Mercurial > repos > iuc > annotatemyids
annotate annotateMyIDs.xml @ 7:1aae04680c4b draft
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 |
rev | line source |
---|---|
7
1aae04680c4b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 372ac44c1eed0a02c842d8dc65a5d484ed2ba29f
iuc
parents:
6
diff
changeset
|
1 <tool id="annotatemyids" name="annotateMyIDs" version="3.7.0+galaxy1"> |
0
442e2d79b05c
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> |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
3 <requirements> |
5
b467a89be0c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit b8cb10b5fe2aa448e3621828829194567d5ae50d
iuc
parents:
4
diff
changeset
|
4 <requirement type="package" version="3.7.0">bioconductor-org.hs.eg.db</requirement> |
b467a89be0c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit b8cb10b5fe2aa448e3621828829194567d5ae50d
iuc
parents:
4
diff
changeset
|
5 <requirement type="package" version="3.7.0">bioconductor-org.mm.eg.db</requirement> |
b467a89be0c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit b8cb10b5fe2aa448e3621828829194567d5ae50d
iuc
parents:
4
diff
changeset
|
6 <requirement type="package" version="3.7.0">bioconductor-org.dm.eg.db</requirement> |
b467a89be0c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit b8cb10b5fe2aa448e3621828829194567d5ae50d
iuc
parents:
4
diff
changeset
|
7 <requirement type="package" version="3.7.0">bioconductor-org.dr.eg.db</requirement> |
7
1aae04680c4b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 372ac44c1eed0a02c842d8dc65a5d484ed2ba29f
iuc
parents:
6
diff
changeset
|
8 <requirement type="package" version="3.7.0">bioconductor-org.rn.eg.db</requirement> |
0
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
9 </requirements> |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
10 <version_command><![CDATA[ |
7
1aae04680c4b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 372ac44c1eed0a02c842d8dc65a5d484ed2ba29f
iuc
parents:
6
diff
changeset
|
11 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: ") |
0
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
12 ]]></version_command> |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
13 <command detect_errors="exit_code"><![CDATA[ |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
14 #if $rscriptOpt: |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
15 cp '${annotatemyids_script}' '${out_rscript}' && |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
16 #end if |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
17 Rscript '${annotatemyids_script}' |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
18 ]]> |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
19 </command> |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
20 <configfiles> |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
21 <configfile name="annotatemyids_script"><![CDATA[ |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
22 options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } ) |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
23 |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
24 # we need that to not crash galaxy with an UTF8 error on German LC settings. |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
25 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
26 |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
27 id_type <- "${id_type}" |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
28 organism <- "${organism}" |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
29 output_cols <- "${output_cols}" |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
30 file_has_header <- ${file_has_header} |
2
9ab35a2245ce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 348750c48bc5e4f9ecad408519cdd2c68ac749ab
iuc
parents:
1
diff
changeset
|
31 remove_dups <- ${remove_dups} |
0
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
32 |
6
ecc913a7334b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit a0c51ab52c4e3f296d5577ee3af26c4c1465e1e9
iuc
parents:
5
diff
changeset
|
33 input <- read.table('$id_file', header=file_has_header, sep="\t", quote="") |
ecc913a7334b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit a0c51ab52c4e3f296d5577ee3af26c4c1465e1e9
iuc
parents:
5
diff
changeset
|
34 ids <- as.character(input[, 1]) |
0
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
35 |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
36 if(organism == "Hs"){ |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
37 suppressPackageStartupMessages(library(org.Hs.eg.db)) |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
38 db <- org.Hs.eg.db |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
39 } else if (organism == "Mm"){ |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
40 suppressPackageStartupMessages(library(org.Mm.eg.db)) |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
41 db <- org.Mm.eg.db |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
42 } else if (organism == "Dm"){ |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
43 suppressPackageStartupMessages(library(org.Dm.eg.db)) |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
44 db <- org.Dm.eg.db |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
45 } else if (organism == "Dr"){ |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
46 suppressPackageStartupMessages(library(org.Dr.eg.db)) |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
47 db <- org.Dr.eg.db |
7
1aae04680c4b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 372ac44c1eed0a02c842d8dc65a5d484ed2ba29f
iuc
parents:
6
diff
changeset
|
48 } else if (organism == "Rn"){ |
1aae04680c4b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 372ac44c1eed0a02c842d8dc65a5d484ed2ba29f
iuc
parents:
6
diff
changeset
|
49 suppressPackageStartupMessages(library(org.Rn.eg.db)) |
1aae04680c4b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 372ac44c1eed0a02c842d8dc65a5d484ed2ba29f
iuc
parents:
6
diff
changeset
|
50 db <- org.Rn.eg.db |
0
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
51 } else { |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
52 cat(paste("Organism type not supported", organism)) |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
53 } |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
54 |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
55 cols <- unlist(strsplit(output_cols, ",")) |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
56 result <- select(db, keys=ids, keytype=id_type, columns=cols) |
2
9ab35a2245ce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 348750c48bc5e4f9ecad408519cdd2c68ac749ab
iuc
parents:
1
diff
changeset
|
57 |
9ab35a2245ce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 348750c48bc5e4f9ecad408519cdd2c68ac749ab
iuc
parents:
1
diff
changeset
|
58 if(remove_dups) { |
9ab35a2245ce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 348750c48bc5e4f9ecad408519cdd2c68ac749ab
iuc
parents:
1
diff
changeset
|
59 result <- result[!duplicated(result$${id_type}),] |
9ab35a2245ce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 348750c48bc5e4f9ecad408519cdd2c68ac749ab
iuc
parents:
1
diff
changeset
|
60 } |
9ab35a2245ce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 348750c48bc5e4f9ecad408519cdd2c68ac749ab
iuc
parents:
1
diff
changeset
|
61 |
0
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
62 write.table(result, file='$out_tab', sep="\t", row.names=FALSE, quote=FALSE) |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
63 |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
64 ]]></configfile> |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
65 </configfiles> |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
66 <inputs> |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
67 <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." /> |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
68 <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" /> |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
69 <param name="organism" type="select" label="Organism" help="Select the organism the identifiers are from"> |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
70 <option value="Hs" selected="true">Human</option> |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
71 <option value="Mm">Mouse</option> |
7
1aae04680c4b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 372ac44c1eed0a02c842d8dc65a5d484ed2ba29f
iuc
parents:
6
diff
changeset
|
72 <option value="Rn">Rat</option> |
0
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
73 <option value="Dm">Fruit fly</option> |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
74 <option value="Dr">Zebrafish</option> |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
75 </param> |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
76 <param name="id_type" type="select" label="ID Type" help="Select the type of IDs in your input file"> |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
77 <option value="ENSEMBL" selected="true">Ensembl Gene</option> |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
78 <option value="ENSEMBLPROT">Ensembl Protein</option> |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
79 <option value="ENSEMBLTRANS">Ensembl Transcript</option> |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
80 <option value="ENTREZID">Entrez</option> |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
81 <option value="FLYBASE">FlyBase</option> |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
82 <option value="GO">GO</option> |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
83 <option value="PATH">KEGG</option> |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
84 <option value="MGI">MGI</option> |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
85 <option value="REFSEQ">RefSeq</option> |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
86 <option value="SYMBOL">Gene Symbol</option> |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
87 <option value="ZFIN">Zfin</option> |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
88 </param> |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
89 <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"> |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
90 <option value="ALIAS">ALIAS</option> |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
91 <option value="DESCRIPTION">DESCRIPTION</option> |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
92 <option value="ENSEMBL" selected="True">ENSEMBL</option> |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
93 <option value="ENTREZID" selected="True">ENTREZID</option> |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
94 <option value="EVIDENCE">EVIDENCE</option> |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
95 <option value="SYMBOL" selected="True">SYMBOL</option> |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
96 <option value="GENENAME" selected="True">GENENAME</option> |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
97 <option value="REFSEQ">REFSEQ</option> |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
98 <option value="GO">GO</option> |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
99 <option value="ONTOLOGY">ONTOLOGY</option> |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
100 <option value="PATH">KEGG</option> |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
101 </param> |
2
9ab35a2245ce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 348750c48bc5e4f9ecad408519cdd2c68ac749ab
iuc
parents:
1
diff
changeset
|
102 <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
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
103 <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" /> |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
104 </inputs> |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
105 <outputs> |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
106 <data name="out_tab" format="tabular" from_work_dir="*.tab" label="${tool.name} on ${on_string}: Annotated IDs" /> |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
107 <data name="out_rscript" format="txt" from_work_dir="*.txt" label="${tool.name} on ${on_string}: Rscript"> |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
108 <filter>rscriptOpt is True</filter> |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
109 </data> |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
110 </outputs> |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
111 <tests> |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
112 <!-- Ensure output table works --> |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
113 <test expect_num_outputs="1"> |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
114 <param name="id_file" value="genelist.txt" ftype="tabular"/> |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
115 <param name="id_type" value="SYMBOL"/> |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
116 <param name="organism" value="Hs"/> |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
117 <output name="out_tab" file="out.tab" /> |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
118 </test> |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
119 <!-- Ensure Ensembl IDs input and Rscript output work --> |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
120 <test expect_num_outputs="2"> |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
121 <param name="id_file" value="ensembl_ids.tab" ftype="tabular"/> |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
122 <param name="id_type" value="ENSEMBL"/> |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
123 <param name="organism" value="Hs"/> |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
124 <param name="rscriptOpt" value="True" /> |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
125 <output name="out_tab" file="out_ensembl.tab" /> |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
126 <output name="out_rscript" file="out_rscript.txt" compare="sim_size" /> |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
127 </test> |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
128 <!-- Ensure GO and KEGG output work --> |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
129 <test expect_num_outputs="1"> |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
130 <param name="id_file" value="ensembl_ids.tab" ftype="tabular"/> |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
131 <param name="id_type" value="ENSEMBL"/> |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
132 <param name="organism" value="Hs"/> |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
133 <param name="output_cols" value="ENSEMBL,GO,ONTOLOGY,EVIDENCE" /> |
2
9ab35a2245ce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 348750c48bc5e4f9ecad408519cdd2c68ac749ab
iuc
parents:
1
diff
changeset
|
134 <output name="out_tab" file="out_gokegg.tab" /> |
9ab35a2245ce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 348750c48bc5e4f9ecad408519cdd2c68ac749ab
iuc
parents:
1
diff
changeset
|
135 </test> |
9ab35a2245ce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 348750c48bc5e4f9ecad408519cdd2c68ac749ab
iuc
parents:
1
diff
changeset
|
136 <!-- Ensure duplicate Gene ID removal works --> |
9ab35a2245ce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 348750c48bc5e4f9ecad408519cdd2c68ac749ab
iuc
parents:
1
diff
changeset
|
137 <test expect_num_outputs="1"> |
9ab35a2245ce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 348750c48bc5e4f9ecad408519cdd2c68ac749ab
iuc
parents:
1
diff
changeset
|
138 <param name="id_file" value="ensembl_ids.tab" ftype="tabular"/> |
9ab35a2245ce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 348750c48bc5e4f9ecad408519cdd2c68ac749ab
iuc
parents:
1
diff
changeset
|
139 <param name="id_type" value="ENSEMBL"/> |
9ab35a2245ce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 348750c48bc5e4f9ecad408519cdd2c68ac749ab
iuc
parents:
1
diff
changeset
|
140 <param name="organism" value="Hs"/> |
9ab35a2245ce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 348750c48bc5e4f9ecad408519cdd2c68ac749ab
iuc
parents:
1
diff
changeset
|
141 <param name="output_cols" value="ENSEMBL,GO,ONTOLOGY,EVIDENCE" /> |
9ab35a2245ce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 348750c48bc5e4f9ecad408519cdd2c68ac749ab
iuc
parents:
1
diff
changeset
|
142 <param name="remove_dups" value="True" /> |
9ab35a2245ce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 348750c48bc5e4f9ecad408519cdd2c68ac749ab
iuc
parents:
1
diff
changeset
|
143 <output name="out_tab" file="out_gokegg_dupsrem.tab" /> |
0
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
144 </test> |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
145 </tests> |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
146 <help><![CDATA[ |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
147 |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
148 .. class:: infomark |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
149 |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
150 **What it does** |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
151 |
7
1aae04680c4b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 372ac44c1eed0a02c842d8dc65a5d484ed2ba29f
iuc
parents:
6
diff
changeset
|
152 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_. |
0
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
153 |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
154 Examples of what this tool can be used for are: |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
155 |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
156 * adding gene names to IDs |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
157 * mapping between IDs e.g. Entrez, Ensembl, Symbols |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
158 * adding GO and KEGG identifiers |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
159 |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
160 .. _Bioconductor: https://www.bioconductor.org/ |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
161 .. _here: http://bioconductor.org/packages/release/data/annotation/manuals/org.Hs.eg.db/man/org.Hs.eg.db.pdf |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
162 |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
163 ----- |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
164 |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
165 **Inputs** |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
166 |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
167 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. |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
168 |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
169 Example: |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
170 |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
171 =============== ======================= |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
172 **GeneID** *Additional Columns...* |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
173 --------------- ----------------------- |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
174 ENSG00000091831 |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
175 ENSG00000082175 |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
176 ENSG00000141736 |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
177 ENSG00000012048 |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
178 ENSG00000139618 |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
179 ENSG00000129514 |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
180 ENSG00000171862 |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
181 ENSG00000141510 |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
182 =============== ======================= |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
183 |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
184 ID types supported for input are: |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
185 |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
186 * **ENSEMBL**: Ensembl gene IDs |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
187 * **ENSEMBLPROT**: Ensembl protein IDs |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
188 * **ENSEMBLTRANS**: Ensembl transcript IDs |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
189 * **ENTREZID**: Entrez gene Identifiers |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
190 * **FLYBASE**: FlyBase accession numbers |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
191 * **GO**: GO Identifiers |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
192 * **MGI**: Jackson Laboratory MGI gene accession numbers |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
193 * **PATH**: KEGG Pathway Identifiers |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
194 * **REFSEQ**: Refseq Identifiers |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
195 * **SYMBOL**: The official gene symbol |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
196 * **ZFIN**: Zfin accession numbers |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
197 |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
198 .. class:: warningmark |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
199 |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
200 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. |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
201 |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
202 .. _AnnotationDBi: https://www.bioconductor.org/packages/devel/bioc/manuals/AnnotationDbi/man/AnnotationDbi.pdf |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
203 |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
204 ----- |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
205 |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
206 **Outputs** |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
207 |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
208 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. |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
209 |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
210 Example: |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
211 |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
212 =============== ============ ========== ================================= |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
213 **ENSEMBL** **ENTREZID** **SYMBOL** **GENENAME** |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
214 --------------- ------------ ---------- --------------------------------- |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
215 ENSG00000091831 2099 ESR1 estrogen receptor 1 |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
216 ENSG00000082175 5241 PGR progesterone receptor |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
217 ENSG00000141736 2064 ERBB2 erb-b2 receptor tyrosine kinase 2 |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
218 ENSG00000012048 672 BRCA1 breast cancer 1 |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
219 ENSG00000139618 675 BRCA2 breast cancer 2 |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
220 ENSG00000129514 3169 FOXA1 forkhead box A1 |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
221 ENSG00000171862 5728 PTEN phosphatase and tensin homolog |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
222 ENSG00000141510 7157 TP53 tumor protein p53 |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
223 =============== ============ ========== ================================= |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
224 |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
225 Columns available for output include many of the ID columns already described under Inputs above and also: |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
226 |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
227 * **ALIAS**: Commonly used gene symbols |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
228 * **DESCRIPTION**: The description of the associated gene |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
229 * **EVIDENCE**: Evidence codes for GO associations with a gene of interest |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
230 * **GENENAME**: The full gene name |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
231 * **ONTOLOGY**: For GO Identifiers, which Gene Ontology (BP, CC, or MF) |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
232 |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
233 ]]></help> |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
234 <citations> |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
235 <citation type="bibtex"> |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
236 @unpublished{None, |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
237 author = {Mark Dunning}, |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
238 title = {annotateMyIDs}, |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
239 year = {2017}, |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
240 eprint = {None}, |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
241 url = {} |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
242 }</citation> |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
243 </citations> |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
244 </tool> |