Mercurial > repos > kpbioteam > clusterprofiler_bitr
diff clusterProfiler_bitr.xml @ 0:e7a71e686f53 draft
planemo upload for repository https://github.com/kpbioteam/clusterProfiler_bitr commit 470dccce41afc79ef1cc7a6722b50d0c258e0f4f
| author | kpbioteam |
|---|---|
| date | Mon, 19 Mar 2018 14:03:04 -0400 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/clusterProfiler_bitr.xml Mon Mar 19 14:03:04 2018 -0400 @@ -0,0 +1,103 @@ +<tool id="clusterProfiler_bitr" name="clusterProfiler_bitr" version="0.1.0"> + <description>converting ID types</description> + <requirements> + <requirement type="package" version="3.6.0">bioconductor-clusterprofiler</requirement> + <requirement type="package" version="3.5.0">bioconductor-org.hs.eg.db</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + Rscript ${__tool_directory__}/clusterProfiler_bitr.R "$input1" "$input2" "$input3" "$output1" + ]]></command> + <inputs> + <param type="data" name="input1" format="txt" /> + <param name="input2" 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="input3" 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="output1" format="txt" /> + </outputs> + <tests> + <test> + <param name="input1" value="gene.txt"/> + <param name="input2" value="SYMBOL"/> + <param name="input3" value="ENTREZID"/> + <output name="output1" 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>