# HG changeset patch
# User iuc
# Date 1561104229 14400
# Node ID 1aae04680c4b3b83c7771fbdfe3d67ce225e1c6f
# Parent  ecc913a7334bde6f719f46e96962a4b017159774
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 372ac44c1eed0a02c842d8dc65a5d484ed2ba29f

diff -r ecc913a7334b -r 1aae04680c4b annotateMyIDs.xml
--- a/annotateMyIDs.xml	Fri Mar 08 04:39:31 2019 -0500
+++ b/annotateMyIDs.xml	Fri Jun 21 04:03:49 2019 -0400
@@ -1,13 +1,14 @@
-<tool id="annotatemyids" name="annotateMyIDs" version="3.7.0">
+<tool id="annotatemyids" name="annotateMyIDs" version="3.7.0+galaxy1">
     <description>annotate a generic set of identifiers</description>
     <requirements>
         <requirement type="package" version="3.7.0">bioconductor-org.hs.eg.db</requirement>
         <requirement type="package" version="3.7.0">bioconductor-org.mm.eg.db</requirement>
         <requirement type="package" version="3.7.0">bioconductor-org.dm.eg.db</requirement>
         <requirement type="package" version="3.7.0">bioconductor-org.dr.eg.db</requirement>
+        <requirement type="package" version="3.7.0">bioconductor-org.rn.eg.db</requirement>
     </requirements>
     <version_command><![CDATA[
-echo $(R --version | grep version | grep -v GNU)", org.Hs.eg.db version" $(R --vanilla --slave -e "library(org.Hs.eg.db); cat(sessionInfo()\$otherPkgs\$org.Hs.eg.db\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", org.Dr.eg.db version" $(R --vanilla --slave -e "library(org.Dr.eg.db); cat(sessionInfo()\$otherPkgs\$org.Dr.eg.db\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", org.Dm.eg.db version" $(R --vanilla --slave -e "library(org.Dm.eg.db); cat(sessionInfo()\$otherPkgs\$org.Dm.eg.db\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", org.Mm.eg.db version" $(R --vanilla --slave -e "library(org.Mm.eg.db); cat(sessionInfo()\$otherPkgs\$org.Mm.eg.db\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
+echo $(R --version | grep version | grep -v GNU)", org.Hs.eg.db version" $(R --vanilla --slave -e "library(org.Hs.eg.db); cat(sessionInfo()\$otherPkgs\$org.Hs.eg.db\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", org.Dr.eg.db version" $(R --vanilla --slave -e "library(org.Dr.eg.db); cat(sessionInfo()\$otherPkgs\$org.Dr.eg.db\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", org.Dm.eg.db version" $(R --vanilla --slave -e "library(org.Dm.eg.db); cat(sessionInfo()\$otherPkgs\$org.Dm.eg.db\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", org.Mm.eg.db version" $(R --vanilla --slave -e "library(org.Mm.eg.db); cat(sessionInfo()\$otherPkgs\$org.Mm.eg.db\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", org.Rn.eg.db version" $(R --vanilla --slave -e "library(org.Rn.eg.db); cat(sessionInfo()\$otherPkgs\$org.Rn.eg.db\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
     ]]></version_command>
     <command detect_errors="exit_code"><![CDATA[
         #if $rscriptOpt:
@@ -44,6 +45,9 @@
 } else if (organism == "Dr"){
     suppressPackageStartupMessages(library(org.Dr.eg.db))
     db <- org.Dr.eg.db
+} else if (organism == "Rn"){
+    suppressPackageStartupMessages(library(org.Rn.eg.db))
+    db <- org.Rn.eg.db
 } else {
     cat(paste("Organism type not supported", organism))
 }
@@ -65,6 +69,7 @@
         <param name="organism" type="select" label="Organism" help="Select the organism the identifiers are from">
             <option value="Hs" selected="true">Human</option>
             <option value="Mm">Mouse</option>
+            <option value="Rn">Rat</option>
             <option value="Dm">Fruit fly</option>
             <option value="Dr">Zebrafish</option>
         </param>
@@ -144,7 +149,7 @@
 
 **What it does**
 
-This tool can get annotation for a generic set of IDs, using the Bioconductor_ annotation data packages. Supported organisms are human, mouse, fruit fly and zebrafish. The org.db packages that are used here are primarily based on mapping using Entrez Gene identifiers. More information on the annotation packages can be found at the Bioconductor website, for example, information on the human annotation package (org.Hs.eg.db) can be found here_.
+This tool can get annotation for a generic set of IDs, using the Bioconductor_ annotation data packages. Supported organisms are human, mouse, rat, fruit fly and zebrafish. The org.db packages that are used here are primarily based on mapping using Entrez Gene identifiers. More information on the annotation packages can be found at the Bioconductor website, for example, information on the human annotation package (org.Hs.eg.db) can be found here_.
 
 Examples of what this tool can be used for are: