annotate clusterProfiler_bitr.xml @ 8:8556126fd733 draft

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<tool id="clusterprofiler_bitr" name="Cluster Profiler Bitr" version="0.1.0">
    <description>converting ID types</description>
    <requirements>
        <requirement type="package" version="3.10.1">bioconductor-clusterprofiler</requirement>
        <requirement type="package" version="3.7.0">bioconductor-org.hs.eg.db</requirement>
    </requirements>
<command detect_errors="exit_code"><![CDATA[
        Rscript '$clusterprofiler_bitr_script'
    ]]></command>
    <configfiles>
        <configfile name="clusterprofiler_bitr_script"><![CDATA[
require("clusterProfiler", quietly = TRUE)
require("org.Hs.eg.db", quietly = TRUE)

gene <- c(read.table('$genelist'))
gene.df = bitr(gene\$V1, fromType='$fromType', toType='$toType', OrgDb="org.Hs.eg.db")

write.table(gene.df,file = '$translation',row.names = FALSE)
        
        ]]>
        </configfile>
    </configfiles> 
    <inputs>
        <param type="data" name="genelist" format="txt" />
        <param name="fromType" type="select" label="Input Type Gene ID" help="User should provides fromType geneID (translator input type)">
                        <option value="SYMBOL">SYMBOL</option>
			 <option value="ENTREZID">ENTREZID</option>
			 <option value="ENSEMBL">ENSEMBL</option>
			 <option value="ENSEMBLPROT">ENSEMBLPROT</option>
			<option value="EVIDENCE">EVIDENCE</option>
			<option value="GOALL">GOALL</option>
			
			<option value="ONTOLOGY">ONTOLOGY</option>
			<option value="PMID">PMID</option>
			
			<option value="PFAM">PFAM</option>
			
			<option value="OMIM">OMIM</option>
			
			<option value="GO">GO</option>

			<option value="UNIPROT">UNIPROT</option>
			<option value="REFSEQ">REFSEQ</option>
			<option value="PATH">PATH</option>
			
			<option value="MAP">MAP</option>
			
			<option value="GENENAME">GENENAME</option>
			<option value="ENZYME">ENZYME</option>
			<option value="ALIAS">ALIAS</option>

			<option value="UNIGENE">UNIGENE</option>
			<option value="PROSITE">PROSITE</option>
			<option value="ONTOLOGYALL">ONTOLOGYALL</option>
			<option value="IPI">IPI</option>
		
			<option value="EVIDENCEALL">EVIDENCEALL</option>
			<option value="ENSEMBLTRANS">ENSEMBLTRANS</option>
			<option value="ACCNUM">ACCNUM</option>
 </param>

        <param name="toType" type="select" label="Output Type Gene ID" help="User should provides toType geneID (translator output type)">
                        <option value="SYMBOL">SYMBOL</option>
			<option value="ENTREZID">ENTREZID</option>
			<option value="ENSEMBL">ENSEMBL</option>
                         <option value="ENSEMBLPROT">ENSEMBLPROT</option>
                        <option value="EVIDENCE">EVIDENCE</option>
                        <option value="GOALL">GOALL</option>

                        <option value="ONTOLOGY">ONTOLOGY</option>
                        <option value="PMID">PMID</option>

                        <option value="PFAM">PFAM</option>

                        <option value="OMIM">OMIM</option>

                        <option value="GO">GO</option>

                        <option value="UNIPROT">UNIPROT</option>
                        <option value="REFSEQ">REFSEQ</option>
                        <option value="PATH">PATH</option>

                        <option value="MAP">MAP</option>

                        <option value="GENENAME">GENENAME</option>
                        <option value="ENZYME">ENZYME</option>
                        <option value="ALIAS">ALIAS</option>

                        <option value="UNIGENE">UNIGENE</option>
                        <option value="PROSITE">PROSITE</option>
                        <option value="ONTOLOGYALL">ONTOLOGYALL</option>
                        <option value="IPI">IPI</option>

                        <option value="EVIDENCEALL">EVIDENCEALL</option>
                        <option value="ENSEMBLTRANS">ENSEMBLTRANS</option>
                        <option value="ACCNUM">ACCNUM</option>
</param>
    </inputs>
    <outputs>
        <data name="translation" format="txt" />
    </outputs>
    <tests>
        <test>
            <param name="genelist" value="gene.txt"/>
            <param name="fromType" value="SYMBOL"/>
            <param name="toType" value="ENTREZID"/>
            <output name="translation" file="genedf.txt"/>
        </test>
    </tests>
    <help><![CDATA[
        This tool is a Biological Id TRanslator
    ]]></help>
    <citations>
        <citation type="doi">10.1089/omi.2011.0118</citation>
    </citations>
</tool>