# HG changeset patch
# User sblanck
# Date 1513244083 18000
# Node ID ef7d98f9eb5104c04b2a23229ab68d3c4b3dde2d
# Parent  161fe6ba75d72058ccc0faa997162780d2f3221d
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit f981b0fd5431199f51e2db8c680eb3d2d1d741b6

diff -r 161fe6ba75d7 -r ef7d98f9eb51 AffyQCnormalization.R
--- a/AffyQCnormalization.R	Fri Jun 09 05:19:21 2017 -0400
+++ b/AffyQCnormalization.R	Thu Dec 14 04:34:43 2017 -0500
@@ -34,7 +34,7 @@
 suppressPackageStartupMessages(require(limma))
 suppressPackageStartupMessages(require(jsonlite))
 suppressPackageStartupMessages(require(affy))
-suppressPackageStartupMessages(library(affyPLM))
+suppressPackageStartupMessages(require(affyPLM))
 suppressPackageStartupMessages(require(dplyr))
 
 listInput <- trimws( unlist( strsplit(trimws(opt$input), ",") ) )
diff -r 161fe6ba75d7 -r ef7d98f9eb51 AffyQCnormalization.xml
--- a/AffyQCnormalization.xml	Fri Jun 09 05:19:21 2017 -0400
+++ b/AffyQCnormalization.xml	Thu Dec 14 04:34:43 2017 -0500
@@ -3,8 +3,16 @@
     <description>Quality control and normalization of affymetrix expression data</description>
 
     <requirements>
-        <requirement type="package" version="0.2.0">r-smagexp</requirement>
-    </requirements>
+        <requirement type="package">bioconductor-biobase</requirement>
+        <requirement type="package">bioconductor-geoquery</requirement>
+        <requirement type="package">bioconductor-geometadb</requirement>
+        <requirement type="package">bioconductor-limma</requirement>
+        <requirement type="package">bioconductor-biobase</requirement>
+        <requirement type="package">bioconductor-affy</requirement>
+        <requirement type="package">bioconductor-affyPLM</requirement>
+        <requirement type="package">r-jsonlite</requirement>
+        <requirement type="package">r-dplyr</requirement>
+     </requirements>
 
     <stdio>
         <exit_code range="1:" />
diff -r 161fe6ba75d7 -r ef7d98f9eb51 Analyse.xml
--- a/Analyse.xml	Fri Jun 09 05:19:21 2017 -0400
+++ b/Analyse.xml	Thu Dec 14 04:34:43 2017 -0500
@@ -3,8 +3,15 @@
     <description>Performs gene expression analysis thanks to limma</description>
 
     <requirements>
-        <requirement type="package" version="0.2.0">r-smagexp</requirement>
-    </requirements>
+        <requirement type="package">bioconductor-biobase</requirement>
+        <requirement type="package">bioconductor-geoquery</requirement>
+        <requirement type="package">bioconductor-geometadb</requirement>
+        <requirement type="package">bioconductor-limma</requirement>
+        <requirement type="package">bioconductor-biobase</requirement>
+        <requirement type="package">bioconductor-affy</requirement>
+        <requirement type="package">r-jsonlite</requirement>
+        <requirement type="package">r-dplyr</requirement>
+     </requirements>
 
     <stdio>
         <exit_code range="1:" />
diff -r 161fe6ba75d7 -r ef7d98f9eb51 GEOQuery.xml
--- a/GEOQuery.xml	Fri Jun 09 05:19:21 2017 -0400
+++ b/GEOQuery.xml	Thu Dec 14 04:34:43 2017 -0500
@@ -3,9 +3,9 @@
     <description>GEOQuery wrapper</description>
 
     <requirements>
-        <requirement type="package" version="0.2.0">r-smagexp</requirement>
+        <requirement type="package">bioconductor-geoquery</requirement>
+        <requirement type="package">r-optparse</requirement>
     </requirements>
-
     <stdio>
         <exit_code range="1:" />
         <regex match="Warning" source="both" level="warning"/>
diff -r 161fe6ba75d7 -r ef7d98f9eb51 ImportDataFromMatrix.xml
--- a/ImportDataFromMatrix.xml	Fri Jun 09 05:19:21 2017 -0400
+++ b/ImportDataFromMatrix.xml	Thu Dec 14 04:34:43 2017 -0500
@@ -3,8 +3,16 @@
     <description>Quality control and normalization of a custom matrix expression data</description>
 
     <requirements>
-        <requirement type="package" version="0.2.0">r-smagexp</requirement>		
-    </requirements>
+        <requirement type="package">bioconductor-biobase</requirement>
+        <requirement type="package">bioconductor-geoquery</requirement>
+        <requirement type="package">bioconductor-geometadb</requirement>
+        <requirement type="package">bioconductor-limma</requirement>
+        <requirement type="package">bioconductor-biobase</requirement>
+        <requirement type="package">bioconductor-affy</requirement>
+        <requirement type="package">r-jsonlite</requirement>
+        <requirement type="package">r-dplyr</requirement>
+        <requirement type="package">r-optparse</requirement>
+     </requirements>
 
     <stdio>
         <exit_code range="1:" />
diff -r 161fe6ba75d7 -r ef7d98f9eb51 MetaMA.xml
--- a/MetaMA.xml	Fri Jun 09 05:19:21 2017 -0400
+++ b/MetaMA.xml	Thu Dec 14 04:34:43 2017 -0500
@@ -3,7 +3,13 @@
     <description>Performs meta-analysis thanks to metaMA.</description>
 
     <requirements>
-        <requirement type="package" version="0.2.0">r-smagexp</requirement>
+        <requirement type="package">bioconductor-affy</requirement>
+        <requirement type="package">bioconductor-annaffy</requirement>
+        <requirement type="package">bioconductor-geoquery</requirement>
+        <requirement type="package">bioconductor-org.hs.eg.db</requirement>
+        <requirement type="package">r-venndiagram</requirement>
+        <requirement type="package">r-metama</requirement>
+        <requirement type="package">r-optparse</requirement>
     </requirements>
 
     <stdio>
diff -r 161fe6ba75d7 -r ef7d98f9eb51 MetaRNASeq.R
--- a/MetaRNASeq.R	Fri Jun 09 05:19:21 2017 -0400
+++ b/MetaRNASeq.R	Thu Dec 14 04:34:43 2017 -0500
@@ -26,7 +26,6 @@
 
 #loading libraries
 
-suppressPackageStartupMessages(require(metaMA))
 suppressPackageStartupMessages(require(affy))
 suppressPackageStartupMessages(require(annaffy))
 suppressPackageStartupMessages(require(VennDiagram))
diff -r 161fe6ba75d7 -r ef7d98f9eb51 MetaRNAseq.xml
--- a/MetaRNAseq.xml	Fri Jun 09 05:19:21 2017 -0400
+++ b/MetaRNAseq.xml	Thu Dec 14 04:34:43 2017 -0500
@@ -3,7 +3,13 @@
     <description>Performs meta-analysis thanks to metaRNAseq</description>
 
     <requirements>
-        <requirement type="package" version="0.2.0">r-smagexp</requirement>
+        <requirement type="package">bioconductor-affy</requirement>
+        <requirement type="package">bioconductor-annaffy</requirement>
+        <requirement type="package">bioconductor-geoquery</requirement>
+        <requirement type="package">r-venndiagram</requirement>
+        <requirement type="package">r-jsonlite</requirement> 
+        <requirement type="package">r-metarnaseq</requirement>
+        <requirement type="package">r-optparse</requirement>
     </requirements>	
 
     <stdio>