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changeset 0:e7a71e686f53 draft

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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 90120121398f
files README.md clusterProfiler_bitr.R clusterProfiler_bitr.xml gene.txt genedf.txt test-data/gene.txt test-data/genedf.txt
diffstat 7 files changed, 124 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.md	Mon Mar 19 14:03:04 2018 -0400
@@ -0,0 +1,1 @@
+#This tool is a Biological Id TRanslator (for human genome wide annotation)
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/clusterProfiler_bitr.R	Mon Mar 19 14:03:04 2018 -0400
@@ -0,0 +1,14 @@
+require("clusterProfiler", quietly = TRUE)
+require("org.Hs.eg.db", quietly = TRUE)
+
+args <- commandArgs(trailingOnly = TRUE)
+
+input1 = args[1]
+input2 = args[2]
+input3 = args[3]
+output = args[4]
+
+gene <- c(read.table(input1))
+gene.df = bitr(gene$V1, fromType=input2, toType=input3, OrgDb="org.Hs.eg.db")
+
+write.table(gene.df,file = output,row.names = FALSE)
--- /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>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gene.txt	Mon Mar 19 14:03:04 2018 -0400
@@ -0,0 +1,1 @@
+"GPX3",  "GLRX",   "LBP",   "CRYAB", "DEFB1", "HCLS1",   "SOD2",   "HSPA2"
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/genedf.txt	Mon Mar 19 14:03:04 2018 -0400
@@ -0,0 +1,2 @@
+"SYMBOL" "ENTREZID"
+"GPX3" "2878"
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gene.txt	Mon Mar 19 14:03:04 2018 -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	Mon Mar 19 14:03:04 2018 -0400
@@ -0,0 +1,2 @@
+"SYMBOL" "ENTREZID"
+"GPX3" "2878"