| Previous changeset 2:4a06a7d061fb (2019-04-28) Next changeset 4:03b28a1e2f23 (2019-04-28) |
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Commit message:
Uploaded |
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added:
test-data/gene.txt test-data/genedf.txt |
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removed:
clusterProfiler_bitr.xml |
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| diff -r 4a06a7d061fb -r 230bed1368fc clusterProfiler_bitr.xml --- a/clusterProfiler_bitr.xml Sun Apr 28 03:45:59 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,116 +0,0 @@ -<tool id="clusterprofiler_bitr" name="Cluster Profiler 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 '$clusterprofiler_bitr_script' - ]]></command> - <configfiles> - <configfile name="clusterprofiler_bitr_script"><![CDATA[ -require("clusterProfiler", quietly = TRUE) -require("org.Hs.eg.db", quietly = TRUE) - -gene <- c(read.table('$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> |
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| diff -r 4a06a7d061fb -r 230bed1368fc test-data/gene.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gene.txt Sun Apr 28 07:38:56 2019 -0400 |
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| @@ -0,0 +1,1 @@ +"GPX3", "GLRX", "LBP", "CRYAB", "DEFB1", "HCLS1", "SOD2", "HSPA2" |
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| diff -r 4a06a7d061fb -r 230bed1368fc test-data/genedf.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/genedf.txt Sun Apr 28 07:38:56 2019 -0400 |
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| @@ -0,0 +1,2 @@ +"SYMBOL" "ENTREZID" +"GPX3" "2878" |