Mercurial > repos > iuc > annotatemyids

annotate annotateMyIDs.xml @ 15:2790d367cfbc draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit ce8871b2708d391a99cd7656d84eade6f16a1337
author iuc
date Tue, 29 Aug 2023 22:44:11 +0000
parents dec0e9dbe336
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
12
6feec02cf814 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit a7ca7bc12103e184333ec8ab6e99518a4873c707
iuc
parents: 11
diff changeset
1 <tool id="annotatemyids" name="annotateMyIDs" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
0
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
2 <description>annotate a generic set of identifiers</description>
14
dec0e9dbe336 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 8e82a7fcd4c5d82e92dd59b67d2dcf2bb0b905cb
iuc
parents: 13
diff changeset
3 <macros>
dec0e9dbe336 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 8e82a7fcd4c5d82e92dd59b67d2dcf2bb0b905cb
iuc
parents: 13
diff changeset
4 <token name="@TOOL_VERSION@">3.17.0</token>
15
2790d367cfbc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit ce8871b2708d391a99cd7656d84eade6f16a1337
iuc
parents: 14
diff changeset
5 <token name="@VERSION_SUFFIX@">1</token>
14
dec0e9dbe336 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 8e82a7fcd4c5d82e92dd59b67d2dcf2bb0b905cb
iuc
parents: 13
diff changeset
6 </macros>
11
344471c33167 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 3e791f5bd978eee4cd42787c33d4cccc76612c9e
iuc
parents: 10
diff changeset
7 <xrefs>
344471c33167 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 3e791f5bd978eee4cd42787c33d4cccc76612c9e
iuc
parents: 10
diff changeset
8 <xref type="bio.tools">annotatemyids</xref>
344471c33167 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 3e791f5bd978eee4cd42787c33d4cccc76612c9e
iuc
parents: 10
diff changeset
9 </xrefs>
0
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
10 <requirements>
12
6feec02cf814 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit a7ca7bc12103e184333ec8ab6e99518a4873c707
iuc
parents: 11
diff changeset
11 <requirement type="package" version="@TOOL_VERSION@">bioconductor-org.hs.eg.db</requirement>
6feec02cf814 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit a7ca7bc12103e184333ec8ab6e99518a4873c707
iuc
parents: 11
diff changeset
12 <requirement type="package" version="@TOOL_VERSION@">bioconductor-org.mm.eg.db</requirement>
6feec02cf814 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit a7ca7bc12103e184333ec8ab6e99518a4873c707
iuc
parents: 11
diff changeset
13 <requirement type="package" version="@TOOL_VERSION@">bioconductor-org.dm.eg.db</requirement>
6feec02cf814 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit a7ca7bc12103e184333ec8ab6e99518a4873c707
iuc
parents: 11
diff changeset
14 <requirement type="package" version="@TOOL_VERSION@">bioconductor-org.dr.eg.db</requirement>
6feec02cf814 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit a7ca7bc12103e184333ec8ab6e99518a4873c707
iuc
parents: 11
diff changeset
15 <requirement type="package" version="@TOOL_VERSION@">bioconductor-org.rn.eg.db</requirement>
6feec02cf814 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit a7ca7bc12103e184333ec8ab6e99518a4873c707
iuc
parents: 11
diff changeset
16 <requirement type="package" version="@TOOL_VERSION@">bioconductor-org.at.tair.db</requirement>
6feec02cf814 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit a7ca7bc12103e184333ec8ab6e99518a4873c707
iuc
parents: 11
diff changeset
17 <requirement type="package" version="@TOOL_VERSION@">bioconductor-org.gg.eg.db</requirement>
15
2790d367cfbc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit ce8871b2708d391a99cd7656d84eade6f16a1337
iuc
parents: 14
diff changeset
18 <requirement type="package" version="@TOOL_VERSION@">bioconductor-org.bt.eg.db</requirement>
0
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
19 </requirements>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
20 <version_command><![CDATA[
15
2790d367cfbc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit ce8871b2708d391a99cd7656d84eade6f16a1337
iuc
parents: 14
diff changeset
21 echo $(R --version | grep version | grep -v GNU)", org.Hs.eg.db version" $(R --vanilla --slave -e "library(org.Hs.eg.db); cat(sessionInfo()\$otherPkgs\$org.Hs.eg.db\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", org.Dr.eg.db version" $(R --vanilla --slave -e "library(org.Dr.eg.db); cat(sessionInfo()\$otherPkgs\$org.Dr.eg.db\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", org.Dm.eg.db version" $(R --vanilla --slave -e "library(org.Dm.eg.db); cat(sessionInfo()\$otherPkgs\$org.Dm.eg.db\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", org.Mm.eg.db version" $(R --vanilla --slave -e "library(org.Mm.eg.db); cat(sessionInfo()\$otherPkgs\$org.Mm.eg.db\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", org.Rn.eg.db version" $(R --vanilla --slave -e "library(org.Rn.eg.db); cat(sessionInfo()\$otherPkgs\$org.Rn.eg.db\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", org.Bt.eg.db version" $(R --vanilla --slave -e "library(org.Bt.eg.db); cat(sessionInfo()\$otherPkgs\$org.Bt.eg.db\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
0
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
22 ]]></version_command>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
23 <command detect_errors="exit_code"><![CDATA[
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
24 #if $rscriptOpt:
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
25 cp '${annotatemyids_script}' '${out_rscript}' &&
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
26 #end if
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
27 Rscript '${annotatemyids_script}'
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
28 ]]>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
29 </command>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
30 <configfiles>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
31 <configfile name="annotatemyids_script"><![CDATA[
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
32 options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
33
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
34 # we need that to not crash galaxy with an UTF8 error on German LC settings.
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
35 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
36
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
37 id_type <- "${id_type}"
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
38 organism <- "${organism}"
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
39 output_cols <- "${output_cols}"
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
40 file_has_header <- ${file_has_header}
2
1b3e8d3fde62 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 348750c48bc5e4f9ecad408519cdd2c68ac749ab
iuc
parents: 1
diff changeset
41 remove_dups <- ${remove_dups}
0
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
42
6
a4745bc5a840 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit a0c51ab52c4e3f296d5577ee3af26c4c1465e1e9
iuc
parents: 5
diff changeset
43 input <- read.table('$id_file', header=file_has_header, sep="\t", quote="")
a4745bc5a840 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit a0c51ab52c4e3f296d5577ee3af26c4c1465e1e9
iuc
parents: 5
diff changeset
44 ids <- as.character(input[, 1])
0
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
45
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
46 if(organism == "Hs"){
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
47 suppressPackageStartupMessages(library(org.Hs.eg.db))
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
48 db <- org.Hs.eg.db
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
49 } else if (organism == "Mm"){
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
50 suppressPackageStartupMessages(library(org.Mm.eg.db))
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
51 db <- org.Mm.eg.db
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
52 } else if (organism == "Dm"){
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
53 suppressPackageStartupMessages(library(org.Dm.eg.db))
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
54 db <- org.Dm.eg.db
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
55 } else if (organism == "Dr"){
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
56 suppressPackageStartupMessages(library(org.Dr.eg.db))
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
57 db <- org.Dr.eg.db
7
f23e8ea9dd8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 372ac44c1eed0a02c842d8dc65a5d484ed2ba29f
iuc
parents: 6
diff changeset
58 } else if (organism == "Rn"){
f23e8ea9dd8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 372ac44c1eed0a02c842d8dc65a5d484ed2ba29f
iuc
parents: 6
diff changeset
59 suppressPackageStartupMessages(library(org.Rn.eg.db))
f23e8ea9dd8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 372ac44c1eed0a02c842d8dc65a5d484ed2ba29f
iuc
parents: 6
diff changeset
60 db <- org.Rn.eg.db
11
344471c33167 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 3e791f5bd978eee4cd42787c33d4cccc76612c9e
iuc
parents: 10
diff changeset
61 } else if (organism == "At"){
344471c33167 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 3e791f5bd978eee4cd42787c33d4cccc76612c9e
iuc
parents: 10
diff changeset
62 suppressPackageStartupMessages(library(org.At.tair.db))
344471c33167 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 3e791f5bd978eee4cd42787c33d4cccc76612c9e
iuc
parents: 10
diff changeset
63 db <- org.At.tair.db
12
6feec02cf814 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit a7ca7bc12103e184333ec8ab6e99518a4873c707
iuc
parents: 11
diff changeset
64 } else if (organism == "Gg"){
6feec02cf814 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit a7ca7bc12103e184333ec8ab6e99518a4873c707
iuc
parents: 11
diff changeset
65 suppressPackageStartupMessages(library(org.Gg.eg.db))
6feec02cf814 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit a7ca7bc12103e184333ec8ab6e99518a4873c707
iuc
parents: 11
diff changeset
66 db <- org.Gg.eg.db
15
2790d367cfbc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit ce8871b2708d391a99cd7656d84eade6f16a1337
iuc
parents: 14
diff changeset
67 } else if (organism == "Bt"){
2790d367cfbc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit ce8871b2708d391a99cd7656d84eade6f16a1337
iuc
parents: 14
diff changeset
68 suppressPackageStartupMessages(library(org.Bt.eg.db))
2790d367cfbc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit ce8871b2708d391a99cd7656d84eade6f16a1337
iuc
parents: 14
diff changeset
69 db <- org.Bt.eg.db
0
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
70 } else {
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
71 cat(paste("Organism type not supported", organism))
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
72 }
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
73
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
74 cols <- unlist(strsplit(output_cols, ","))
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
75 result <- select(db, keys=ids, keytype=id_type, columns=cols)
2
1b3e8d3fde62 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 348750c48bc5e4f9ecad408519cdd2c68ac749ab
iuc
parents: 1
diff changeset
76
1b3e8d3fde62 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 348750c48bc5e4f9ecad408519cdd2c68ac749ab
iuc
parents: 1
diff changeset
77 if(remove_dups) {
1b3e8d3fde62 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 348750c48bc5e4f9ecad408519cdd2c68ac749ab
iuc
parents: 1
diff changeset
78 result <- result[!duplicated(result$${id_type}),]
1b3e8d3fde62 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 348750c48bc5e4f9ecad408519cdd2c68ac749ab
iuc
parents: 1
diff changeset
79 }
1b3e8d3fde62 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 348750c48bc5e4f9ecad408519cdd2c68ac749ab
iuc
parents: 1
diff changeset
80
0
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
81 write.table(result, file='$out_tab', sep="\t", row.names=FALSE, quote=FALSE)
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
82
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
83 ]]></configfile>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
84 </configfiles>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
85 <inputs>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
86 <param name="id_file" type="data" format="tabular" label="File with IDs" help="A tabular file with the first column containing one of the supported types of identifier, see Help below." />
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
87 <param name="file_has_header" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="False" label="File has header?" help="If this option is set to Yes, the tool will assume that the input file has a column header in the first row and the identifers commence on the second line. Default: No" />
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
88 <param name="organism" type="select" label="Organism" help="Select the organism the identifiers are from">
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
89 <option value="Hs" selected="true">Human</option>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
90 <option value="Mm">Mouse</option>
7
f23e8ea9dd8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 372ac44c1eed0a02c842d8dc65a5d484ed2ba29f
iuc
parents: 6
diff changeset
91 <option value="Rn">Rat</option>
0
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
92 <option value="Dm">Fruit fly</option>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
93 <option value="Dr">Zebrafish</option>
11
344471c33167 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 3e791f5bd978eee4cd42787c33d4cccc76612c9e
iuc
parents: 10
diff changeset
94 <option value="At">Arabidopsis thaliana</option>
12
6feec02cf814 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit a7ca7bc12103e184333ec8ab6e99518a4873c707
iuc
parents: 11
diff changeset
95 <option value="Gg">Gallus gallus</option>
15
2790d367cfbc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit ce8871b2708d391a99cd7656d84eade6f16a1337
iuc
parents: 14
diff changeset
96 <option value="Bt">Bos taurus</option>
0
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
97 </param>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
98 <param name="id_type" type="select" label="ID Type" help="Select the type of IDs in your input file">
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
99 <option value="ENSEMBL" selected="true">Ensembl Gene</option>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
100 <option value="ENSEMBLPROT">Ensembl Protein</option>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
101 <option value="ENSEMBLTRANS">Ensembl Transcript</option>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
102 <option value="ENTREZID">Entrez</option>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
103 <option value="FLYBASE">FlyBase</option>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
104 <option value="GO">GO</option>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
105 <option value="PATH">KEGG</option>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
106 <option value="MGI">MGI</option>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
107 <option value="REFSEQ">RefSeq</option>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
108 <option value="SYMBOL">Gene Symbol</option>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
109 <option value="ZFIN">Zfin</option>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
110 </param>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
111 <param name="output_cols" type="select" multiple="True" display="checkboxes" label="Output columns" help="Choose the columns you want in the output table. Note that selecting some columns such as GO or KEGG could make the table very large as some genes may be associated with many terms. Default: ENSEMBL, ENTREZID, SYMBOL, GENENAME">
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
112 <option value="ALIAS">ALIAS</option>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
113 <option value="ENSEMBL" selected="True">ENSEMBL</option>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
114 <option value="ENTREZID" selected="True">ENTREZID</option>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
115 <option value="EVIDENCE">EVIDENCE</option>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
116 <option value="SYMBOL" selected="True">SYMBOL</option>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
117 <option value="GENENAME" selected="True">GENENAME</option>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
118 <option value="REFSEQ">REFSEQ</option>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
119 <option value="GO">GO</option>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
120 <option value="ONTOLOGY">ONTOLOGY</option>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
121 <option value="PATH">KEGG</option>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
122 </param>
2
1b3e8d3fde62 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 348750c48bc5e4f9ecad408519cdd2c68ac749ab
iuc
parents: 1
diff changeset
123 <param name="remove_dups" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="False" label="Remove duplicates?" help="If this option is set to Yes, only the first occurrence of each input Gene ID will be kept. Default: No" />
0
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
124 <param name="rscriptOpt" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="False" label="Output Rscript?" help="If this option is set to Yes, the Rscript used to annotate the IDs will be provided as a text file in the output. Default: No" />
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
125 </inputs>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
126 <outputs>
10
40e7cdca3e8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 341ee309143af2e0d639fd7eb20d6bc03596b28a"
iuc
parents: 9
diff changeset
127 <data name="out_tab" format="tabular" label="${tool.name} on ${on_string}: Annotated IDs" />
40e7cdca3e8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 341ee309143af2e0d639fd7eb20d6bc03596b28a"
iuc
parents: 9
diff changeset
128 <data name="out_rscript" format="txt" label="${tool.name} on ${on_string}: Rscript">
0
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
129 <filter>rscriptOpt is True</filter>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
130 </data>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
131 </outputs>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
132 <tests>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
133 <!-- Ensure output table works -->
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
134 <test expect_num_outputs="1">
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
135 <param name="id_file" value="genelist.txt" ftype="tabular"/>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
136 <param name="id_type" value="SYMBOL"/>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
137 <param name="organism" value="Hs"/>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
138 <output name="out_tab" file="out.tab" />
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
139 </test>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
140 <!-- Ensure Ensembl IDs input and Rscript output work -->
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
141 <test expect_num_outputs="2">
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
142 <param name="id_file" value="ensembl_ids.tab" ftype="tabular"/>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
143 <param name="id_type" value="ENSEMBL"/>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
144 <param name="organism" value="Hs"/>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
145 <param name="rscriptOpt" value="True" />
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
146 <output name="out_tab" file="out_ensembl.tab" />
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
147 <output name="out_rscript" file="out_rscript.txt" compare="sim_size" />
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
148 </test>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
149 <!-- Ensure GO and KEGG output work -->
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
150 <test expect_num_outputs="1">
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
151 <param name="id_file" value="ensembl_ids.tab" ftype="tabular"/>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
152 <param name="id_type" value="ENSEMBL"/>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
153 <param name="organism" value="Hs"/>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
154 <param name="output_cols" value="ENSEMBL,GO,ONTOLOGY,EVIDENCE" />
13
c99c6e951106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 669d17e476ed4e3a57c697e42f690f9650e855d8
iuc
parents: 12
diff changeset
155 <output name="out_tab">
c99c6e951106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 669d17e476ed4e3a57c697e42f690f9650e855d8
iuc
parents: 12
diff changeset
156 <assert_contents>
c99c6e951106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 669d17e476ed4e3a57c697e42f690f9650e855d8
iuc
parents: 12
diff changeset
157 <has_n_columns n="4"/>
c99c6e951106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 669d17e476ed4e3a57c697e42f690f9650e855d8
iuc
parents: 12
diff changeset
158 <has_n_lines min="700"/>
c99c6e951106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 669d17e476ed4e3a57c697e42f690f9650e855d8
iuc
parents: 12
diff changeset
159 <has_text_matching expression="ENSG00000012048" min="80"/>
c99c6e951106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 669d17e476ed4e3a57c697e42f690f9650e855d8
iuc
parents: 12
diff changeset
160 </assert_contents>
c99c6e951106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 669d17e476ed4e3a57c697e42f690f9650e855d8
iuc
parents: 12
diff changeset
161 </output>
2
1b3e8d3fde62 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 348750c48bc5e4f9ecad408519cdd2c68ac749ab
iuc
parents: 1
diff changeset
162 </test>
1b3e8d3fde62 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 348750c48bc5e4f9ecad408519cdd2c68ac749ab
iuc
parents: 1
diff changeset
163 <!-- Ensure duplicate Gene ID removal works -->
1b3e8d3fde62 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 348750c48bc5e4f9ecad408519cdd2c68ac749ab
iuc
parents: 1
diff changeset
164 <test expect_num_outputs="1">
1b3e8d3fde62 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 348750c48bc5e4f9ecad408519cdd2c68ac749ab
iuc
parents: 1
diff changeset
165 <param name="id_file" value="ensembl_ids.tab" ftype="tabular"/>
1b3e8d3fde62 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 348750c48bc5e4f9ecad408519cdd2c68ac749ab
iuc
parents: 1
diff changeset
166 <param name="id_type" value="ENSEMBL"/>
1b3e8d3fde62 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 348750c48bc5e4f9ecad408519cdd2c68ac749ab
iuc
parents: 1
diff changeset
167 <param name="organism" value="Hs"/>
1b3e8d3fde62 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 348750c48bc5e4f9ecad408519cdd2c68ac749ab
iuc
parents: 1
diff changeset
168 <param name="output_cols" value="ENSEMBL,GO,ONTOLOGY,EVIDENCE" />
1b3e8d3fde62 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 348750c48bc5e4f9ecad408519cdd2c68ac749ab
iuc
parents: 1
diff changeset
169 <param name="remove_dups" value="True" />
13
c99c6e951106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 669d17e476ed4e3a57c697e42f690f9650e855d8
iuc
parents: 12
diff changeset
170 <output name="out_tab">
c99c6e951106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 669d17e476ed4e3a57c697e42f690f9650e855d8
iuc
parents: 12
diff changeset
171 <assert_contents>
c99c6e951106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 669d17e476ed4e3a57c697e42f690f9650e855d8
iuc
parents: 12
diff changeset
172 <has_n_columns n="4"/>
c99c6e951106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 669d17e476ed4e3a57c697e42f690f9650e855d8
iuc
parents: 12
diff changeset
173 <has_n_lines n="9"/>
c99c6e951106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 669d17e476ed4e3a57c697e42f690f9650e855d8
iuc
parents: 12
diff changeset
174 <has_text_matching expression="ENSG00000012048" n="1"/>
c99c6e951106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 669d17e476ed4e3a57c697e42f690f9650e855d8
iuc
parents: 12
diff changeset
175 </assert_contents>
c99c6e951106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 669d17e476ed4e3a57c697e42f690f9650e855d8
iuc
parents: 12
diff changeset
176 </output>
0
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
177 </test>
11
344471c33167 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 3e791f5bd978eee4cd42787c33d4cccc76612c9e
iuc
parents: 10
diff changeset
178 <!-- Arabidopsis database -->
344471c33167 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 3e791f5bd978eee4cd42787c33d4cccc76612c9e
iuc
parents: 10
diff changeset
179 <test expect_num_outputs="1">
344471c33167 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 3e791f5bd978eee4cd42787c33d4cccc76612c9e
iuc
parents: 10
diff changeset
180 <param name="id_file" value="genelist_arabidopsis.txt" ftype="tabular"/>
344471c33167 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 3e791f5bd978eee4cd42787c33d4cccc76612c9e
iuc
parents: 10
diff changeset
181 <param name="id_type" value="SYMBOL"/>
344471c33167 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 3e791f5bd978eee4cd42787c33d4cccc76612c9e
iuc
parents: 10
diff changeset
182 <param name="organism" value="At"/>
344471c33167 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 3e791f5bd978eee4cd42787c33d4cccc76612c9e
iuc
parents: 10
diff changeset
183 <param name="output_cols" value="GO,ENTREZID" />
13
c99c6e951106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 669d17e476ed4e3a57c697e42f690f9650e855d8
iuc
parents: 12
diff changeset
184 <output name="out_tab">
c99c6e951106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 669d17e476ed4e3a57c697e42f690f9650e855d8
iuc
parents: 12
diff changeset
185 <assert_contents>
c99c6e951106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 669d17e476ed4e3a57c697e42f690f9650e855d8
iuc
parents: 12
diff changeset
186 <has_n_columns n="5"/>
c99c6e951106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 669d17e476ed4e3a57c697e42f690f9650e855d8
iuc
parents: 12
diff changeset
187 <has_n_lines min="20"/>
c99c6e951106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 669d17e476ed4e3a57c697e42f690f9650e855d8
iuc
parents: 12
diff changeset
188 <has_text_matching expression="CLE13" min="5"/>
c99c6e951106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 669d17e476ed4e3a57c697e42f690f9650e855d8
iuc
parents: 12
diff changeset
189 </assert_contents>
c99c6e951106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 669d17e476ed4e3a57c697e42f690f9650e855d8
iuc
parents: 12
diff changeset
190 </output>
11
344471c33167 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 3e791f5bd978eee4cd42787c33d4cccc76612c9e
iuc
parents: 10
diff changeset
191 </test>
12
6feec02cf814 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit a7ca7bc12103e184333ec8ab6e99518a4873c707
iuc
parents: 11
diff changeset
192 <!-- Gallus gallus database -->
6feec02cf814 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit a7ca7bc12103e184333ec8ab6e99518a4873c707
iuc
parents: 11
diff changeset
193 <test expect_num_outputs="1">
6feec02cf814 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit a7ca7bc12103e184333ec8ab6e99518a4873c707
iuc
parents: 11
diff changeset
194 <param name="id_file" value="genelist_gallus.txt" ftype="tabular"/>
6feec02cf814 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit a7ca7bc12103e184333ec8ab6e99518a4873c707
iuc
parents: 11
diff changeset
195 <param name="id_type" value="SYMBOL"/>
6feec02cf814 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit a7ca7bc12103e184333ec8ab6e99518a4873c707
iuc
parents: 11
diff changeset
196 <param name="organism" value="Gg"/>
6feec02cf814 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit a7ca7bc12103e184333ec8ab6e99518a4873c707
iuc
parents: 11
diff changeset
197 <param name="output_cols" value="GO,ENTREZID" />
13
c99c6e951106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 669d17e476ed4e3a57c697e42f690f9650e855d8
iuc
parents: 12
diff changeset
198 <output name="out_tab">
c99c6e951106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 669d17e476ed4e3a57c697e42f690f9650e855d8
iuc
parents: 12
diff changeset
199 <assert_contents>
c99c6e951106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 669d17e476ed4e3a57c697e42f690f9650e855d8
iuc
parents: 12
diff changeset
200 <has_n_columns n="5"/>
c99c6e951106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 669d17e476ed4e3a57c697e42f690f9650e855d8
iuc
parents: 12
diff changeset
201 <has_n_lines min="40"/>
c99c6e951106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 669d17e476ed4e3a57c697e42f690f9650e855d8
iuc
parents: 12
diff changeset
202 <has_text_matching expression="TENM2" min="20"/>
c99c6e951106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 669d17e476ed4e3a57c697e42f690f9650e855d8
iuc
parents: 12
diff changeset
203 </assert_contents>
c99c6e951106 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 669d17e476ed4e3a57c697e42f690f9650e855d8
iuc
parents: 12
diff changeset
204 </output>
12
6feec02cf814 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit a7ca7bc12103e184333ec8ab6e99518a4873c707
iuc
parents: 11
diff changeset
205 </test>
15
2790d367cfbc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit ce8871b2708d391a99cd7656d84eade6f16a1337
iuc
parents: 14
diff changeset
206 <!-- Bos taurus database -->
2790d367cfbc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit ce8871b2708d391a99cd7656d84eade6f16a1337
iuc
parents: 14
diff changeset
207 <test expect_num_outputs="1">
2790d367cfbc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit ce8871b2708d391a99cd7656d84eade6f16a1337
iuc
parents: 14
diff changeset
208 <param name="id_file" value="genelist.txt" ftype="tabular"/>
2790d367cfbc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit ce8871b2708d391a99cd7656d84eade6f16a1337
iuc
parents: 14
diff changeset
209 <param name="id_type" value="SYMBOL"/>
2790d367cfbc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit ce8871b2708d391a99cd7656d84eade6f16a1337
iuc
parents: 14
diff changeset
210 <param name="organism" value="Bt"/>
2790d367cfbc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit ce8871b2708d391a99cd7656d84eade6f16a1337
iuc
parents: 14
diff changeset
211 <param name="output_cols" value="ENSEMBL" />
2790d367cfbc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit ce8871b2708d391a99cd7656d84eade6f16a1337
iuc
parents: 14
diff changeset
212 <output name="out_tab">
2790d367cfbc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit ce8871b2708d391a99cd7656d84eade6f16a1337
iuc
parents: 14
diff changeset
213 <assert_contents>
2790d367cfbc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit ce8871b2708d391a99cd7656d84eade6f16a1337
iuc
parents: 14
diff changeset
214 <has_n_columns n="2"/>
2790d367cfbc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit ce8871b2708d391a99cd7656d84eade6f16a1337
iuc
parents: 14
diff changeset
215 <has_n_lines min="9"/>
2790d367cfbc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit ce8871b2708d391a99cd7656d84eade6f16a1337
iuc
parents: 14
diff changeset
216 <has_text_matching expression="ENSBTAG00000007159"/>
2790d367cfbc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit ce8871b2708d391a99cd7656d84eade6f16a1337
iuc
parents: 14
diff changeset
217 <has_text_matching expression="ENSBTAG00000009498"/>
2790d367cfbc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit ce8871b2708d391a99cd7656d84eade6f16a1337
iuc
parents: 14
diff changeset
218 </assert_contents>
2790d367cfbc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit ce8871b2708d391a99cd7656d84eade6f16a1337
iuc
parents: 14
diff changeset
219 </output>
2790d367cfbc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit ce8871b2708d391a99cd7656d84eade6f16a1337
iuc
parents: 14
diff changeset
220 </test>
0
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
221 </tests>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
222 <help><![CDATA[
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
223
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
224 .. class:: infomark
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
225
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
226 **What it does**
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
227
7
f23e8ea9dd8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 372ac44c1eed0a02c842d8dc65a5d484ed2ba29f
iuc
parents: 6
diff changeset
228 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
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
229
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
230 Examples of what this tool can be used for are:
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
231
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
232 * adding gene names to IDs
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
233 * mapping between IDs e.g. Entrez, Ensembl, Symbols
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
234 * adding GO and KEGG identifiers
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
235
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
236 .. _Bioconductor: https://www.bioconductor.org/
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
237 .. _here: http://bioconductor.org/packages/release/data/annotation/manuals/org.Hs.eg.db/man/org.Hs.eg.db.pdf
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
238
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
239 -----
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
240
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
241 **Inputs**
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
242
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
243 A tab-delimited file with identifiers in the first column. If the file contains a header row, select the file has a header option in the tool form above.
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
244
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
245 Example:
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
246
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
247 =============== =======================
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
248 **GeneID** *Additional Columns...*
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
249 --------------- -----------------------
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
250 ENSG00000091831
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
251 ENSG00000082175
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
252 ENSG00000141736
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
253 ENSG00000012048
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
254 ENSG00000139618
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
255 ENSG00000129514
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
256 ENSG00000171862
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
257 ENSG00000141510
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
258 =============== =======================
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
259
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
260 ID types supported for input are:
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
261
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
262 * **ENSEMBL**: Ensembl gene IDs
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
263 * **ENSEMBLPROT**: Ensembl protein IDs
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
264 * **ENSEMBLTRANS**: Ensembl transcript IDs
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
265 * **ENTREZID**: Entrez gene Identifiers
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
266 * **FLYBASE**: FlyBase accession numbers
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
267 * **GO**: GO Identifiers
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
268 * **MGI**: Jackson Laboratory MGI gene accession numbers
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
269 * **PATH**: KEGG Pathway Identifiers
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
270 * **REFSEQ**: Refseq Identifiers
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
271 * **SYMBOL**: The official gene symbol
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
272 * **ZFIN**: Zfin accession numbers
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
273
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
274 .. class:: warningmark
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
275
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
276 This tool uses the ``select`` function from the Bioconductor AnnotationDBi_ package. Note that if you request columns that have multiple matches for your IDs, select will return *one row in the output for each possible match*. This has the effect that if you request multiple columns and some of them have a many-to-one relationship to the IDs, things will continue to multiply accordingly. So it's not a good idea to request a large number of columns unless you know what you are asking for should have a one-to-one relationship with the initial set of IDs. In general, if you need to retrieve a column like **GO** or **KEGG**, that has a many-to-one relationship to the original IDs, it is most useful to extract that separately.
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
277
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
278 .. _AnnotationDBi: https://www.bioconductor.org/packages/devel/bioc/manuals/AnnotationDbi/man/AnnotationDbi.pdf
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
279
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
280 -----
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
281
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
282 **Outputs**
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
283
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
284 If the input IDs are Ensembl, the default output will be similar to below, containing four columns. Other columns, such as GO and KEGG terms, can be selected above to be added as additional columns.
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
285
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
286 Example:
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
287
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
288 =============== ============ ========== =================================
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
289 **ENSEMBL** **ENTREZID** **SYMBOL** **GENENAME**
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
290 --------------- ------------ ---------- ---------------------------------
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
291 ENSG00000091831 2099 ESR1 estrogen receptor 1
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
292 ENSG00000082175 5241 PGR progesterone receptor
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
293 ENSG00000141736 2064 ERBB2 erb-b2 receptor tyrosine kinase 2
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
294 ENSG00000012048 672 BRCA1 breast cancer 1
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
295 ENSG00000139618 675 BRCA2 breast cancer 2
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
296 ENSG00000129514 3169 FOXA1 forkhead box A1
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
297 ENSG00000171862 5728 PTEN phosphatase and tensin homolog
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
298 ENSG00000141510 7157 TP53 tumor protein p53
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
299 =============== ============ ========== =================================
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
300
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
301 Columns available for output include many of the ID columns already described under Inputs above and also:
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
302
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
303 * **ALIAS**: Commonly used gene symbols
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
304 * **EVIDENCE**: Evidence codes for GO associations with a gene of interest
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
305 * **GENENAME**: The full gene name
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
306 * **ONTOLOGY**: For GO Identifiers, which Gene Ontology (BP, CC, or MF)
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
307
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
308 ]]></help>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
309 <citations>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
310 <citation type="bibtex">
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
311 @unpublished{None,
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
312 author = {Mark Dunning},
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
313 title = {annotateMyIDs},
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
314 year = {2017},
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
315 eprint = {None},
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
316 url = {}
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
317 }</citation>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
318 </citations>
af97bb1b9435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
iuc
parents:
diff changeset
319 </tool>