.0874061922919609\t-0.161127944358748\t0.871992631384028\tNA\n-FBgn0030599\t2.95619777580832\t0.182676699085778\t0.140734565657972\t1.29802297134123\t0.1942794414749\tNA\n+FBgn0030595\t0.90385617240921\t0.0140835782063791\t0.0874061821542703\t0.161127941517018\t0.871992633622158\tNA\n FBgn0030608\t0\tNA\tNA\tNA\tNA\tNA\n-FBgn0030614\t0.210705028699836\t-0.0343775337066376\t0.043774177282677\t-0.785338202580956\t0.432255302814996\tNA\n-FBgn0030617\t0.267076655602412\t-0.0501740241110423\t0.0527678420425947\t-0.950844722256055\t0.341683206164236\tNA\n-FBgn0030618\t0.205882296391466\t-0.00423405109284277\t0.0447574791725155\t-0.0945998561832053\t0.924632664074002\tNA\n-FBgn0030619\t0.080862070626247\t-0.023087221762983\t0.0399975293297779\t-0.577216196846307\t0.563793416905248\tNA\n+FBgn0030614\t0.210705028699836\t0.034377529798995\t0.0437741723334843\t0.785338202104588\t0.432255303094221\tNA\n+FBgn0030617\t0.267076655602412\t0.0501740190961892\t0.0527678364632217\t0.950844727756834\t0.341683203371434\tNA\n+FBgn0030618\t0.205882296391466\t0.00423405052771355\t0.0447574735163511\t0.0945998555116551\t0.924632664607429\tNA\n+FBgn0030619\t0.080862070626247\t0.0230872191457161\t0.0399975247953908\t0.577216196847676\t0.563793416904323\tNA\n FBgn0030620\t0\tNA\tNA\tNA\tNA\tNA\n FBgn0030621\t0\tNA\tNA\tNA\tNA\tNA\n FBgn0030622\t0\tNA\tNA\tNA\tNA\tNA\n FBgn0030623\t0\tNA\tNA\tNA\tNA\tNA\n FBgn0030624\t0\tNA\tNA\tNA\tNA\tNA\n-FBgn0030634\t2.70235590865947\t0.192428979172224\t0.136399442066759\t1.41077541268858\t0.158310846510837\tNA\n FBgn0030640\t0\tNA\tNA\tNA\tNA\tNA\n-FBgn0030663\t1.2590203447849\t-0.0316273257119708\t0.104066964547581\t-0.303913214433292\t0.761194010025528\tNA\n-FBgn0030665\t2.18244927278868\t0.152547462937079\t0.143519425684929\t1.06290463614291\t0.287825200353307\tNA\n-FBgn0030684\t1.7810355028069\t0.138568750756954\t0.112043714971323\t1.23673827481015\t0.216184264196814\tNA\n-FBgn0030688\t0.827337508607711\t-0.0122149688945211\t0.0936310087832147\t-0.130458584749445\t0.896203618636089\tNA\n+FBgn0030663\t1.2590203447849\t0.0316273222798865\t0.104066953284795\t0.303913214345129\t0.761194010092697\tNA\n+FBgn0030688\t0.827337508607711\t0.0122149676539822\t0.0936309991990391\t0.130458584854102\t0.896203618553293\tNA\n'

diff -r 8702e49e68b6 -r d38fd393402e test-data/deseq2_out_filtered.tab
--- a/test-data/deseq2_out_filtered.tab Tue May 31 06:23:49 2016 -0400
+++ b/test-data/deseq2_out_filtered.tab Thu Sep 22 05:49:52 2016 -0400

diff -r 8702e49e68b6 -r d38fd393402e tool_dependencies.xml
--- a/tool_dependencies.xml Tue May 31 06:23:49 2016 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,6 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="deseq2" version="1.8.2">
-       <repository changeset_revision="623321e04b2d" name="package_deseq2_1_8_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
-</tool_dependency>