Mercurial > repos > iuc > annotatemyids
annotate annotateMyIDs.xml @ 0:442e2d79b05c draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
author | iuc |
---|---|
date | Wed, 03 Jan 2018 15:25:26 -0500 |
parents | |
children | 2e1b256f732f |
rev | line source |
---|---|
0
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
1 <tool id="annotateMyIDs" name="annotateMyIDs" version="3.5.0.0"> |
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> |
442e2d79b05c
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> |
442e2d79b05c
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> |
442e2d79b05c
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> |
442e2d79b05c
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> |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
8 </requirements> |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
9 <version_command><![CDATA[ |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
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: ")", optparse version" $(R --vanilla --slave -e "library(optparse); cat(sessionInfo()\$otherPkgs\$optparse\$Version)" 2> /dev/null | grep -v -i "WARNING: ") |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
11 ]]></version_command> |
442e2d79b05c
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[ |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
13 #if $rscriptOpt: |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
14 cp '${annotatemyids_script}' '${out_rscript}' && |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
15 #end if |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
16 Rscript '${annotatemyids_script}' |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
17 ]]> |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
18 </command> |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
19 <configfiles> |
442e2d79b05c
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[ |
442e2d79b05c
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 ) } ) |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
22 |
442e2d79b05c
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. |
442e2d79b05c
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") |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
25 |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
26 id_type <- "${id_type}" |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
27 organism <- "${organism}" |
442e2d79b05c
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}" |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
29 file_has_header <- ${file_has_header} |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
30 |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
31 ids <- as.character(read.table('$id_file', header=file_has_header)[,1]) |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
32 |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
33 if(organism == "Hs"){ |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
34 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
|
35 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
|
36 } 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
|
37 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
|
38 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
|
39 } 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
|
40 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
|
41 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
|
42 } 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
|
43 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
|
44 db <- 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
|
45 } else { |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
46 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
|
47 } |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
48 |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
49 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
|
50 result <- select(db, keys=ids, keytype=id_type, columns=cols) |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
51 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
|
52 |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
53 ]]></configfile> |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
54 </configfiles> |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
55 <inputs> |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
56 <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
|
57 <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
|
58 <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
|
59 <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
|
60 <option value="Mm">Mouse</option> |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
61 <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
|
62 <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
|
63 </param> |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
64 <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
|
65 <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
|
66 <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
|
67 <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
|
68 <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
|
69 <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
|
70 <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
|
71 <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
|
72 <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
|
73 <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
|
74 <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
|
75 <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
|
76 </param> |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
77 <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
|
78 <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
|
79 <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
|
80 <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
|
81 <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
|
82 <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
|
83 <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
|
84 <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
|
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="GO">GO</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="ONTOLOGY">ONTOLOGY</option> |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
88 <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
|
89 </param> |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
90 <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
|
91 </inputs> |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
92 <outputs> |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
93 <data name="out_tab" format="tabular" from_work_dir="*.tab" label="${tool.name} on ${on_string}: Annotated IDs" /> |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
94 <data name="out_rscript" format="txt" from_work_dir="*.txt" label="${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
|
95 <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
|
96 </data> |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
97 </outputs> |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
98 <tests> |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
99 <!-- 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
|
100 <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
|
101 <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
|
102 <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
|
103 <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
|
104 <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
|
105 </test> |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
106 <!-- 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
|
107 <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
|
108 <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
|
109 <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
|
110 <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
|
111 <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
|
112 <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
|
113 <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
|
114 </test> |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
115 <!-- 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
|
116 <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
|
117 <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
|
118 <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
|
119 <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
|
120 <param name="output_cols" value="ENSEMBL,GO,ONTOLOGY,EVIDENCE" /> |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
121 <output name="out_tab" file="out_gokegg.tab" compare="contains" /> |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
122 </test> |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
123 </tests> |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
124 <help><![CDATA[ |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
125 |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
126 .. class:: infomark |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
127 |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
128 **What it does** |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
129 |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
130 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_. |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
131 |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
132 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
|
133 |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
134 * 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
|
135 * 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
|
136 * 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
|
137 |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
138 .. _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
|
139 .. _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
|
140 |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
141 ----- |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
142 |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
143 **Inputs** |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
144 |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
145 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
|
146 |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
147 Example: |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
148 |
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 **GeneID** *Additional Columns...* |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
151 --------------- ----------------------- |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
152 ENSG00000091831 |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
153 ENSG00000082175 |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
154 ENSG00000141736 |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
155 ENSG00000012048 |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
156 ENSG00000139618 |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
157 ENSG00000129514 |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
158 ENSG00000171862 |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
159 ENSG00000141510 |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
160 =============== ======================= |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
161 |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
162 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
|
163 |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
164 * **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
|
165 * **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
|
166 * **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
|
167 * **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
|
168 * **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
|
169 * **GO**: GO Identifiers |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
170 * **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
|
171 * **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
|
172 * **REFSEQ**: Refseq Identifiers |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
173 * **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
|
174 * **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
|
175 |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
176 .. class:: warningmark |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
177 |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
178 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
|
179 |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
180 .. _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
|
181 |
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 **Outputs** |
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 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
|
187 |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
188 Example: |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
189 |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
190 =============== ============ ========== ================================= |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
191 **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
|
192 --------------- ------------ ---------- --------------------------------- |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
193 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
|
194 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
|
195 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
|
196 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
|
197 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
|
198 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
|
199 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
|
200 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
|
201 =============== ============ ========== ================================= |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
202 |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
203 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
|
204 |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
205 * **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
|
206 * **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
|
207 * **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
|
208 * **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
|
209 * **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
|
210 |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
211 ]]></help> |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
212 <citations> |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
213 <citation type="bibtex"> |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
214 @unpublished{None, |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
215 author = {Mark Dunning}, |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
216 title = {annotateMyIDs}, |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
217 year = {2017}, |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
218 eprint = {None}, |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
219 url = {} |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
220 }</citation> |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
221 </citations> |
442e2d79b05c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff
changeset
|
222 </tool> |