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(-) [+]
line wrap: on
line diff
--- 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>