# HG changeset patch # User iuc # Date 1517303206 18000 # Node ID c469357cf454ca5fd130038f62b6cf7b9d9acb11 # Parent 1844cd48af49beab61a5f5216d77d2234e1532ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 22882a8eabae0dcc15938423852d1325303b0b78 diff -r 1844cd48af49 -r c469357cf454 edger.R --- a/edger.R Tue Nov 07 08:17:41 2017 -0500 +++ b/edger.R Tue Jan 30 04:06:46 2018 -0500 @@ -486,9 +486,9 @@ sumStatus <- summary(status) # Collect counts for differential expression - upCount[i] <- sumStatus["1", ] - downCount[i] <- sumStatus["-1", ] - flatCount[i] <- sumStatus["0", ] + upCount[i] <- sumStatus["Up"] + downCount[i] <- sumStatus["Down"] + flatCount[i] <- sumStatus["NotSig"] # Write top expressions table top <- topTags(res, n=Inf, sort.by="PValue") diff -r 1844cd48af49 -r c469357cf454 edger.xml --- a/edger.xml Tue Nov 07 08:17:41 2017 -0500 +++ b/edger.xml Tue Jan 30 04:06:46 2018 -0500 @@ -1,20 +1,19 @@ - + Perform differential expression of count data - bioconductor-edger + bioconductor-edger r-rjson r-getopt + r-statmod - r-scales - - r-statmod + r-scales /dev/null | grep -v -i "WARNING: ")", scales version" $(R --vanilla --slave -e "library(scales); cat(sessionInfo()\$otherPkgs\$scales\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", rjson version" $(R --vanilla --slave -e "library(rjson); cat(sessionInfo()\$otherPkgs\$rjson\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", getopt version" $(R --vanilla --slave -e "library(getopt); cat(sessionInfo()\$otherPkgs\$getopt\$Version)" 2> /dev/null | grep -v -i "WARNING: ") +echo $(R --version | grep version | grep -v GNU)", edgeR version" $(R --vanilla --slave -e "library(edgeR); cat(sessionInfo()\$otherPkgs\$edgeR\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", scales version" $(R --vanilla --slave -e "library(scales); cat(sessionInfo()\$otherPkgs\$scales\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", rjson version" $(R --vanilla --slave -e "library(rjson); cat(sessionInfo()\$otherPkgs\$rjson\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", getopt version" $(R --vanilla --slave -e "library(getopt); cat(sessionInfo()\$otherPkgs\$getopt\$Version)" 2> /dev/null | grep -v -i "WARNING: ") ]]>