Mercurial > repos > iuc > annotatemyids

changeset 7:1aae04680c4b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 372ac44c1eed0a02c842d8dc65a5d484ed2ba29f
author iuc
date Fri, 21 Jun 2019 04:03:49 -0400
parents ecc913a7334b
children b5d8e5475247
files annotateMyIDs.xml
diffstat 1 files changed, 8 insertions(+), 3 deletions(-) [+]
line wrap: on
line diff
--- 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: