diff annotateMyIDs.xml @ 12:fe3ca740a485 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit a7ca7bc12103e184333ec8ab6e99518a4873c707

--- a/annotateMyIDs.xml	Fri Jul 01 12:24:49 2022 +0000
+++ b/annotateMyIDs.xml	Tue Sep 13 09:25:40 2022 +0000
@@ -1,15 +1,20 @@
-<tool id="annotatemyids" name="annotateMyIDs" version="3.14.0+galaxy0">
+<tool id="annotatemyids" name="annotateMyIDs" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
     <description>annotate a generic set of identifiers</description>
     <xrefs>
         <xref type="bio.tools">annotatemyids</xref>
     </xrefs>
+    <macros>
+        <token name="@TOOL_VERSION@">3.14.0</token>
+        <token name="@VERSION_SUFFIX@">1</token>
+    </macros>
     <requirements>
-        <requirement type="package" version="3.14.0">bioconductor-org.hs.eg.db</requirement>
-        <requirement type="package" version="3.14.0">bioconductor-org.mm.eg.db</requirement>
-        <requirement type="package" version="3.14.0">bioconductor-org.dm.eg.db</requirement>
-        <requirement type="package" version="3.14.0">bioconductor-org.dr.eg.db</requirement>
-        <requirement type="package" version="3.14.0">bioconductor-org.rn.eg.db</requirement>
-        <requirement type="package" version="3.14.0">bioconductor-org.at.tair.db</requirement>
+        <requirement type="package" version="@TOOL_VERSION@">bioconductor-org.hs.eg.db</requirement>
+        <requirement type="package" version="@TOOL_VERSION@">bioconductor-org.mm.eg.db</requirement>
+        <requirement type="package" version="@TOOL_VERSION@">bioconductor-org.dm.eg.db</requirement>
+        <requirement type="package" version="@TOOL_VERSION@">bioconductor-org.dr.eg.db</requirement>
+        <requirement type="package" version="@TOOL_VERSION@">bioconductor-org.rn.eg.db</requirement>
+        <requirement type="package" version="@TOOL_VERSION@">bioconductor-org.at.tair.db</requirement>
+        <requirement type="package" version="@TOOL_VERSION@">bioconductor-org.gg.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: ")", 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: ")
@@ -55,6 +60,9 @@
 } else if (organism == "At"){
     suppressPackageStartupMessages(library(org.At.tair.db))
     db <- org.At.tair.db
+} else if (organism == "Gg"){
+    suppressPackageStartupMessages(library(org.Gg.eg.db))
+    db <- org.Gg.eg.db
 } else {
     cat(paste("Organism type not supported", organism))
 }
@@ -80,6 +88,7 @@
             <option value="Dm">Fruit fly</option>
             <option value="Dr">Zebrafish</option>
             <option value="At">Arabidopsis thaliana</option>
+            <option value="Gg">Gallus gallus</option>
         </param>
         <param name="id_type" type="select" label="ID Type" help="Select the type of IDs in your input file">
             <option value="ENSEMBL" selected="true">Ensembl Gene</option>
@@ -157,6 +166,14 @@
             <param name="output_cols" value="GO,ENTREZID" />
             <output name="out_tab" file="out_arabidopsis.tab" />
         </test>
+        <!-- Gallus gallus database -->
+        <test expect_num_outputs="1">
+            <param name="id_file" value="genelist_gallus.txt" ftype="tabular"/>
+            <param name="id_type" value="SYMBOL"/>
+            <param name="organism" value="Gg"/>
+            <param name="output_cols" value="GO,ENTREZID" />
+            <output name="out_tab" file="out_gallus.tab" />
+        </test>
     </tests>
     <help><![CDATA[