comparison annotateMyIDs.xml @ 15:cd2480f35935 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit ce8871b2708d391a99cd7656d84eade6f16a1337

14:3e1f6f6d557e

<tool id="annotatemyids" name="annotateMyIDs" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
    <description>annotate a generic set of identifiers</description>
    <macros>
        <token name="@TOOL_VERSION@">3.17.0</token>
        <token name="@VERSION_SUFFIX@">0</token>
    </macros>
    <xrefs>
        <xref type="bio.tools">annotatemyids</xref>
    </xrefs>
    <requirements>

        <requirement type="package" version="@TOOL_VERSION@">bioconductor-org.dm.eg.db</requirement>
        <requirement type="package" version="@TOOL_VERSION@">bioconductor-org.dr.eg.db</requirement>
        <requirement type="package" version="@TOOL_VERSION@">bioconductor-org.rn.eg.db</requirement>
        <requirement type="package" version="@TOOL_VERSION@">bioconductor-org.at.tair.db</requirement>
        <requirement type="package" version="@TOOL_VERSION@">bioconductor-org.gg.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.At.tair.db))
    db <- org.At.tair.db
} else if (organism == "Gg"){
    suppressPackageStartupMessages(library(org.Gg.eg.db))
    db <- org.Gg.eg.db
} else {
    cat(paste("Organism type not supported", organism))
}

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

            <option value="Rn">Rat</option>
            <option value="Dm">Fruit fly</option>
            <option value="Dr">Zebrafish</option>
            <option value="At">Arabidopsis thaliana</option>
            <option value="Gg">Gallus gallus</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>
            <option value="ENSEMBLPROT">Ensembl Protein</option>
            <option value="ENSEMBLTRANS">Ensembl Transcript</option>

                    <has_n_lines min="40"/>
                    <has_text_matching expression="TENM2" min="20"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[

.. class:: infomark

15:cd2480f35935

<tool id="annotatemyids" name="annotateMyIDs" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
    <description>annotate a generic set of identifiers</description>
    <macros>
        <token name="@TOOL_VERSION@">3.17.0</token>
        <token name="@VERSION_SUFFIX@">1</token>
    </macros>
    <xrefs>
        <xref type="bio.tools">annotatemyids</xref>
    </xrefs>
    <requirements>

        <requirement type="package" version="@TOOL_VERSION@">bioconductor-org.dm.eg.db</requirement>
        <requirement type="package" version="@TOOL_VERSION@">bioconductor-org.dr.eg.db</requirement>
        <requirement type="package" version="@TOOL_VERSION@">bioconductor-org.rn.eg.db</requirement>
        <requirement type="package" version="@TOOL_VERSION@">bioconductor-org.at.tair.db</requirement>
        <requirement type="package" version="@TOOL_VERSION@">bioconductor-org.gg.eg.db</requirement>
        <requirement type="package" version="@TOOL_VERSION@">bioconductor-org.bt.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: ")", 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: ")
    ]]></version_command>
    <command detect_errors="exit_code"><![CDATA[
        #if $rscriptOpt:
            cp '${annotatemyids_script}' '${out_rscript}' &&
        #end if

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

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

            <option value="Rn">Rat</option>
            <option value="Dm">Fruit fly</option>
            <option value="Dr">Zebrafish</option>
            <option value="At">Arabidopsis thaliana</option>
            <option value="Gg">Gallus gallus</option>
            <option value="Bt">Bos taurus</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>
            <option value="ENSEMBLPROT">Ensembl Protein</option>
            <option value="ENSEMBLTRANS">Ensembl Transcript</option>

                    <has_n_lines min="40"/>
                    <has_text_matching expression="TENM2" min="20"/>
                </assert_contents>
            </output>
        </test>
        <!-- Bos taurus database -->
        <test expect_num_outputs="1">
            <param name="id_file" value="genelist.txt" ftype="tabular"/>
            <param name="id_type" value="SYMBOL"/>
            <param name="organism" value="Bt"/>
            <param name="output_cols" value="ENSEMBL" />
            <output name="out_tab">
                <assert_contents>
                    <has_n_columns n="2"/>
                    <has_n_lines min="9"/>
                    <has_text_matching expression="ENSBTAG00000007159"/>
                    <has_text_matching expression="ENSBTAG00000009498"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[

.. class:: infomark