# 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 @@
-<tool id="edger" name="edgeR" version="3.16.5">
+<tool id="edger" name="edgeR" version="3.20.7.0">
     <description>
         Perform differential expression of count data
     </description>
 
     <requirements>
-        <requirement type="package" version="3.16.5">bioconductor-edger</requirement>
+        <requirement type="package" version="3.20.7">bioconductor-edger</requirement>
         <requirement type="package" version="0.2.15">r-rjson</requirement>
         <requirement type="package" version="1.20.0">r-getopt</requirement>
+        <requirement type="package" version="1.4.30">r-statmod</requirement>
         <!-- required for alpha function used with plotMD -->
-        <requirement type="package" version="0.4.1">r-scales</requirement>
-        <!-- This should be in limma conda now - check why still needed? -->
-        <requirement type="package" version="1.4.30">r-statmod</requirement>
+        <requirement type="package" version="0.5.0">r-scales</requirement>
     </requirements>
 
     <version_command><![CDATA[
-        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: ")
+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: ")
     ]]></version_command>
 
     <command detect_errors="exit_code"><![CDATA[
diff -r 1844cd48af49 -r c469357cf454 test-data/edgeR_Mut-WT_2fact.tsv
--- a/test-data/edgeR_Mut-WT_2fact.tsv	Tue Nov 07 08:17:41 2017 -0500
+++ b/test-data/edgeR_Mut-WT_2fact.tsv	Tue Jan 30 04:06:46 2018 -0500
@@ -1,7 +1,7 @@
 "GeneID"	"logFC"	"logCPM"	"F"	"PValue"	"FDR"
-"11287"	0.189281291475186	17.6499778192954	198.646314971919	7.90598427634257e-09	4.74359056580554e-08
+"11287"	0.189281291475186	17.6499778192954	198.646314971919	7.90598427634242e-09	4.74359056580545e-08
 "11298"	-0.13798041694802	17.6843133699537	96.2224552671758	4.15830411749776e-06	1.24749123524933e-05
 "11304"	0.458490715244216	15.526484673111	14.5864146735617	0.00244295799161999	0.00488591598323999
-"11303"	-0.0560600217169691	17.8909334307093	6.5300693781724	0.0442859767053646	0.0664289650580469
-"11305"	-0.0585095825423414	18.1629882429457	1.07140336604322	0.32103822810743	0.385245873728916
-"11302"	-0.0716631320244627	10.0898336653124	0.376796260571098	0.878304702615846	0.878304702615846
+"11303"	-0.0560600217169691	17.8909334307093	6.53006937817236	0.0442859767053646	0.0664289650580469
+"11305"	-0.0585095825423414	18.1629882429457	1.07140336604322	0.32103822810743	0.385245873728915
+"11302"	-0.0716631320244627	10.0898336653124	0.376796260569999	0.878304702615846	0.878304702615846
diff -r 1844cd48af49 -r c469357cf454 test-data/edgeR_Mut-WT_2fact_anno.tsv
--- a/test-data/edgeR_Mut-WT_2fact_anno.tsv	Tue Nov 07 08:17:41 2017 -0500
+++ b/test-data/edgeR_Mut-WT_2fact_anno.tsv	Tue Jan 30 04:06:46 2018 -0500
@@ -1,7 +1,7 @@
 "EntrezID"	"Symbol"	"GeneName"	"Chr"	"Length"	"logFC"	"logCPM"	"F"	"PValue"	"FDR"
-11287	"Pzp"	"pregnancy zone protein"	6	4681	0.189281947498313	17.6499778192954	198.646315096405	7.90598424818912e-09	4.74359054891347e-08
+11287	"Pzp"	"pregnancy zone protein"	6	4681	0.189281947498313	17.6499778192954	198.646315096405	7.90598424818915e-09	4.74359054891349e-08
 11298	"Aanat"	"arylalkylamine N-acetyltransferase"	11	1455	-0.137980416947824	17.6843133699537	96.2224553233548	4.15830411749738e-06	1.24749123524921e-05
 11304	"Abca4"	"ATP-binding cassette, sub-family A (ABC1), member 4"	3	7248	0.45849071524422	15.526484673111	14.5864146737822	0.00244295799149183	0.00488591598298366
 11303	"Abca1"	"ATP-binding cassette, sub-family A (ABC1), member 1"	4	10260	-0.0560600215744048	17.8909334307093	6.53006938009001	0.0442859767053567	0.066428965058035
 11305	"Abca2"	"ATP-binding cassette, sub-family A (ABC1), member 2"	2	8061	-0.0585095828508861	18.1629882429457	1.07140336564628	0.321038228193371	0.385245873832045
-11302	"Aatk"	"apoptosis-associated tyrosine kinase"	11	5743	-0.0716631320197652	10.0898336653124	0.376796260576848	0.878304702615841	0.878304702615841
+11302	"Aatk"	"apoptosis-associated tyrosine kinase"	11	5743	-0.0716631320197652	10.0898336653124	0.376796260576849	0.878304702615839	0.878304702615839
diff -r 1844cd48af49 -r c469357cf454 test-data/edgeR_WT-Mut_2fact_anno.tsv
--- a/test-data/edgeR_WT-Mut_2fact_anno.tsv	Tue Nov 07 08:17:41 2017 -0500
+++ b/test-data/edgeR_WT-Mut_2fact_anno.tsv	Tue Jan 30 04:06:46 2018 -0500
@@ -1,7 +1,7 @@
 "EntrezID"	"Symbol"	"GeneName"	"Chr"	"Length"	"logFC"	"logCPM"	"F"	"PValue"	"FDR"
-11287	"Pzp"	"pregnancy zone protein"	6	4681	-0.189281947498313	17.6499778192954	198.646315096405	7.90598424818912e-09	4.74359054891347e-08
+11287	"Pzp"	"pregnancy zone protein"	6	4681	-0.189281947498313	17.6499778192954	198.646315096405	7.90598424818915e-09	4.74359054891349e-08
 11298	"Aanat"	"arylalkylamine N-acetyltransferase"	11	1455	0.137980416947824	17.6843133699537	96.2224553233548	4.15830411749738e-06	1.24749123524921e-05
 11304	"Abca4"	"ATP-binding cassette, sub-family A (ABC1), member 4"	3	7248	-0.45849071524422	15.526484673111	14.5864146737822	0.00244295799149183	0.00488591598298366
 11303	"Abca1"	"ATP-binding cassette, sub-family A (ABC1), member 1"	4	10260	0.0560600215744048	17.8909334307093	6.53006938009001	0.0442859767053567	0.066428965058035
 11305	"Abca2"	"ATP-binding cassette, sub-family A (ABC1), member 2"	2	8061	0.0585095828508861	18.1629882429457	1.07140336564628	0.321038228193371	0.385245873832045
-11302	"Aatk"	"apoptosis-associated tyrosine kinase"	11	5743	0.0716631320197652	10.0898336653124	0.376796260576848	0.878304702615841	0.878304702615841
+11302	"Aatk"	"apoptosis-associated tyrosine kinase"	11	5743	0.0716631320197652	10.0898336653124	0.376796260576849	0.878304702615839	0.878304702615839