Mercurial > repos > iuc > annotatemyids

annotate annotateMyIDs.xml @ 2:1b3e8d3fde62 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 348750c48bc5e4f9ecad408519cdd2c68ac749ab
author iuc
date Sun, 11 Mar 2018 05:17:08 -0400
parents 11a9c9573c07
children b3db1e0bf574
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
2
1b3e8d3fde62 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 348750c48bc5e4f9ecad408519cdd2c68ac749ab
iuc
parents: 1
diff changeset
1 <tool id="annotatemyids" name="annotateMyIDs" version="3.5.0.1">
0
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
2 <description>annotate a generic set of identifiers</description>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
3 <requirements>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
4 <requirement type="package" version="3.5.0">bioconductor-org.hs.eg.db</requirement>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
5 <requirement type="package" version="3.5.0">bioconductor-org.mm.eg.db</requirement>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
6 <requirement type="package" version="3.5.0">bioconductor-org.dm.eg.db</requirement>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
7 <requirement type="package" version="3.5.0">bioconductor-org.dr.eg.db</requirement>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
8 </requirements>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
9 <version_command><![CDATA[
2
1b3e8d3fde62 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 348750c48bc5e4f9ecad408519cdd2c68ac749ab
iuc
parents: 1
diff changeset
10 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: ")
0
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
11 ]]></version_command>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
12 <command detect_errors="exit_code"><![CDATA[
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
13 #if $rscriptOpt:
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
14 cp '${annotatemyids_script}' '${out_rscript}' &&
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
15 #end if
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
16 Rscript '${annotatemyids_script}'
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
17 ]]>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
18 </command>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
19 <configfiles>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
20 <configfile name="annotatemyids_script"><![CDATA[
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
21 options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
22
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
23 # we need that to not crash galaxy with an UTF8 error on German LC settings.
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
24 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
25
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
26 id_type <- "${id_type}"
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
27 organism <- "${organism}"
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
28 output_cols <- "${output_cols}"
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
29 file_has_header <- ${file_has_header}
2
1b3e8d3fde62 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 348750c48bc5e4f9ecad408519cdd2c68ac749ab
iuc
parents: 1
diff changeset
30 remove_dups <- ${remove_dups}
0
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
31
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
32 ids <- as.character(read.table('$id_file', header=file_has_header)[,1])
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
33
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
34 if(organism == "Hs"){
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
35 suppressPackageStartupMessages(library(org.Hs.eg.db))
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
36 db <- org.Hs.eg.db
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
37 } else if (organism == "Mm"){
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
38 suppressPackageStartupMessages(library(org.Mm.eg.db))
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
39 db <- org.Mm.eg.db
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
40 } else if (organism == "Dm"){
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
41 suppressPackageStartupMessages(library(org.Dm.eg.db))
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
42 db <- org.Dm.eg.db
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
43 } else if (organism == "Dr"){
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
44 suppressPackageStartupMessages(library(org.Dr.eg.db))
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
45 db <- org.Dr.eg.db
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
46 } else {
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
47 cat(paste("Organism type not supported", organism))
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
48 }
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
49
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
50 cols <- unlist(strsplit(output_cols, ","))
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
51 result <- select(db, keys=ids, keytype=id_type, columns=cols)
2
1b3e8d3fde62 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 348750c48bc5e4f9ecad408519cdd2c68ac749ab
iuc
parents: 1
diff changeset
52
1b3e8d3fde62 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 348750c48bc5e4f9ecad408519cdd2c68ac749ab
iuc
parents: 1
diff changeset
53 if(remove_dups) {
1b3e8d3fde62 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 348750c48bc5e4f9ecad408519cdd2c68ac749ab
iuc
parents: 1
diff changeset
54 result <- result[!duplicated(result$${id_type}),]
1b3e8d3fde62 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 348750c48bc5e4f9ecad408519cdd2c68ac749ab
iuc
parents: 1
diff changeset
55 }
1b3e8d3fde62 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 348750c48bc5e4f9ecad408519cdd2c68ac749ab
iuc
parents: 1
diff changeset
56
0
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
57 write.table(result, file='$out_tab', sep="\t", row.names=FALSE, quote=FALSE)
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
58
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
59 ]]></configfile>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
60 </configfiles>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
61 <inputs>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
62 <param name="id_file" type="data" format="tabular" label="File with IDs" help="A tabular file with the first column containing one of the supported types of identifier, see Help below." />
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
63 <param name="file_has_header" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="False" label="File has header?" help="If this option is set to Yes, the tool will assume that the input file has a column header in the first row and the identifers commence on the second line. Default: No" />
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
64 <param name="organism" type="select" label="Organism" help="Select the organism the identifiers are from">
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
65 <option value="Hs" selected="true">Human</option>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
66 <option value="Mm">Mouse</option>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
67 <option value="Dm">Fruit fly</option>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
68 <option value="Dr">Zebrafish</option>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
69 </param>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
70 <param name="id_type" type="select" label="ID Type" help="Select the type of IDs in your input file">
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
71 <option value="ENSEMBL" selected="true">Ensembl Gene</option>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
72 <option value="ENSEMBLPROT">Ensembl Protein</option>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
73 <option value="ENSEMBLTRANS">Ensembl Transcript</option>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
74 <option value="ENTREZID">Entrez</option>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
75 <option value="FLYBASE">FlyBase</option>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
76 <option value="GO">GO</option>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
77 <option value="PATH">KEGG</option>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
78 <option value="MGI">MGI</option>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
79 <option value="REFSEQ">RefSeq</option>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
80 <option value="SYMBOL">Gene Symbol</option>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
81 <option value="ZFIN">Zfin</option>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
82 </param>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
83 <param name="output_cols" type="select" multiple="True" display="checkboxes" label="Output columns" help="Choose the columns you want in the output table. Note that selecting some columns such as GO or KEGG could make the table very large as some genes may be associated with many terms. Default: ENSEMBL, ENTREZID, SYMBOL, GENENAME">
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
84 <option value="ALIAS">ALIAS</option>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
85 <option value="DESCRIPTION">DESCRIPTION</option>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
86 <option value="ENSEMBL" selected="True">ENSEMBL</option>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
87 <option value="ENTREZID" selected="True">ENTREZID</option>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
88 <option value="EVIDENCE">EVIDENCE</option>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
89 <option value="SYMBOL" selected="True">SYMBOL</option>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
90 <option value="GENENAME" selected="True">GENENAME</option>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
91 <option value="REFSEQ">REFSEQ</option>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
92 <option value="GO">GO</option>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
93 <option value="ONTOLOGY">ONTOLOGY</option>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
94 <option value="PATH">KEGG</option>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
95 </param>
2
1b3e8d3fde62 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 348750c48bc5e4f9ecad408519cdd2c68ac749ab
iuc
parents: 1
diff changeset
96 <param name="remove_dups" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="False" label="Remove duplicates?" help="If this option is set to Yes, only the first occurrence of each input Gene ID will be kept. Default: No" />
0
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
97 <param name="rscriptOpt" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="False" label="Output Rscript?" help="If this option is set to Yes, the Rscript used to annotate the IDs will be provided as a text file in the output. Default: No" />
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
98 </inputs>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
99 <outputs>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
100 <data name="out_tab" format="tabular" from_work_dir="*.tab" label="${tool.name} on ${on_string}: Annotated IDs" />
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
101 <data name="out_rscript" format="txt" from_work_dir="*.txt" label="${tool.name} on ${on_string}: Rscript">
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
102 <filter>rscriptOpt is True</filter>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
103 </data>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
104 </outputs>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
105 <tests>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
106 <!-- Ensure output table works -->
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
107 <test expect_num_outputs="1">
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
108 <param name="id_file" value="genelist.txt" ftype="tabular"/>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
109 <param name="id_type" value="SYMBOL"/>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
110 <param name="organism" value="Hs"/>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
111 <output name="out_tab" file="out.tab" />
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
112 </test>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
113 <!-- Ensure Ensembl IDs input and Rscript output work -->
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
114 <test expect_num_outputs="2">
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
115 <param name="id_file" value="ensembl_ids.tab" ftype="tabular"/>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
116 <param name="id_type" value="ENSEMBL"/>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
117 <param name="organism" value="Hs"/>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
118 <param name="rscriptOpt" value="True" />
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
119 <output name="out_tab" file="out_ensembl.tab" />
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
120 <output name="out_rscript" file="out_rscript.txt" compare="sim_size" />
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
121 </test>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
122 <!-- Ensure GO and KEGG output work -->
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
123 <test expect_num_outputs="1">
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
124 <param name="id_file" value="ensembl_ids.tab" ftype="tabular"/>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
125 <param name="id_type" value="ENSEMBL"/>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
126 <param name="organism" value="Hs"/>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
127 <param name="output_cols" value="ENSEMBL,GO,ONTOLOGY,EVIDENCE" />
2
1b3e8d3fde62 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 348750c48bc5e4f9ecad408519cdd2c68ac749ab
iuc
parents: 1
diff changeset
128 <output name="out_tab" file="out_gokegg.tab" />
1b3e8d3fde62 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 348750c48bc5e4f9ecad408519cdd2c68ac749ab
iuc
parents: 1
diff changeset
129 </test>
1b3e8d3fde62 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 348750c48bc5e4f9ecad408519cdd2c68ac749ab
iuc
parents: 1
diff changeset
130 <!-- Ensure duplicate Gene ID removal works -->
1b3e8d3fde62 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 348750c48bc5e4f9ecad408519cdd2c68ac749ab
iuc
parents: 1
diff changeset
131 <test expect_num_outputs="1">
1b3e8d3fde62 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 348750c48bc5e4f9ecad408519cdd2c68ac749ab
iuc
parents: 1
diff changeset
132 <param name="id_file" value="ensembl_ids.tab" ftype="tabular"/>
1b3e8d3fde62 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 348750c48bc5e4f9ecad408519cdd2c68ac749ab
iuc
parents: 1
diff changeset
133 <param name="id_type" value="ENSEMBL"/>
1b3e8d3fde62 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 348750c48bc5e4f9ecad408519cdd2c68ac749ab
iuc
parents: 1
diff changeset
134 <param name="organism" value="Hs"/>
1b3e8d3fde62 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 348750c48bc5e4f9ecad408519cdd2c68ac749ab
iuc
parents: 1
diff changeset
135 <param name="output_cols" value="ENSEMBL,GO,ONTOLOGY,EVIDENCE" />
1b3e8d3fde62 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 348750c48bc5e4f9ecad408519cdd2c68ac749ab
iuc
parents: 1
diff changeset
136 <param name="remove_dups" value="True" />
1b3e8d3fde62 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 348750c48bc5e4f9ecad408519cdd2c68ac749ab
iuc
parents: 1
diff changeset
137 <output name="out_tab" file="out_gokegg_dupsrem.tab" />
0
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
138 </test>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
139 </tests>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
140 <help><![CDATA[
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
141
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
142 .. class:: infomark
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
143
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
144 **What it does**
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
145
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
146 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_.
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
147
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
148 Examples of what this tool can be used for are:
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
149
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
150 * adding gene names to IDs
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
151 * mapping between IDs e.g. Entrez, Ensembl, Symbols
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
152 * adding GO and KEGG identifiers
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
153
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
154 .. _Bioconductor: https://www.bioconductor.org/
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
155 .. _here: http://bioconductor.org/packages/release/data/annotation/manuals/org.Hs.eg.db/man/org.Hs.eg.db.pdf
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
156
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
157 -----
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
158
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
159 **Inputs**
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
160
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
161 A tab-delimited file with identifiers in the first column. If the file contains a header row, select the file has a header option in the tool form above.
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
162
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
163 Example:
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
164
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
165 =============== =======================
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
166 **GeneID** *Additional Columns...*
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
167 --------------- -----------------------
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
168 ENSG00000091831
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
169 ENSG00000082175
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
170 ENSG00000141736
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
171 ENSG00000012048
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
172 ENSG00000139618
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
173 ENSG00000129514
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
174 ENSG00000171862
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
175 ENSG00000141510
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
176 =============== =======================
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
177
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
178 ID types supported for input are:
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
179
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
180 * **ENSEMBL**: Ensembl gene IDs
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
181 * **ENSEMBLPROT**: Ensembl protein IDs
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
182 * **ENSEMBLTRANS**: Ensembl transcript IDs
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
183 * **ENTREZID**: Entrez gene Identifiers
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
184 * **FLYBASE**: FlyBase accession numbers
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
185 * **GO**: GO Identifiers
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
186 * **MGI**: Jackson Laboratory MGI gene accession numbers
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
187 * **PATH**: KEGG Pathway Identifiers
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
188 * **REFSEQ**: Refseq Identifiers
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
189 * **SYMBOL**: The official gene symbol
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
190 * **ZFIN**: Zfin accession numbers
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
191
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
192 .. class:: warningmark
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
193
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
194 This tool uses the ``select`` function from the Bioconductor AnnotationDBi_ package. Note that if you request columns that have multiple matches for your IDs, select will return *one row in the output for each possible match*. This has the effect that if you request multiple columns and some of them have a many-to-one relationship to the IDs, things will continue to multiply accordingly. So it's not a good idea to request a large number of columns unless you know what you are asking for should have a one-to-one relationship with the initial set of IDs. In general, if you need to retrieve a column like **GO** or **KEGG**, that has a many-to-one relationship to the original IDs, it is most useful to extract that separately.
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
195
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
196 .. _AnnotationDBi: https://www.bioconductor.org/packages/devel/bioc/manuals/AnnotationDbi/man/AnnotationDbi.pdf
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
197
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
198 -----
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
199
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
200 **Outputs**
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
201
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
202 If the input IDs are Ensembl, the default output will be similar to below, containing four columns. Other columns, such as GO and KEGG terms, can be selected above to be added as additional columns.
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
203
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
204 Example:
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
205
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
206 =============== ============ ========== =================================
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
207 **ENSEMBL** **ENTREZID** **SYMBOL** **GENENAME**
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
208 --------------- ------------ ---------- ---------------------------------
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
209 ENSG00000091831 2099 ESR1 estrogen receptor 1
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
210 ENSG00000082175 5241 PGR progesterone receptor
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
211 ENSG00000141736 2064 ERBB2 erb-b2 receptor tyrosine kinase 2
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
212 ENSG00000012048 672 BRCA1 breast cancer 1
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
213 ENSG00000139618 675 BRCA2 breast cancer 2
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
214 ENSG00000129514 3169 FOXA1 forkhead box A1
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
215 ENSG00000171862 5728 PTEN phosphatase and tensin homolog
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
216 ENSG00000141510 7157 TP53 tumor protein p53
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
217 =============== ============ ========== =================================
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
218
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
219 Columns available for output include many of the ID columns already described under Inputs above and also:
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
220
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
221 * **ALIAS**: Commonly used gene symbols
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
222 * **DESCRIPTION**: The description of the associated gene
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
223 * **EVIDENCE**: Evidence codes for GO associations with a gene of interest
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
224 * **GENENAME**: The full gene name
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
225 * **ONTOLOGY**: For GO Identifiers, which Gene Ontology (BP, CC, or MF)
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
226
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
227 ]]></help>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
228 <citations>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
229 <citation type="bibtex">
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
230 @unpublished{None,
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
231 author = {Mark Dunning},
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
232 title = {annotateMyIDs},
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
233 year = {2017},
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
234 eprint = {None},
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
235 url = {}
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
236 }</citation>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
237 </citations>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
238 </tool>