Mercurial > repos > iuc > deseq2
changeset 8:57e2f9454d9e draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 50db5cdaef2ff3e54a63670108eb6e4ade2a630f
| author | iuc |
|---|---|
| date | Tue, 04 Apr 2017 10:17:29 -0400 |
| parents | cb23006f34ff |
| children | 6f91b8ce6e07 |
| files | deseq2.xml test-data/deseq2_out.tab test-data/deseq2_tximport_out.tab |
| diffstat | 3 files changed, 3435 insertions(+), 3438 deletions(-) [+] |
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--- a/deseq2.xml Mon Mar 20 17:23:27 2017 -0400 +++ b/deseq2.xml Tue Apr 04 10:17:29 2017 -0400 @@ -1,7 +1,7 @@ -<tool id="deseq2" name="DESeq2" version="2.11.38"> +<tool id="deseq2" name="DESeq2" version="2.11.39"> <description>Determines differentially expressed features from count tables</description> <requirements> - <requirement type="package" version="1.12.4">bioconductor-deseq2</requirement> + <requirement type="package" version="1.14.1">bioconductor-deseq2</requirement> </requirements> <stdio> <regex match="Execution halted" @@ -24,7 +24,6 @@ </version_command> <command> <![CDATA[ - #if $tximport.tximport_selector == 'tximport': #if $tximport.mapping_format.mapping_format_selector == 'gtf': ln -s '$tximport.mapping_format.gtf_file' mapping.gtf && @@ -209,7 +208,6 @@ 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 - **Inputs** 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. @@ -249,7 +247,6 @@ which controls false discovery rate (FDR) ====== ========================================================== - .. _DESeq2: http://master.bioconductor.org/packages/release/bioc/html/DESeq2.html ]]> </help>
--- a/test-data/deseq2_out.tab Mon Mar 20 17:23:27 2017 -0400 +++ b/test-data/deseq2_out.tab Tue Apr 04 10:17:29 2017 -0400 @@ -1,3179 +1,3130 @@ -FBgn0003360 1933.95040021558 -2.83947882860311 0.131398735103526 -21.6096359402999 1.45793503518353e-103 4.22509573196188e-100 -FBgn0029167 1648.81894046778 -2.12874859471823 0.110943514269587 -19.1876795027916 4.69124302384403e-82 6.79761114155e-79 -FBgn0025111 655.359768612902 2.56439431726834 0.137673641648878 18.6266178954469 1.95494155109008e-77 1.88847353835302e-74 -FBgn0029896 211.4755450268 -2.08770414088624 0.146427809890345 -14.2575658438766 4.02241730340987e-46 2.91424133632045e-43 -FBgn0000071 151.249383869297 2.07707140413389 0.16829300159233 12.3419951185216 5.38058421332163e-35 3.11858661004122e-32 -FBgn0027279 1317.42349329018 -1.15808854122062 0.0978228860467626 -11.8386257860662 2.46458088202281e-32 1.19039256601702e-29 -FBgn0023479 1361.36610109448 -1.42289412002226 0.123339462716259 -11.5364060186934 8.6462804814041e-31 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--- a/test-data/deseq2_tximport_out.tab Mon Mar 20 17:23:27 2017 -0400 +++ b/test-data/deseq2_tximport_out.tab Tue Apr 04 10:17:29 2017 -0400 @@ -1,4 +1,4 @@ -WASH7P 9900.55558083217 -4.23770412981225 0.206202033070674 -20.5512238007848 7.50472789083548e-94 3.00189115633419e-93 -DDX11L1 537.947385623122 0.311741396087371 0.207236221043698 1.50428045115548 0.132509170400216 0.265018340800432 -MIR6859-1 1535.69554043224 0.215149819818111 0.188163332682435 1.1434205418822 0.252864027682612 0.337152036910149 -MIR6859-2 80.7433269754715 -0.177756822115013 0.275440925762787 -0.645353705600378 0.51869799671008 0.51869799671008 +WASH7P 9900.55558083217 -4.23770405949884 0.206202398724737 -20.5511870167709 7.51041665825148e-94 3.00416666330059e-93 +DDX11L1 537.947385623122 0.311741386141816 0.207236860051557 1.50427576476627 0.132510376563798 0.265020753127596 +MIR6859-1 1535.69554043224 0.215149819624812 0.188163354844762 1.14342040618012 0.252864083997862 0.33715211199715 +MIR6859-2 80.7433269754715 -0.177756825325613 0.275440631693817 -0.645354406256263 0.5186975427612 0.5186975427612