diff TEiso/GFFToBed_Wrapper.xml @ 0:3d22562b4489 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/TEiso/GFFToBed_Wrapper.xml	Fri Apr 29 09:11:18 2016 -0400
@@ -0,0 +1,53 @@
+<tool id="GFFToBed" name="GFFToBed" version="1.0">
+    <description>GFFToBed 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>
+   GFFToBed.py --version
+    </version_command>
+    <command interpreter="python">
+    GFFToBedWrapper_Wrapper.py -i $inputFile -o $outputFile
+    </command>
+    <inputs>
+        <param name="inputFile" type="data" format="gff" label="indicate a transcript GTF file of cufflinks."/>
+    </inputs>
+    <outputs>
+        <data  name="outputFile" format="bed" label="${tool.name} on ${on_string} (BED)"/>
+    </outputs>
+    <help><![CDATA[
+      
+**GFFToBed_wrapper converts a result GTF file of Cufflinks into a bed file.**
+
+
+**what it does :**
+
+converts a result GTF file of Cufflinks into a bed file. 
+
+It can take: Chromosome, Start, End, ID, Target, strand
+
+-----
+
+**input format :**
+
+.. class:: infomark
+
+2L	DmelCaf1_2_2_REPET_TEs	match	47519	52563	0.0	+	.	ID=ms1_dmel_chr2L_RIX-comp_DmelCaf1_2_2-B-P58.20-Map11;Target=RIX-comp_DmelCaf1_2_2-B-P58.20-Map11 6 5050;Identity=99.8
+
+
+-----
+
+**output format :**
+
+2L	47519	52563	ms1_dmel_chr2L_RIX-comp_DmelCaf1_2_2-B-P58.20-Map11		RIX-comp_DmelCaf1_2_2-B-P58.20-Map11 6 5050		+
+
+-----
+
+
+-----
+
+**reference :**
+
+]]>
+    </help>
+</tool>