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comparison annotateMyIDs.xml @ 7:f23e8ea9dd8a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 372ac44c1eed0a02c842d8dc65a5d484ed2ba29f
author iuc
date Fri, 21 Jun 2019 04:03:28 -0400
parents a4745bc5a840
children 3c1c293b6955
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6:a4745bc5a840 7:f23e8ea9dd8a
1 <tool id="annotatemyids" name="annotateMyIDs" version="3.7.0"> 1 <tool id="annotatemyids" name="annotateMyIDs" version="3.7.0+galaxy1">
2 <description>annotate a generic set of identifiers</description> 2 <description>annotate a generic set of identifiers</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="3.7.0">bioconductor-org.hs.eg.db</requirement> 4 <requirement type="package" version="3.7.0">bioconductor-org.hs.eg.db</requirement>
5 <requirement type="package" version="3.7.0">bioconductor-org.mm.eg.db</requirement> 5 <requirement type="package" version="3.7.0">bioconductor-org.mm.eg.db</requirement>
6 <requirement type="package" version="3.7.0">bioconductor-org.dm.eg.db</requirement> 6 <requirement type="package" version="3.7.0">bioconductor-org.dm.eg.db</requirement>
7 <requirement type="package" version="3.7.0">bioconductor-org.dr.eg.db</requirement> 7 <requirement type="package" version="3.7.0">bioconductor-org.dr.eg.db</requirement>
8 <requirement type="package" version="3.7.0">bioconductor-org.rn.eg.db</requirement>
8 </requirements> 9 </requirements>
9 <version_command><![CDATA[ 10 <version_command><![CDATA[
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: ") 11 echo $(R --version | grep version | grep -v GNU)", org.Hs.eg.db version" $(R --vanilla --slave -e "library(org.Hs.eg.db); cat(sessionInfo()\$otherPkgs\$org.Hs.eg.db\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", org.Dr.eg.db version" $(R --vanilla --slave -e "library(org.Dr.eg.db); cat(sessionInfo()\$otherPkgs\$org.Dr.eg.db\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", org.Dm.eg.db version" $(R --vanilla --slave -e "library(org.Dm.eg.db); cat(sessionInfo()\$otherPkgs\$org.Dm.eg.db\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", org.Mm.eg.db version" $(R --vanilla --slave -e "library(org.Mm.eg.db); cat(sessionInfo()\$otherPkgs\$org.Mm.eg.db\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", org.Rn.eg.db version" $(R --vanilla --slave -e "library(org.Rn.eg.db); cat(sessionInfo()\$otherPkgs\$org.Rn.eg.db\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
11 ]]></version_command> 12 ]]></version_command>
12 <command detect_errors="exit_code"><![CDATA[ 13 <command detect_errors="exit_code"><![CDATA[
13 #if $rscriptOpt: 14 #if $rscriptOpt:
14 cp '${annotatemyids_script}' '${out_rscript}' && 15 cp '${annotatemyids_script}' '${out_rscript}' &&
15 #end if 16 #end if
42 suppressPackageStartupMessages(library(org.Dm.eg.db)) 43 suppressPackageStartupMessages(library(org.Dm.eg.db))
43 db <- org.Dm.eg.db 44 db <- org.Dm.eg.db
44 } else if (organism == "Dr"){ 45 } else if (organism == "Dr"){
45 suppressPackageStartupMessages(library(org.Dr.eg.db)) 46 suppressPackageStartupMessages(library(org.Dr.eg.db))
46 db <- org.Dr.eg.db 47 db <- org.Dr.eg.db
48 } else if (organism == "Rn"){
49 suppressPackageStartupMessages(library(org.Rn.eg.db))
50 db <- org.Rn.eg.db
47 } else { 51 } else {
48 cat(paste("Organism type not supported", organism)) 52 cat(paste("Organism type not supported", organism))
49 } 53 }
50 54
51 cols <- unlist(strsplit(output_cols, ",")) 55 cols <- unlist(strsplit(output_cols, ","))
63 <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." /> 67 <param name="id_file" type="data" format="tabular" label="File with IDs" help="A tabular file with the first column containing one of the supported types of identifier, see Help below." />
64 <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" /> 68 <param name="file_has_header" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="False" label="File has header?" help="If this option is set to Yes, the tool will assume that the input file has a column header in the first row and the identifers commence on the second line. Default: No" />
65 <param name="organism" type="select" label="Organism" help="Select the organism the identifiers are from"> 69 <param name="organism" type="select" label="Organism" help="Select the organism the identifiers are from">
66 <option value="Hs" selected="true">Human</option> 70 <option value="Hs" selected="true">Human</option>
67 <option value="Mm">Mouse</option> 71 <option value="Mm">Mouse</option>
72 <option value="Rn">Rat</option>
68 <option value="Dm">Fruit fly</option> 73 <option value="Dm">Fruit fly</option>
69 <option value="Dr">Zebrafish</option> 74 <option value="Dr">Zebrafish</option>
70 </param> 75 </param>
71 <param name="id_type" type="select" label="ID Type" help="Select the type of IDs in your input file"> 76 <param name="id_type" type="select" label="ID Type" help="Select the type of IDs in your input file">
72 <option value="ENSEMBL" selected="true">Ensembl Gene</option> 77 <option value="ENSEMBL" selected="true">Ensembl Gene</option>
142 147
143 .. class:: infomark 148 .. class:: infomark
144 149
145 **What it does** 150 **What it does**
146 151
147 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_. 152 This tool can get annotation for a generic set of IDs, using the Bioconductor_ annotation data packages. Supported organisms are human, mouse, rat, fruit fly and zebrafish. The org.db packages that are used here are primarily based on mapping using Entrez Gene identifiers. More information on the annotation packages can be found at the Bioconductor website, for example, information on the human annotation package (org.Hs.eg.db) can be found here_.
148 153
149 Examples of what this tool can be used for are: 154 Examples of what this tool can be used for are:
150 155
151 * adding gene names to IDs 156 * adding gene names to IDs
152 * mapping between IDs e.g. Entrez, Ensembl, Symbols 157 * mapping between IDs e.g. Entrez, Ensembl, Symbols