changeset 15:cd2480f35935 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit ce8871b2708d391a99cd7656d84eade6f16a1337

--- a/annotateMyIDs.xml	Sat Jul 22 11:14:36 2023 +0000
+++ b/annotateMyIDs.xml	Tue Aug 29 22:44:27 2023 +0000
@@ -2,7 +2,7 @@
     <description>annotate a generic set of identifiers</description>
     <macros>
         <token name="@TOOL_VERSION@">3.17.0</token>
-        <token name="@VERSION_SUFFIX@">0</token>
+        <token name="@VERSION_SUFFIX@">1</token>
     </macros>
     <xrefs>
         <xref type="bio.tools">annotatemyids</xref>
@@ -15,9 +15,10 @@
         <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>
+        <requirement type="package" version="@TOOL_VERSION@">bioconductor-org.bt.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: ")
+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: ")", org.Bt.eg.db version" $(R --vanilla --slave -e "library(org.Bt.eg.db); cat(sessionInfo()\$otherPkgs\$org.Bt.eg.db\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
     ]]></version_command>
     <command detect_errors="exit_code"><![CDATA[
         #if $rscriptOpt:
@@ -63,6 +64,9 @@
 } else if (organism == "Gg"){
     suppressPackageStartupMessages(library(org.Gg.eg.db))
     db <- org.Gg.eg.db
+} else if (organism == "Bt"){
+    suppressPackageStartupMessages(library(org.Bt.eg.db))
+    db <- org.Bt.eg.db
 } else {
     cat(paste("Organism type not supported", organism))
 }
@@ -89,6 +93,7 @@
             <option value="Dr">Zebrafish</option>
             <option value="At">Arabidopsis thaliana</option>
             <option value="Gg">Gallus gallus</option>
+            <option value="Bt">Bos taurus</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>
@@ -198,6 +203,21 @@
                 </assert_contents>
             </output>
         </test>
+        <!-- Bos taurus database -->
+        <test expect_num_outputs="1">
+            <param name="id_file" value="genelist.txt" ftype="tabular"/>
+            <param name="id_type" value="SYMBOL"/>
+            <param name="organism" value="Bt"/>
+            <param name="output_cols" value="ENSEMBL" />
+            <output name="out_tab">
+                <assert_contents>
+                    <has_n_columns n="2"/>
+                    <has_n_lines min="9"/>
+                    <has_text_matching expression="ENSBTAG00000007159"/>
+                    <has_text_matching expression="ENSBTAG00000009498"/>
+                </assert_contents>
+            </output>
+        </test>
     </tests>
     <help><![CDATA[