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clusterProfiler_bitr.xml |
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| diff -r c5d67efb4c94 -r dd045606e0bd clusterProfiler_bitr.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/clusterProfiler_bitr.xml Sun Apr 28 13:26:44 2019 -0400 |
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| @@ -0,0 +1,116 @@ +<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="3.5.0">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> |