| Next changeset 1:89bbd1dbf48d (2015-10-14) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371 |
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added:
deseq2.xml test-data/GSM461176_untreat_single.counts test-data/GSM461177_untreat_paired.counts test-data/GSM461178_untreat_paired.counts test-data/GSM461179_treat_single.counts test-data/GSM461180_treat_paired.counts test-data/GSM461181_treat_paired.counts test-data/GSM461182_untreat_single.counts test-data/deseq2_out.tab test-data/deseq2_out_filtered.tab tool_dependencies.xml |
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| diff -r 000000000000 -r d983d19fbbab deseq2.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/deseq2.xml Mon Sep 28 05:07:29 2015 -0400 |
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| b'@@ -0,0 +1,185 @@\n+<tool id="deseq2" name="DESeq2" version="2.1.8.0">\n+ <description>Determines differentially expressed features from count tables</description>\n+ <requirements>\n+ <!-- odering is crucial, otherwise R will override the ENV variables from deseq2 -->\n+ <requirement type="package" version="1.8.1">deseq2</requirement>\n+ </requirements>\n+ <stdio>\n+ <regex match="Execution halted"\n+ source="both"\n+ level="fatal"\n+ description="Execution halted." />\n+ <regex match="Error in"\n+ source="both"\n+ level="fatal"\n+ description="An undefined error occured, please check your intput carefully and contact your administrator." />\n+ <regex match="Fatal error"\n+ source="both"\n+ level="fatal"\n+ description="An undefined error occured, please check your intput carefully and contact your administrator." />\n+ </stdio>\n+ <version_command>\n+ <![CDATA[\n+ echo $(R --version | grep version | grep -v GNU)", DESeq2 version" $(R --vanilla --slave -e "library(DESeq2); cat(sessionInfo()\\$otherPkgs\\$DESeq2\\$Version)" 2> /dev/null | grep -v -i "WARNING: ")\n+ ]]>\n+ </version_command>\n+ <command>\n+ <![CDATA[\n+ #import json\n+ Rscript \\$DESEQ2_ROOT_PATH/DESeq2/script/deseq2.R\n+ -o "$deseq_out"\n+ #if $pdf:\n+ -p "$plots"\n+ #end if\n+ #set $temp_factor_names = list()\n+ #for $factor in $rep_factorName:\n+ #set $temp_factor = list()\n+ #for $level in $factor.rep_factorLevel:\n+ #set $count_files = list()\n+ #for $file in $level.countsFile:\n+ $count_files.append(str($file))\n+ #end for\n+ $temp_factor.append( {str($level.factorLevel): $count_files} )\n+ #end for\n+ $temp_factor_names.append([str($factor.factorName), $temp_factor])\n+ #end for\n+ -f \'#echo json.dumps(temp_factor_names)#\'\n+ -t "$fit_type"\n+ #if $outlier_replace_off:\n+ -a\n+ #end if\n+ #if $outlier_filter_off:\n+ -b\n+ #end if\n+ #if $many_contrasts:\n+ -m\n+ #end if\n+ ]]>\n+ </command>\n+ <inputs>\n+ <repeat name="rep_factorName" title="Factor" min="1">\n+ <param name="factorName" type="text" value="FactorName" label="Specify a factor name" \n+ help="Only letters, numbers and underscores will be retained in this field">\n+ <sanitizer>\n+ <valid initial="string.letters,string.digits"><add value="_" /></valid>\n+ </sanitizer>\n+ </param>\n+ <repeat name="rep_factorLevel" title="Factor level" min="2" default="2">\n+ <param name="factorLevel" type="text" value="FactorLevel" label="Specify a factor level"\n+ help="Only letters, numbers and underscores will be retained in this field">\n+ <sanitizer>\n+ <valid initial="string.letters,string.digits"><add value="_" /></valid>\n+ </sanitizer>\n+ </param>\n+ <param name="countsFile" type="data" format="tabular" multiple="true" label="Counts file(s)"/>\n+ </repeat>\n+ </repeat>\n+ <param name="pdf" type="boolean" truevalue="1" falsevalue="0" checked="true"\n+ label="Visualising the analysis results"\n+ help="output an additional PDF files" />\n+ <param name="many_contrasts" type="boolean" truevalue="1" falsevalue="0" checked="false"\n+ label="Output all levels vs all levels of primary factor (use when you have >2 levels for primary factor)"\n+ help=" DESeq2 performs independent \xef\xac\x81ltering by default using the mean of normalized counts as a \xef\xac\x81lt'..b'le="true"/>\n+ </collection>\n+ <data format="pdf" name="plots" label="DESeq2 plots on ${on_string}">\n+ <filter>pdf == True</filter>\n+ </data>\n+ </outputs>\n+ <tests>\n+ <test>\n+ <repeat name="rep_factorName">\n+ <param name="factorName" value="Treatment"/>\n+ <repeat name="rep_factorLevel">\n+ <param name="factorLevel" value="Treated"/>\n+ <param name="countsFile" value="GSM461179_treat_single.counts,GSM461180_treat_paired.counts,GSM461181_treat_paired.counts"/>\n+ </repeat>\n+ <repeat name="rep_factorLevel">\n+ <param name="factorLevel" value="Untreated"/>\n+ <param name="countsFile" value="GSM461176_untreat_single.counts,GSM461177_untreat_paired.counts,GSM461178_untreat_paired.counts,GSM461182_untreat_single.counts"/>\n+ </repeat>\n+ </repeat>\n+ <param name="pdf" value="no"/>\n+ <output name="deseq_out" file="deseq2_out.tab"/>\n+ <output name="deseq_out_filtered" file="deseq2_out_filtered.tab"/>\n+ </test>\n+ </tests>\n+ <help>\n+<![CDATA[\n+.. class:: infomark\n+\n+**What it does** \n+\n+Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution\n+\n+\n+**Inputs**\n+\n+DESeq2_ takes count tables that generated from the htseq-count as input. Count tables must be generated for each sample individually. DESeq2 is capable of handling multiple factors that effect your experiment. The first factor you input is considered as the primary factor that affects gene expressions. You also input several secondary factors that might influence your experiment. But the final output will be changes in genes due to primary factor in presence of secondary factors. Each factor has two levels/states. You need to select appropriate count table from your history for each factor level.\n+\n+The following table gives some examples of factors and their levels:\n+\n+========= ============== ===============\n+Factor Factor level 1 Factor level 2 \n+--------- -------------- ---------------\n+Treatment Treated Untreated\n+--------- -------------- ---------------\n+Condition Knockdown Wildtype\n+--------- -------------- ---------------\n+TimePoint Day4 Day1\n+--------- -------------- ---------------\n+SeqType SingleEnd PairedEnd\n+--------- -------------- ---------------\n+Gender Female Male\n+========= ============== ===============\n+\n+*Note*: Output log2 fold changes are based on primary factor level 1 vs. factor level2. Here the order of factor levels is important. For example, for the factor \'Treatment\' given in above table, DESeq2 computes fold changes of \'Treated\' samples against \'Untreated\', i.e. the values correspond to up or down regulations of genes in Treated samples.\n+\n+**Output**\n+\n+DESeq2_ generates a tabular file containing the different columns and optional visualized results as PDF.\n+\n+====== ==========================================================\n+Column Description\n+------ ----------------------------------------------------------\n+ 1 Gene Identifiers\n+ 2 mean normalised counts, averaged over all samples from both conditions\n+ 3 the logarithm (to basis 2) of the fold change (See the note in inputs section)\n+ 4 standard error estimate for the log2 fold change estimate\n+ 5 p value for the statistical significance of this change\n+ 6 p value adjusted for multiple testing with the Benjamini-Hochberg procedure\n+ which controls false discovery rate (FDR)\n+====== ==========================================================\n+\n+\n+.. _DESeq2: http://master.bioconductor.org/packages/release/bioc/html/DESeq2.html\n+]]>\n+ </help>\n+ <citations>\n+ <citation type="doi">10.1186/s13059-014-0550-8</citation>\n+ </citations>\n+</tool>\n' |
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| diff -r 000000000000 -r d983d19fbbab test-data/GSM461176_untreat_single.counts --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/GSM461176_untreat_single.counts Mon Sep 28 05:07:29 2015 -0400 |
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| b'@@ -0,0 +1,4004 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| diff -r 000000000000 -r d983d19fbbab test-data/GSM461177_untreat_paired.counts --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/GSM461177_untreat_paired.counts Mon Sep 28 05:07:29 2015 -0400 |
| b |
| b'@@ -0,0 +1,4004 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|
| b |
| diff -r 000000000000 -r d983d19fbbab test-data/GSM461178_untreat_paired.counts --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/GSM461178_untreat_paired.counts Mon Sep 28 05:07:29 2015 -0400 |
| b |
| b'@@ -0,0 +1,4004 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|
| b |
| diff -r 000000000000 -r d983d19fbbab test-data/GSM461179_treat_single.counts --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/GSM461179_treat_single.counts Mon Sep 28 05:07:29 2015 -0400 |
| b |
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|
| b |
| diff -r 000000000000 -r d983d19fbbab test-data/GSM461180_treat_paired.counts --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/GSM461180_treat_paired.counts Mon Sep 28 05:07:29 2015 -0400 |
| b |
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|
| b |
| diff -r 000000000000 -r d983d19fbbab test-data/GSM461181_treat_paired.counts --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/GSM461181_treat_paired.counts Mon Sep 28 05:07:29 2015 -0400 |
| b |
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|
| b |
| diff -r 000000000000 -r d983d19fbbab test-data/GSM461182_untreat_single.counts --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/GSM461182_untreat_single.counts Mon Sep 28 05:07:29 2015 -0400 |
| b |
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n0030386\t0\n+FBgn0030389\t0\n+FBgn0030390\t0\n+FBgn0030391\t101\n+FBgn0030394\t3\n+FBgn0030395\t0\n+FBgn0030396\t10\n+FBgn0030398\t0\n+FBgn0030399\t1\n+FBgn0030400\t301\n+FBgn0030403\t294\n+FBgn0030406\t41\n+FBgn0030407\t16\n+FBgn0030408\t0\n+FBgn0030409\t0\n+FBgn0030410\t27\n+FBgn0030411\t26\n+FBgn0030412\t412\n+FBgn0030417\t9\n+FBgn0030418\t97\n+FBgn0030420\t343\n+FBgn0030421\t93\n+FBgn0030425\t2\n+FBgn0030429\t1\n+FBgn0030431\t174\n+FBgn0030432\t9\n+FBgn0030433\t136\n+FBgn0030434\t224\n+FBgn0030435\t240\n+FBgn0030437\t0\n+FBgn0030438\t1\n+FBgn0030439\t0\n+FBgn0030440\t0\n+FBgn0030441\t0\n+FBgn0030443\t0\n+FBgn0030447\t157\n+FBgn0030448\t111\n+FBgn0030449\t0\n+FBgn0030451\t298\n+FBgn0030452\t341\n+FBgn0030455\t1\n+FBgn0030456\t227\n+FBgn0030457\t169\n+FBgn0030459\t1\n+FBgn0030460\t127\n+FBgn0030462\t0\n+FBgn0030465\t165\n+FBgn0030466\t705\n+FBgn0030467\t237\n+FBgn0030468\t452\n+FBgn0030469\t357\n+FBgn0030474\t239\n+FBgn0030477\t0\n+FBgn0030478\t427\n+FBgn0030479\t50\n+FBgn0030480\t72\n+FBgn0030481\t123\n+FBgn0030482\t1315\n+FBgn0030483\t0\n+FBgn0030484\t275\n+FBgn0030485\t70\n+FBgn0030486\t534\n+FBgn0030491\t0\n+FBgn0030492\t0\n+FBgn0030493\t0\n+FBgn0030494\t0\n+FBgn0030495\t0\n+FBgn0030499\t186\n+FBgn0030500\t158\n+FBgn0030501\t299\n+FBgn0030502\t735\n+FBgn0030503\t33\n+FBgn0030504\t894\n+FBgn0030505\t397\n+FBgn0030506\t108\n+FBgn0030507\t141\n+FBgn0030508\t0\n+FBgn0030509\t0\n+FBgn0030510\t93\n+FBgn0030511\t57\n+FBgn0030512\t369\n+FBgn0030514\t452\n+FBgn0030518\t101\n+FBgn0030519\t355\n+FBgn0030520\t1140\n+FBgn0030521\t1299\n+FBgn0030522\t83\n+FBgn0030524\t5\n+FBgn0030525\t1\n+FBgn0030528\t40\n+FBgn0030529\t2773\n+FBgn0030530\t450\n+FBgn0030532\t444\n+FBgn0030536\t1\n+FBgn0030537\t0\n+FBgn0030538\t0\n+FBgn0030539\t0\n+FBgn0030540\t0\n+FBgn0030541\t0\n+FBgn0030542\t0\n+FBgn0030543\t0\n+FBgn0030544\t0\n+FBgn0030545\t100\n+FBgn0030551\t1\n+FBgn0030552\t131\n+FBgn0030554\t95\n+FBgn0030555\t59\n+FBgn0030556\t395\n+FBgn0030558\t0\n+FBgn0030559\t1\n+FBgn0030562\t16\n+FBgn0030563\t0\n+FBgn0030566\t0\n+FBgn0030569\t0\n+FBgn0030570\t0\n+FBgn0030571\t59\n+FBgn0030572\t87\n+FBgn0030573\t10\n+FBgn0030574\t1\n+FBgn0030575\t14\n+FBgn0030576\t91\n+FBgn0030577\t0\n+FBgn0030578\t0\n+FBgn0030581\t133\n+FBgn0030582\t329\n+FBgn0030583\t12\n+FBgn0030584\t92\n+FBgn0030586\t0\n+FBgn0030587\t0\n+FBgn0030588\t54\n+FBgn0030589\t0\n+FBgn0030590\t4\n+FBgn0030591\t1\n+FBgn0030592\t1\n+FBgn0030593\t4\n+FBgn0030594\t2\n+FBgn0030595\t1\n+FBgn0030596\t1\n+FBgn0030597\t1\n+FBgn0030598\t5\n+FBgn0030599\t6\n+FBgn0030600\t619\n+FBgn0030603\t230\n+FBgn0030605\t170\n+FBgn0030606\t180\n+FBgn0030607\t0\n+FBgn0030608\t0\n+FBgn0030610\t74\n+FBgn0030611\t45\n+FBgn0030612\t161\n+FBgn0030613\t0\n+FBgn0030614\t0\n+FBgn0030615\t19\n+FBgn0030616\t6362\n+FBgn0030617\t0\n+FBgn0030618\t0\n+FBgn0030619\t0\n+FBgn0030620\t0\n+FBgn0030621\t0\n+FBgn0030622\t0\n+FBgn0030623\t0\n+FBgn0030624\t0\n+FBgn0030625\t85\n+FBgn0030626\t118\n+FBgn0030627\t268\n+FBgn0030628\t175\n+FBgn0030629\t41\n+FBgn0030630\t145\n+FBgn0030631\t349\n+FBgn0030634\t2\n+FBgn0030636\t1\n+FBgn0030638\t277\n+FBgn0030640\t0\n+FBgn0030641\t4\n+FBgn0030642\t4\n+FBgn0030643\t3\n+FBgn0030645\t29\n+FBgn0030646\t75\n+FBgn0030647\t5\n+FBgn0030648\t88\n+FBgn0030653\t28\n+FBgn0030654\t39\n+FBgn0030655\t91\n+FBgn0030657\t30\n+FBgn0030658\t336\n+FBgn0030659\t123\n+FBgn0030660\t61\n+FBgn0030661\t5\n+FBgn0030662\t108\n+FBgn0030663\t0\n+FBgn0030664\t2\n+FBgn0030665\t2\n+FBgn0030666\t5\n+FBgn0030667\t27\n+FBgn0030668\t79\n+FBgn0030669\t75\n+FBgn0030670\t247\n+FBgn0030671\t78\n+FBgn0030672\t2028\n+FBgn0030673\t31\n+FBgn0030674\t2711\n+FBgn0030675\t21\n+FBgn0030676\t0\n+FBgn0030678\t76\n+FBgn0030679\t110\n+FBgn0030680\t153\n+FBgn0030683\t102\n+FBgn0030684\t3\n+FBgn0030685\t753\n+FBgn0030686\t138\n+FBgn0030687\t255\n+FBgn0030688\t1\n+FBgn0030691\t9\n+FBgn0030692\t241\n+FBgn0030693\t126\n+FBgn0030694\t55\n+no_feature\t165407\n+ambiguous\t48373\n+too_low_aQual\t0\n+not_aligned\t0\n+alignment_not_unique\t6896814\n' |
| b |
| diff -r 000000000000 -r d983d19fbbab test-data/deseq2_out.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/deseq2_out.tab Mon Sep 28 05:07:29 2015 -0400 |
| b |
| b'@@ -0,0 +1,3999 @@\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\t1.3712'..b'8176183\tNA\n+FBgn0030477\t0.661041167025807\t0.0081984754077381\t0.0850498283643641\t0.0963961428894931\t0.923205955387942\tNA\n+FBgn0030483\t2.080205027065\t-0.0239949304720301\t0.0987342413330125\t-0.243025420037407\t0.807985705326572\tNA\n+FBgn0030491\t1.23119801662681\t-0.0641480310242875\t0.10788944820293\t-0.594571870491276\t0.552129687688108\tNA\n+FBgn0030492\t0\tNA\tNA\tNA\tNA\tNA\n+FBgn0030493\t0.105352514349918\t-0.025474153197091\t0.0405830546409886\t-0.627704183986246\t0.530197743961967\tNA\n+FBgn0030494\t0\tNA\tNA\tNA\tNA\tNA\n+FBgn0030495\t0\tNA\tNA\tNA\tNA\tNA\n+FBgn0030508\t2.87475877539332\t-0.0248438786809049\t0.146943510346916\t-0.169070948572356\t0.865740835619969\tNA\n+FBgn0030509\t0.105352514349918\t-0.025474153197091\t0.0405830546409886\t-0.627704183986246\t0.530197743961967\tNA\n+FBgn0030525\t1.80722574742121\t0.0474905207215449\t0.125449836571252\t0.378561838098304\t0.705013265285825\tNA\n+FBgn0030536\t1.19456732550319\t0.0654391088021302\t0.0865521136606593\t0.756065981920374\t0.449609636576436\tNA\n+FBgn0030537\t0.0923751652987496\t0.0204895066777026\t0.0402731980486052\t0.508762841554675\t0.610918468176183\tNA\n+FBgn0030538\t0.080862070626247\t-0.023087221762983\t0.0399975293297779\t-0.577216196846307\t0.563793416905248\tNA\n+FBgn0030539\t0.181391852667795\t-0.000922878168198612\t0.0431227595100373\t-0.0214011853296124\t0.982925628026842\tNA\n+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+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+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+FBgn0030570\t0\tNA\tNA\tNA\tNA\tNA\n+FBgn0030577\t0.269423611141796\t0.0265926273358347\t0.0432208169475914\t0.615273593002195\t0.538374053776731\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+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+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' |
| b |
| diff -r 000000000000 -r d983d19fbbab test-data/deseq2_out_filtered.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/deseq2_out_filtered.tab Mon Sep 28 05:07:29 2015 -0400 |
| b |
| b'@@ -0,0 +1,3999 @@\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\t1.3712'..b'8176183\tNA\n+FBgn0030477\t0.661041167025807\t0.0081984754077381\t0.0850498283643641\t0.0963961428894931\t0.923205955387942\tNA\n+FBgn0030483\t2.080205027065\t-0.0239949304720301\t0.0987342413330125\t-0.243025420037407\t0.807985705326572\tNA\n+FBgn0030491\t1.23119801662681\t-0.0641480310242875\t0.10788944820293\t-0.594571870491276\t0.552129687688108\tNA\n+FBgn0030492\t0\tNA\tNA\tNA\tNA\tNA\n+FBgn0030493\t0.105352514349918\t-0.025474153197091\t0.0405830546409886\t-0.627704183986246\t0.530197743961967\tNA\n+FBgn0030494\t0\tNA\tNA\tNA\tNA\tNA\n+FBgn0030495\t0\tNA\tNA\tNA\tNA\tNA\n+FBgn0030508\t2.87475877539332\t-0.0248438786809049\t0.146943510346916\t-0.169070948572356\t0.865740835619969\tNA\n+FBgn0030509\t0.105352514349918\t-0.025474153197091\t0.0405830546409886\t-0.627704183986246\t0.530197743961967\tNA\n+FBgn0030525\t1.80722574742121\t0.0474905207215449\t0.125449836571252\t0.378561838098304\t0.705013265285825\tNA\n+FBgn0030536\t1.19456732550319\t0.0654391088021302\t0.0865521136606593\t0.756065981920374\t0.449609636576436\tNA\n+FBgn0030537\t0.0923751652987496\t0.0204895066777026\t0.0402731980486052\t0.508762841554675\t0.610918468176183\tNA\n+FBgn0030538\t0.080862070626247\t-0.023087221762983\t0.0399975293297779\t-0.577216196846307\t0.563793416905248\tNA\n+FBgn0030539\t0.181391852667795\t-0.000922878168198612\t0.0431227595100373\t-0.0214011853296124\t0.982925628026842\tNA\n+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+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+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+FBgn0030570\t0\tNA\tNA\tNA\tNA\tNA\n+FBgn0030577\t0.269423611141796\t0.0265926273358347\t0.0432208169475914\t0.615273593002195\t0.538374053776731\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+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+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' |
| b |
| diff -r 000000000000 -r d983d19fbbab tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Mon Sep 28 05:07:29 2015 -0400 |
| b |
| @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="deseq2" version="1.8.1"> + <repository changeset_revision="245e19b70f1d" name="package_deseq2_1_8_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency> |