diff TEiso/GFFToBed_Wrapper.xml @ 1:15d6811e6bf5 draft

Uploaded

--- a/TEiso/GFFToBed_Wrapper.xml	Fri Apr 29 09:11:18 2016 -0400
+++ b/TEiso/GFFToBed_Wrapper.xml	Tue May 24 08:59:28 2016 -0400
@@ -1,5 +1,5 @@
 <tool id="GFFToBed" name="GFFToBed" version="1.0">
-    <description>GFFToBed can convert a result GTF file of Cufflinks into a bed file.</description>
+    <description>GFFToBed can convert a result GTF file into a bed file.</description>
     <requirements>
         <requirement type="package" version="1.0">TEiso_Tools</requirement>
     </requirements>
@@ -7,7 +7,7 @@
    GFFToBed.py --version
     </version_command>
     <command interpreter="python">
-    GFFToBedWrapper_Wrapper.py -i $inputFile -o $outputFile
+    GFFToBed_Wrapper.py -i $inputFile -o $outputFile
     </command>
     <inputs>
         <param name="inputFile" type="data" format="gff" label="indicate a transcript GTF file of cufflinks."/>
@@ -16,37 +16,35 @@
         <data  name="outputFile" format="bed" label="${tool.name} on ${on_string} (BED)"/>
     </outputs>
     <help><![CDATA[
-      
-**GFFToBed_wrapper converts a result GTF file of Cufflinks into a bed file.**
+
 
+**GFFToBed_wrapper converts a result GTF file 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
+converts a result GFF3 file into a bed file
+ 
+it can take: Chromosome, Start, End, ID, Target, strand.
 
 -----
 
-**input format :**
+**example :**
+
+a GFF3 file of the Transposable elements as input file: ::
 
-.. 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
-
+    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 :**
+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	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	-
 
 
------
-
-**reference :**
 
 ]]>
     </help>