| Previous changeset 129:a95f5496d330 (2014-11-28) Next changeset 131:21b218a7429f (2015-01-06) |
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Commit message:
with tests |
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modified:
test-data/edgeRtest1out.html test-data/edgeRtest1out.xls |
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| diff -r a95f5496d330 -r a9ffdf5f7d2a test-data/edgeRtest1out.html --- a/test-data/edgeRtest1out.html Fri Nov 28 06:45:33 2014 -0500 +++ b/test-data/edgeRtest1out.html Thu Jan 01 21:53:07 2015 -0500 |
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| b'@@ -8,26 +8,26 @@\n <body> \n <div class="toolFormBody"> \n \n-<div class="infomessage">Galaxy Tool "DifferentialCounts" run at 06/10/2014 15:33:02</div><br/>\n+<div class="infomessage">Galaxy Tool "Differential_Counts" run at 28/12/2014 21:02:37</div><br/>\n <div class="toolFormTitle">DESeq2 images and outputs</div>\n (Click on a thumbnail image to download the corresponding original PDF image)<br/>\n <div><table class="simple" cellpadding="2" cellspacing="2">\n <tr>\n-<td><a href="DESeq2_DifferentialCounts_MA_plot.pdf"><img src="DESeq2_DifferentialCounts_MA_plot.png" title="Click to download a PDF of DESeq2_DifferentialCounts_MA_plot.pdf" hspace="5" width="400" \n- alt="Image called DESeq2_DifferentialCounts_MA_plot.pdf"/></a></td>\n+<td><a href="DESeq2_edgeRtest_MA_plot.pdf"><img src="DESeq2_edgeRtest_MA_plot.png" title="Click to download a PDF of DESeq2_edgeRtest_MA_plot.pdf" hspace="5" width="400" \n+ alt="Image called DESeq2_edgeRtest_MA_plot.pdf"/></a></td>\n \n-<td><a href="DESeq2_DifferentialCounts_PCA_plot.pdf"><img src="DESeq2_DifferentialCounts_PCA_plot.png" title="Click to download a PDF of DESeq2_DifferentialCounts_PCA_plot.pdf" hspace="5" width="400" \n- alt="Image called DESeq2_DifferentialCounts_PCA_plot.pdf"/></a></td>\n+<td><a href="DESeq2_edgeRtest_PCA_plot.pdf"><img src="DESeq2_edgeRtest_PCA_plot.png" title="Click to download a PDF of DESeq2_edgeRtest_PCA_plot.pdf" hspace="5" width="400" \n+ alt="Image called DESeq2_edgeRtest_PCA_plot.pdf"/></a></td>\n \n-<td><a href="DESeq2_DifferentialCounts_dispersion_estimates.pdf"><img src="DESeq2_DifferentialCounts_dispersion_estimates.png" title="Click to download a PDF of DESeq2_DifferentialCounts_dispersion_estimates.pdf" hspace="5" width="400" \n- alt="Image called DESeq2_DifferentialCounts_dispersion_estimates.pdf"/></a></td>\n+<td><a href="DESeq2_edgeRtest_dispersion_estimates.pdf"><img src="DESeq2_edgeRtest_dispersion_estimates.png" title="Click to download a PDF of DESeq2_edgeRtest_dispersion_estimates.pdf" hspace="5" width="400" \n+ alt="Image called DESeq2_edgeRtest_dispersion_estimates.pdf"/></a></td>\n </tr>\n <tr>\n-<td><a href="DESeq2_DifferentialCounts_qqplot.pdf"><img src="DESeq2_DifferentialCounts_qqplot.png" title="Click to download a PDF of DESeq2_DifferentialCounts_qqplot.pdf" hspace="5" width="400" \n- alt="Image called DESeq2_DifferentialCounts_qqplot.pdf"/></a></td>\n+<td><a href="DESeq2_edgeRtest_qqplot.pdf"><img src="DESeq2_edgeRtest_qqplot.png" title="Click to download a PDF of DESeq2_edgeRtest_qqplot.pdf" hspace="5" width="400" \n+ alt="Image called DESeq2_edgeRtest_qqplot.pdf"/></a></td>\n \n-<td><a href="DESeq2_DifferentialCounts_sample_distance_plot.pdf"><img src="DESeq2_DifferentialCounts_sample_distance_plot.png" title="Click to download a PDF of DESeq2_DifferentialCounts_sample_distance_plot.pdf" hspace="5" width="400" \n- alt="Image called DESeq2_DifferentialCounts_sample_distance_plot.pdf"/></a></td>\n+<td><a href="DESeq2_edgeRtest_sample_distance_plot.pdf"><img src="DESeq2_edgeRtest_sample_distance_plot.png" title="Click to download a PDF of DESeq2_edgeRtest_sample_distance_plot.pdf" hspace="5" width="400" \n+ alt="Image called DESeq2_edgeRtest_sample_distance_plot.pdf"/></a></td>\n \n <td> </td>\n </tr></table></div>\n@@ -40,116 +40,180 @@\n \n Contig baseMean log2FoldChange lfcSE stat pvalue padj NReads URL\n \n-Mir122a Mir122a 10112.31117 10.433687 0.3440661 30.324653 5.425198e-202 4.568017e-199 90428 <a href=\'http://www.genecards.org/index.php?path=/Search/keyword/Mir122a\'>Mir122a</a>\n+Mir192 Mi'..b'</tr>\n-<tr><td><a href="VOOM_DifferentialCounts_qqplot.pdf">VOOM_DifferentialCounts_qqplot.pdf</a></td><td>17.5 KB</td></tr>\n-<tr class="odd_row"><td><a href="Venn_DifferentialCounts_significant_genes_overlap.pdf">Venn_DifferentialCounts_significant_genes_overlap.pdf</a></td><td>9.7 KB</td></tr>\n-<tr><td><a href="edgeR.log">edgeR.log</a></td><td>13.1 KB</td></tr>\n-<tr class="odd_row"><td><a href="edgeR_DifferentialCounts_BCV_vs_abundance.pdf">edgeR_DifferentialCounts_BCV_vs_abundance.pdf</a></td><td>17.4 KB</td></tr>\n-<tr><td><a href="edgeR_DifferentialCounts_GoodnessofFit.pdf">edgeR_DifferentialCounts_GoodnessofFit.pdf</a></td><td>13.1 KB</td></tr>\n-<tr class="odd_row"><td><a href="edgeR_DifferentialCounts_MDSplot.pdf">edgeR_DifferentialCounts_MDSplot.pdf</a></td><td>5.0 KB</td></tr>\n-<tr><td><a href="edgeR_DifferentialCounts_qqplot.pdf">edgeR_DifferentialCounts_qqplot.pdf</a></td><td>15.2 KB</td></tr>\n-<tr class="odd_row"><td><a href="edgeR_DifferentialCounts_raw_norm_counts_box.pdf">edgeR_DifferentialCounts_raw_norm_counts_box.pdf</a></td><td>7.8 KB</td></tr>\n-<tr><td><a href="edgeR_DifferentialCounts_smearplot.pdf">edgeR_DifferentialCounts_smearplot.pdf</a></td><td>16.6 KB</td></tr>\n-<tr class="odd_row"><td><a href="edgeR_DifferentialCounts_top_100_heatmap.pdf">edgeR_DifferentialCounts_top_100_heatmap.pdf</a></td><td>11.5 KB</td></tr>\n-<tr><td><a href="sample_counts_histogram.pdf">sample_counts_histogram.pdf</a></td><td>11.0 KB</td></tr>\n+<tr class="odd_row"><td><a href="DESeq2_edgeRtest_MA_plot.pdf">DESeq2_edgeRtest_MA_plot.pdf</a></td><td>15.0 KB</td></tr>\n+<tr><td><a href="DESeq2_edgeRtest_PCA_plot.pdf">DESeq2_edgeRtest_PCA_plot.pdf</a></td><td>4.9 KB</td></tr>\n+<tr class="odd_row"><td><a href="DESeq2_edgeRtest_dispersion_estimates.pdf">DESeq2_edgeRtest_dispersion_estimates.pdf</a></td><td>190.6 KB</td></tr>\n+<tr><td><a href="DESeq2_edgeRtest_qqplot.pdf">DESeq2_edgeRtest_qqplot.pdf</a></td><td>13.3 KB</td></tr>\n+<tr class="odd_row"><td><a href="DESeq2_edgeRtest_sample_distance_plot.pdf">DESeq2_edgeRtest_sample_distance_plot.pdf</a></td><td>9.5 KB</td></tr>\n+<tr><td><a href="Differential.log">Differential.log</a></td><td>1.4 KB</td></tr>\n+<tr class="odd_row"><td><a href="Differential_Counts.Rscript">Differential_Counts.Rscript</a></td><td>28.3 KB</td></tr>\n+<tr><td><a href="Differential_Counts_error.log">Differential_Counts_error.log</a></td><td>1.8 KB</td></tr>\n+<tr class="odd_row"><td><a href="Differential_Counts_runner.log">Differential_Counts_runner.log</a></td><td>1.3 KB</td></tr>\n+<tr><td><a href="Differential_rowsum_bar_charts.pdf">Differential_rowsum_bar_charts.pdf</a></td><td>6.3 KB</td></tr>\n+<tr class="odd_row"><td><a href="Differential_venn_edgeRtest_significant_genes_overlap.pdf">Differential_venn_edgeRtest_significant_genes_overlap.pdf</a></td><td>9.7 KB</td></tr>\n+<tr><td><a href="VOOM.log">VOOM.log</a></td><td>10.1 KB</td></tr>\n+<tr class="odd_row"><td><a href="VOOM_edgeRtest_mean_variance_plot.pdf">VOOM_edgeRtest_mean_variance_plot.pdf</a></td><td>18.3 KB</td></tr>\n+<tr><td><a href="VOOM_edgeRtest_qqplot.pdf">VOOM_edgeRtest_qqplot.pdf</a></td><td>17.5 KB</td></tr>\n+<tr class="odd_row"><td><a href="edgeR.log">edgeR.log</a></td><td>10.4 KB</td></tr>\n+<tr><td><a href="edgeR_edgeRtest_BCV_vs_abundance.pdf">edgeR_edgeRtest_BCV_vs_abundance.pdf</a></td><td>17.4 KB</td></tr>\n+<tr class="odd_row"><td><a href="edgeR_edgeRtest_GoodnessofFit.pdf">edgeR_edgeRtest_GoodnessofFit.pdf</a></td><td>13.1 KB</td></tr>\n+<tr><td><a href="edgeR_edgeRtest_MDSplot.pdf">edgeR_edgeRtest_MDSplot.pdf</a></td><td>4.9 KB</td></tr>\n+<tr class="odd_row"><td><a href="edgeR_edgeRtest_qqplot.pdf">edgeR_edgeRtest_qqplot.pdf</a></td><td>15.2 KB</td></tr>\n+<tr><td><a href="edgeR_edgeRtest_smearplot.pdf">edgeR_edgeRtest_smearplot.pdf</a></td><td>16.7 KB</td></tr>\n+<tr class="odd_row"><td><a href="edgeR_edgeRtest_top_100_heatmap.pdf">edgeR_edgeRtest_top_100_heatmap.pdf</a></td><td>11.2 KB</td></tr>\n </table></div><br/>\n </div></body></html>\n \n' |
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| diff -r a95f5496d330 -r a9ffdf5f7d2a test-data/edgeRtest1out.xls --- a/test-data/edgeRtest1out.xls Fri Nov 28 06:45:33 2014 -0500 +++ b/test-data/edgeRtest1out.xls Thu Jan 01 21:53:07 2015 -0500 |
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| b'@@ -1,1142 +1,1142 @@\n-Name\tlogFC\tlogCPM\tLR\tPValue\tadj.p.value\tDispersion\ttotreads\tLiver_X11706Liv_CAAAAG_L003_R1_001_trimmed.fastq_bwa.sam.bam\tLiver_X11700Liv_ATTCCT_L003_R1_001_trimmed.fastq_bwa.sam.bam\tLiver_X11698Liv_ACTGAT_L003_R1_001_trimmed.fastq_bwa.sam.bam\tLiver_X11699Liv_ATGAGC_L003_R1_001_trimmed.fastq_bwa.sam.bam\tHeart_X11706He_AGTTCC_L001_R1_001_trimmed.fastq_bwa.sam.bam\tHeart_X11699He_GGCTAC_L001_R1_001_trimmed.fastq_bwa.sam.bam\tHeart_X11698He_TAGCTT_L001_R1_001_trimmed.fastq_bwa.sam.bam\tHeart_X11700He_CTTGTA_L001_R1_001_trimmed.fastq_bwa.sam.bam\tLiver_X11706Liv_CAAAAG_L003_R1_001_trimmed.fastq_bwa.sam.bam\tLiver_X11700Liv_ATTCCT_L003_R1_001_trimmed.fastq_bwa.sam.bam\tLiver_X11698Liv_ACTGAT_L003_R1_001_trimmed.fastq_bwa.sam.bam\tLiver_X11699Liv_ATGAGC_L003_R1_001_trimmed.fastq_bwa.sam.bam\tHeart_X11706He_AGTTCC_L001_R1_001_trimmed.fastq_bwa.sam.bam\tHeart_X11699He_GGCTAC_L001_R1_001_trimmed.fastq_bwa.sam.bam\tHeart_X11698He_TAGCTT_L001_R1_001_trimmed.fastq_bwa.sam.bam\tHeart_X11700He_CTTGTA_L001_R1_001_trimmed.fastq_bwa.sam.bam\n-Mir208a\t-11.8407506325994\t8.46501715136261\t594.169461788588\t3.10454340520719e-131\t3.54228402534141e-128\t0.0517121951525415\t4638\t0\t0\t0\t0.539638866040004\t398.994619637285\t739.374891373071\t901.627384247207\t673.126883915814\t0\t0\t0\t1\t1060\t956\t1693\t928\n-Mir149\t-7.00898388335122\t8.86176664758882\t484.303208159111\t2.47390942083987e-107\t1.41136532458914e-104\t0.0495993679492896\t6164\t18.1338061399734\t6.7041218845597\t4.90063242902982\t5.93467521388658\t754.954773589966\t422.708450804407\t1774.96378211422\t686.472355755848\t25\t9\t8\t16\t1399\t1123\t2295\t1289\n-Mir208b\t-13.2916347677151\t9.90594480087289\t417.697578727504\t7.73746551125031e-93\t2.94281604944553e-90\t0.105080963479123\t14756\t0.773404698088987\t0\t0\t0\t1255.17448088526\t610.90062982945\t4804.9444632202\t811.163589922971\t1\t0\t0\t0\t2049\t1647\t8904\t2155\n-Mir122a\t10.5146833712803\t12.4780878408673\t415.174286432694\t2.74052770257465e-92\t7.81735527159419e-90\t0.108038824620343\t90428\t21591.5602947436\t18051.2206253928\t7296.42910777178\t9073.74748483171\t6.47566639248005\t2.63487012968019\t20.8819268484026\t4.26049561369029\t29767\t24233\t11911\t24463\t12\t7\t27\t8\n-Mir204\t-7.49816212336048\t7.63450677628189\t341.306784912854\t3.31342909192416e-76\t7.56124518777094e-74\t0.0690795842951528\t2601\t3.06289526814364\t0.741834401735822\t0.539638866040004\t3.38769016673167\t441.614082608811\t292.376511489496\t669.500122687819\t402.9922155052\t5\t2\t1\t9\t571\t549\t923\t541\n-Mir499\t-13.5774541855868\t8.70007828481468\t325.791991149153\t7.93076155694377e-73\t1.50816648941214e-70\t0.120422839284927\t6527\t0\t0\t0\t0\t630.331101425477\t543.778775080954\t2540.36533539833\t289.686333877839\t0\t0\t0\t0\t869\t730\t4147\t781\n-Mir490\t-8.53439419160321\t6.99102321339932\t303.171840011248\t6.71036527101623e-68\t1.09378953917565e-65\t0.0794971088607054\t1741\t1.11275160260373\t0.539638866040004\t0\t0.773404698088987\t187.994368954084\t225.58454838127\t558.676823713309\t197.25045526845\t3\t1\t0\t1\t353\t311\t750\t322\n-Mir192\t6.95385326892823\t17.1693636192881\t217.228663189203\t3.63831152188904e-49\t5.18914180809424e-47\t0.127009950205414\t2325567\t480279.658435161\t365245.774587834\t386444.883402629\t195324.997977042\t1734.39931545257\t1190.58488859692\t4662.8569247785\t1731.8914669651\t662133\t490327\t630849\t526600\t3214\t3163\t6029\t3252\n-Mir802\t11.4408053854895\t6.59338011170441\t212.880584185723\t3.23164660393739e-48\t4.09700975010284e-46\t0.122736709116123\t1514\t297.880654054082\t150.940417428822\t161.641581900598\t187.461807002373\t0\t0\t0\t0\t552\t401\t209\t352\t0\t0\t0\t0\n-Mir1948\t7.41814210391099\t7.25273383973858\t195.669583395952\t1.84024805337572e-44\t2.0997230289017e-42\t0.120602206022636\t2404\t672.088682639329\t345.100144708913\t187.866231610125\t459.604800308149\t1.22515810725746\t0.741834401735822\t1.61891659812001\t1.50564007410296\t869\t648\t259\t617\t2\t2\t3\t4\n-Mir194-2\t5.2989500004112\t7.81152218291727\t191.855876570524\t1.25095983644798e-43\t1.29758652126104e-41\t0.0867075108051565\t3570\t954.563555208202\t644.340603349349\t268.922204543012\t326.407136763762\t10.2531384547601\t5.64615027788611\t15.4680939617797\t8.52099122738058\t1316'..b'73498972596457\t0.00166750535258586\t0.967427357317129\t0.979600222217201\t0.367416862910588\t9\t0.376410018525741\t0\t1.06512390342257\t1.07927773208001\t0.744902431617745\t1.54680939617797\t0\t0.725352245598938\t1\t0\t2\t2\t1\t2\t0\t1\n+6330549D23Rik\t0.0365504895754985\t0.766481265149971\t0.00165505138189159\t0.967549154353767\t0.979600222217201\t0.144795356612801\t9\t0.752820037051481\t1.22515810725746\t0\t0.539638866040004\t0.744902431617745\t0.773404698088987\t0.370917200867911\t0.725352245598938\t2\t2\t0\t1\t1\t1\t1\t1\n+Gm16291\t-0.0497984136905431\t1.04049827004916\t0.00165184486677905\t0.96758058758877\t0.979600222217201\t0.760533853439203\t14\t0.752820037051481\t0.612579053628728\t2.66280975855643\t0\t2.23470729485323\t1.54680939617797\t0\t0.725352245598938\t2\t1\t5\t0\t3\t2\t0\t1\n+Gm4890\t-0.0259416163380367\t0.436081268353407\t0.00151936462515234\t0.968907109122493\t0.98007359176309\t0.663367644323302\t4\t0\t0\t1.06512390342257\t0\t0\t0\t0.741834401735823\t0\t0\t0\t2\t0\t0\t0\t2\t0\n+5430402O13Rik\t-0.0215659699049333\t0.436296133284018\t0.00131072419039668\t0.971119756290488\t0.980573134449068\t0.66336084861507\t4\t0\t0\t0\t1.07927773208001\t0\t0\t0.741834401735823\t0\t0\t0\t0\t2\t0\t0\t2\t0\n+Gm6297\t-0.0215659699049333\t0.436296133284018\t0.00131072419039668\t0.971119756290488\t0.980573134449068\t0.66336084861507\t4\t0\t0\t0\t1.07927773208001\t0\t0\t0.741834401735823\t0\t0\t0\t0\t2\t0\t0\t2\t0\n+G730013B05Rik\t-0.0385365765720963\t1.01651726367811\t0.000926357662148547\t0.975719235170337\t0.983633409630645\t0.703663961483763\t14\t2.25846011115444\t0\t1.06512390342257\t0\t1.48980486323549\t1.54680939617797\t0.741834401735823\t0\t6\t0\t2\t0\t2\t2\t2\t0\n+Fut8\t-0.0301535765572007\t0.983272857012977\t0.000914530335813346\t0.975874688608142\t0.983633409630645\t0.461988777734778\t13\t0.376410018525741\t0.612579053628728\t2.66280975855643\t0\t0.744902431617745\t1.54680939617797\t0.741834401735823\t0.725352245598938\t1\t1\t5\t0\t1\t2\t2\t1\n+Mir451\t0.00783986907310383\t10.6424503554937\t0.000668429572201035\t0.979373786499111\t0.986289047127525\t0.0880041428130113\t23834\t1259.46792198713\t1282.12795924493\t1240.8693474873\t2624.26380555254\t1712.5306902892\t1143.86554847361\t1957.70098618084\t1556.60591905532\t3346\t2093\t2330\t4863\t2299\t1479\t5278\t2146\n+Mir3103\t-0.0011092316730465\t0.437273490728585\t0.00054275250380531\t0.981413325432899\t0.987471432380016\t0.663329937374097\t4\t0\t0.612579053628728\t0\t0.539638866040004\t0\t0\t0.741834401735823\t0\t0\t1\t0\t1\t0\t0\t2\t0\n+Mir877\t0.0169238059397901\t2.07117778204749\t0.000493226392977775\t0.982281477037185\t0.987474154448835\t0.411290532451564\t45\t2.25846011115444\t4.2880533754011\t0.532561951711286\t5.93602752644005\t2.23470729485323\t3.09361879235595\t1.85458600433956\t5.8028179647915\t6\t7\t1\t11\t3\t4\t5\t8\n+Mirlet7a-2\t0.00692268187132084\t3.52904314853656\t0.000229292382525781\t0.987918571764677\t0.991638607573432\t0.145210168895582\t158\t13.1743506484009\t10.4138439116884\t7.98842927566929\t9.71349958872008\t8.93882917941294\t9.28085637706784\t13.7239364321127\t8.70422694718725\t35\t17\t15\t18\t12\t12\t37\t12\n+Adarb1\t-0.0208372088988242\t1.01574105327976\t0.000220136486121625\t0.988162223322517\t0.991638607573432\t0.682420434692774\t14\t2.25846011115444\t0\t1.06512390342257\t0\t1.48980486323549\t0\t0.741834401735823\t1.45070449119788\t6\t0\t2\t0\t2\t0\t2\t2\n+Zfp821\t0.0194908209613808\t0.438251386312134\t0.000105716899237329\t0.991796397330917\t0.994410974828274\t0.663299009834018\t4\t0\t1.22515810725746\t0\t0\t0\t0\t0.741834401735823\t0\t0\t2\t0\t0\t0\t0\t2\t0\n+Snord7\t-0.00363412912961608\t0.808396104681926\t2.65747690626483e-05\t0.99588686572452\t0.997635569615169\t1.23423123101037\t10\t2.25846011115444\t0\t0\t0\t0.744902431617745\t0\t0.370917200867911\t1.45070449119788\t6\t0\t0\t0\t1\t0\t1\t2\n+D330022K07Rik\t8.83246306215062e-05\t2.3059219632559\t9.35429808279764e-07\t0.999228305160102\t0.999852120027929\t0.587915295555401\t56\t4.89333024083463\t0.612579053628728\t9.05355317909186\t1.07927773208001\t4.46941458970647\t7.73404698088987\t1.11275160260373\t2.90140898239575\t13\t1\t17\t2\t6\t10\t3\t4\n+AA465934\t-0.00551213095838715\t1.05434721413031\t3.43509380940077e-08\t0.999852120027929\t0.999852120027929\t1.50064027311007\t15\t3.38769016673167\t0\t0\t0\t0.744902431617745\t0\t0.741834401735823\t2.17605673679681\t9\t0\t0\t0\t1\t0\t2\t3\n' |