--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/TEiso/CufflinksGTFToBed_Wrapper.xml	Thu Jul 21 07:42:47 2016 -0400
@@ -0,0 +1,51 @@
+<tool id="CufflinksGTFToBed" name="CufflinksGTFToBed" version="1.0">
+    <description>CufflinksGTFToBed can convert a result GTF file of Cufflinks into a bed file.</description>
+    <requirements>
+        <requirement type="package" version="1.0">TEiso_Tools</requirement>
+    </requirements>
+    <version_command>
+   CufflinksGTFToBed.py --version
+    </version_command>
+    <command interpreter="python">
+    CufflinksGTFToBed_Wrapper.py -i $inputFile -o $outputFile
+    </command>
+    <inputs>
+        <param name="inputFile" type="data" format="gtf" label="indicate a transcript GTF file of cufflinks."/>
+    </inputs>
+    <outputs>
+        <data  name="outputFile" format="bed" label="${tool.name} on ${on_string} (BED)"/>
+    </outputs>
+    <help><![CDATA[
+
+
+
+**CufflinksGTFToBed_wrapper converts a result GTF file of Cufflinks into a bed file.**
+
+**what it does :**
+
+Converts a GTF file of transcripts into a bed file. In input file, there are all the information of the transcript and their exon. CufflinksGTFToBed takes only the transcripts to convert into a bed file. 
+ 
+It can take: Chromosome, Start, End, strand, Isoform ID, Gene ID, value of FPKM
+
+-----
+
+**example :**
+
+
+Transcript input file: ::
+
+    2L	cufflinks	transcript	10487	18076	372	-	.	gene_id "CUFF.1"; transcript_id "CUFF.1.1"; FPKM "1.3627628649"; frac "0.197041"; conf_lo "0.805777"; conf_hi "1.919748"; cov "1.706083";
+
+
+      
+
+----
+
+output format: ::
+
+    2L	10487	18076	CUFF.1.1	CUFF.1	-	1.363
+
+
+]]>
+    </help>
+</tool>