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changeset 12:fe3ca740a485 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit a7ca7bc12103e184333ec8ab6e99518a4873c707
author iuc
date Tue, 13 Sep 2022 09:25:40 +0000
parents 4f2967b27e67
children 133f36c29579
files annotateMyIDs.xml test-data/genelist_gallus.txt test-data/out_gallus.tab
diffstat 3 files changed, 71 insertions(+), 7 deletions(-) [+]
line wrap: on
line diff
--- 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[
 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/genelist_gallus.txt	Tue Sep 13 09:25:40 2022 +0000
@@ -0,0 +1,4 @@
+TRIM15
+TENM2
+FZD10
+ADRA1B
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/out_gallus.tab	Tue Sep 13 09:25:40 2022 +0000
@@ -0,0 +1,43 @@
+SYMBOL	GO	EVIDENCE	ONTOLOGY	ENTREZID
+TRIM15	NA	NA	NA	NA
+TENM2	GO:0000122	IDA	BP	373854
+TENM2	GO:0005102	ISS	MF	373854
+TENM2	GO:0005509	IEA	MF	373854
+TENM2	GO:0005634	IDA	CC	373854
+TENM2	GO:0005783	IDA	CC	373854
+TENM2	GO:0005794	IDA	CC	373854
+TENM2	GO:0005886	IDA	CC	373854
+TENM2	GO:0005887	IEA	CC	373854
+TENM2	GO:0005911	ISS	CC	373854
+TENM2	GO:0007157	IBA	BP	373854
+TENM2	GO:0007157	ISS	BP	373854
+TENM2	GO:0007411	ISS	BP	373854
+TENM2	GO:0016605	IDA	CC	373854
+TENM2	GO:0030054	IDA	CC	373854
+TENM2	GO:0030175	IDA	CC	373854
+TENM2	GO:0030425	IDA	CC	373854
+TENM2	GO:0030426	IDA	CC	373854
+TENM2	GO:0035584	ISS	BP	373854
+TENM2	GO:0042803	IBA	MF	373854
+TENM2	GO:0042803	ISS	MF	373854
+TENM2	GO:0043005	IBA	CC	373854
+TENM2	GO:0043005	ISS	CC	373854
+TENM2	GO:0043197	ISS	CC	373854
+TENM2	GO:0045202	ISS	CC	373854
+TENM2	GO:0045211	ISS	CC	373854
+TENM2	GO:0046982	IBA	MF	373854
+TENM2	GO:0046982	ISS	MF	373854
+TENM2	GO:0048666	IBA	BP	373854
+TENM2	GO:0050839	IBA	MF	373854
+TENM2	GO:0050839	ISS	MF	373854
+TENM2	GO:0051491	IDA	BP	373854
+TENM2	GO:0098609	IDA	BP	373854
+FZD10	GO:0004930	IEA	MF	373885
+FZD10	GO:0005886	IBA	CC	373885
+FZD10	GO:0007186	IEA	BP	373885
+FZD10	GO:0016021	IBA	CC	373885
+FZD10	GO:0017147	IBA	MF	373885
+FZD10	GO:0035567	IBA	BP	373885
+FZD10	GO:0042813	IBA	MF	373885
+FZD10	GO:0060070	IBA	BP	373885
+ADRA1B	NA	NA	NA	373890