comparison annotateMyIDs.xml @ 7:1aae04680c4b draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 372ac44c1eed0a02c842d8dc65a5d484ed2ba29f

6:ecc913a7334b

<tool id="annotatemyids" name="annotateMyIDs" version="3.7.0">
    <description>annotate a generic set of identifiers</description>
    <requirements>
        <requirement type="package" version="3.7.0">bioconductor-org.hs.eg.db</requirement>
        <requirement type="package" version="3.7.0">bioconductor-org.mm.eg.db</requirement>
        <requirement type="package" version="3.7.0">bioconductor-org.dm.eg.db</requirement>
        <requirement type="package" version="3.7.0">bioconductor-org.dr.eg.db</requirement>
    </requirements>
    <version_command><![CDATA[
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: ")
    ]]></version_command>
    <command detect_errors="exit_code"><![CDATA[
        #if $rscriptOpt:
            cp '${annotatemyids_script}' '${out_rscript}' &&
        #end if

    suppressPackageStartupMessages(library(org.Dm.eg.db))
    db <- org.Dm.eg.db
} else if (organism == "Dr"){
    suppressPackageStartupMessages(library(org.Dr.eg.db))
    db <- org.Dr.eg.db
} else {
    cat(paste("Organism type not supported", organism))
}

cols <- unlist(strsplit(output_cols, ","))

        <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." />
        <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" />
        <param name="organism" type="select" label="Organism" help="Select the organism the identifiers are from">
            <option value="Hs" selected="true">Human</option>
            <option value="Mm">Mouse</option>
            <option value="Dm">Fruit fly</option>
            <option value="Dr">Zebrafish</option>
        </param>
        <param name="id_type" type="select" label="ID Type" help="Select the type of IDs in your input file">
            <option value="ENSEMBL" selected="true">Ensembl Gene</option>

.. class:: infomark

**What it does**

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_.

Examples of what this tool can be used for are:

* adding gene names to IDs
* mapping between IDs e.g. Entrez, Ensembl, Symbols

7:1aae04680c4b

<tool id="annotatemyids" name="annotateMyIDs" version="3.7.0+galaxy1">
    <description>annotate a generic set of identifiers</description>
    <requirements>
        <requirement type="package" version="3.7.0">bioconductor-org.hs.eg.db</requirement>
        <requirement type="package" version="3.7.0">bioconductor-org.mm.eg.db</requirement>
        <requirement type="package" version="3.7.0">bioconductor-org.dm.eg.db</requirement>
        <requirement type="package" version="3.7.0">bioconductor-org.dr.eg.db</requirement>
        <requirement type="package" version="3.7.0">bioconductor-org.rn.eg.db</requirement>
    </requirements>
    <version_command><![CDATA[
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: ")
    ]]></version_command>
    <command detect_errors="exit_code"><![CDATA[
        #if $rscriptOpt:
            cp '${annotatemyids_script}' '${out_rscript}' &&
        #end if

    suppressPackageStartupMessages(library(org.Dm.eg.db))
    db <- org.Dm.eg.db
} else if (organism == "Dr"){
    suppressPackageStartupMessages(library(org.Dr.eg.db))
    db <- org.Dr.eg.db
} else if (organism == "Rn"){
    suppressPackageStartupMessages(library(org.Rn.eg.db))
    db <- org.Rn.eg.db
} else {
    cat(paste("Organism type not supported", organism))
}

cols <- unlist(strsplit(output_cols, ","))

        <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." />
        <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" />
        <param name="organism" type="select" label="Organism" help="Select the organism the identifiers are from">
            <option value="Hs" selected="true">Human</option>
            <option value="Mm">Mouse</option>
            <option value="Rn">Rat</option>
            <option value="Dm">Fruit fly</option>
            <option value="Dr">Zebrafish</option>
        </param>
        <param name="id_type" type="select" label="ID Type" help="Select the type of IDs in your input file">
            <option value="ENSEMBL" selected="true">Ensembl Gene</option>

.. class:: infomark

**What it does**

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_.

Examples of what this tool can be used for are:

* adding gene names to IDs
* mapping between IDs e.g. Entrez, Ensembl, Symbols