diff TEiso/GFFToBed_Wrapper.xml @ 16:836ce3d9d47a draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/TEiso/GFFToBed_Wrapper.xml	Thu Jul 21 07:42:47 2016 -0400
@@ -0,0 +1,51 @@
+<tool id="GFFToBed" name="GFFToBed" version="1.0">
+    <description>GFFToBed can convert a result GTF file 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">
+    GFFToBed_Wrapper.py -i $inputFile -o $outputFile
+    </command>
+    <inputs>
+        <param name="inputFile" type="data" format="gff" label="indicate a transcript GFF file of cufflinks."/>
+    </inputs>
+    <outputs>
+        <data  name="outputFile" format="bed" label="${tool.name} on ${on_string} (BED)"/>
+    </outputs>
+    <help><![CDATA[
+
+
+**GFFToBed_wrapper converts a result GTF file into a bed file.**
+
+**what it does :**
+
+converts a result GFF3 file into a bed file
+ 
+it can take: Chromosome, Start, End, ID, Target, strand.
+
+-----
+
+**example :**
+
+a GFF3 file of the Transposable elements as input file: ::
+
+    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   
+    2L	DmelCaf1_2_2_REPET_TEs	match	16205	16490	0.0	+	.	ID=ms2_dmel_chr2L_RXX-LARD_DmelCaf1_2_2-L-B578-Map1;Target=RXX-LARD_DmelCaf1_2_2-L-B578-Map1 2551 2828;Identity=97.5
+    2R	DmelCaf1_2_2_REPET_TEs	match	24134   24428   0.0	-	.	ID=ms4350_dmel_chr2R_RXX-LARD-chim_DmelCaf1_2_2-L-B414-Map1;Target=RXX-LARD-chim_DmelCaf1_2_2-L-B414-Map1 2894 3273
+
+-----
+
+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	+
+    2L	16205	16490	ms2_dmel_chr2L_RXX-LARD_DmelCaf1_2_2-L-B578-Map1		RXX-LARD_DmelCaf1_2_2-L-B578-Map1 2551 2828	+
+    2R	24134	24428	ms4350_dmel_chr2R_RXX-LARD-chim_DmelCaf1_2_2-L-B414-Map1	RXX-LARD-chim_DmelCaf1_2_2-L-B414-Map1 2894	3273	-
+
+
+
+]]>
+    </help>
+</tool>