Mercurial > repos > kpbioteam > clusterprofiler_bitr

changeset 8:8556126fd733 draft

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Uploaded
author kpbioteam
date Mon, 29 Apr 2019 12:36:22 -0400
parents aecccadf1dee
children 762c61c71874
files clusterProfiler_bitr.xml
diffstat 1 files changed, 116 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/clusterProfiler_bitr.xml	Mon Apr 29 12:36:22 2019 -0400
@@ -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="3.7.0">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>