Mercurial > repos > kpbioteam > clusterprofiler_bitr

changeset 3:230bed1368fc draft

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Uploaded
author kpbioteam
date Sun, 28 Apr 2019 07:38:56 -0400
parents 4a06a7d061fb
children 03b28a1e2f23
files clusterProfiler_bitr.xml test-data/gene.txt test-data/genedf.txt
diffstat 3 files changed, 3 insertions(+), 116 deletions(-) [+]
line wrap: on
line diff
--- a/clusterProfiler_bitr.xml	Sun Apr 28 03:45:59 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -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>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gene.txt	Sun Apr 28 07:38:56 2019 -0400
@@ -0,0 +1,1 @@
+"GPX3",  "GLRX",   "LBP",   "CRYAB", "DEFB1", "HCLS1",   "SOD2",   "HSPA2"
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/genedf.txt	Sun Apr 28 07:38:56 2019 -0400
@@ -0,0 +1,2 @@
+"SYMBOL" "ENTREZID"
+"GPX3" "2878"