Mercurial > repos > iuc > deseq2
changeset 2:afe2a77c5900 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit e0f819a2fd56eb5ee30a7fd772780693e1f085fa
| author | iuc |
|---|---|
| date | Wed, 02 Dec 2015 17:40:45 -0500 |
| parents | 89bbd1dbf48d |
| children | 248e9c78346e |
| files | deseq2.xml tool_dependencies.xml |
| diffstat | 2 files changed, 6 insertions(+), 4 deletions(-) [+] |
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--- a/deseq2.xml Wed Oct 14 03:25:12 2015 -0400 +++ b/deseq2.xml Wed Dec 02 17:40:45 2015 -0500 @@ -1,4 +1,4 @@ -<tool id="deseq2" name="DESeq2" version="2.1.8.2"> +<tool id="deseq2" name="DESeq2" version="2.1.8.3"> <description>Determines differentially expressed features from count tables</description> <requirements> <!-- odering is crucial, otherwise R will override the ENV variables from deseq2 --> @@ -41,6 +41,7 @@ #end for $temp_factor.append( {str($level.factorLevel): $count_files} ) #end for + $temp_factor.reverse() $temp_factor_names.append([str($factor.factorName), $temp_factor]) #end for -f '#echo json.dumps(temp_factor_names)#' @@ -170,8 +171,9 @@ 2 mean normalised counts, averaged over all samples from both conditions 3 the logarithm (to basis 2) of the fold change (See the note in inputs section) 4 standard error estimate for the log2 fold change estimate - 5 p value for the statistical significance of this change - 6 p value adjusted for multiple testing with the Benjamini-Hochberg procedure + 5 Wald statistic + 6 p value for the statistical significance of this change + 7 p value adjusted for multiple testing with the Benjamini-Hochberg procedure which controls false discovery rate (FDR) ====== ==========================================================
--- a/tool_dependencies.xml Wed Oct 14 03:25:12 2015 -0400 +++ b/tool_dependencies.xml Wed Dec 02 17:40:45 2015 -0500 @@ -1,6 +1,6 @@ <?xml version="1.0"?> <tool_dependency> <package name="deseq2" version="1.8.2"> - <repository changeset_revision="00b14423d00f" name="package_deseq2_1_8_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="623321e04b2d" name="package_deseq2_1_8_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> </tool_dependency>