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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/TEiso/ClosestToStartSite_Wrapper.xml	Fri Apr 29 09:11:18 2016 -0400
@@ -0,0 +1,133 @@
+<tool id="ClosestToStartSite" name="ClosestToStartSite" version="1.0">
+    <description>ClosestToStartSite parses a bed file and create a bed file to create a report about positions of features A to features B.</description>
+    <requirements>
+        <requirement type="package" version="1.0">TEiso_Tools</requirement>
+    </requirements>
+    <version_command>
+   ClosestToStartSite.py --version
+    </version_command>
+    <command interpreter="python">
+    ClosestToStartSite_Wrapper.py -i $inputFile -o $outputFile
+    </command>
+    <inputs>
+        <param name="inputFile" type="data" format="bed" label="indicate a bed file."/>
+    </inputs>
+    <outputs>
+        <data  name="outputFile" format="bed" label="${tool.name} on ${on_string} (BED)"/>
+    </outputs>
+    <help><![CDATA[
+      
+**ClosestToStartSite_wrapper parses a bed file and create a bed file to create a report about positions of features A to features B.**
+
+
+**what it does :**
+
+parses a bed file and create a bed file to create a report about positions of features A to features B
+
+-----
+
+**input format :**
+
+.. class:: infomark
+
+**output format :**
+
+fake	140	532	CUFF.1.1	CUFF.1	+	26875.607
+
+-----
+
+
+
+******  "B_close_TSS"
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+					              F[1]   gene             F[2]
+                                    =========================>
+                     ------------
+                    F[8]        F[9]
+    
+    
+                                   F[1]                     F[2]
+                                    <=========================
+                                                                ---------------
+
+
+******  "B_overlap_TSS"
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+            
+                                    F[1]   gene             F[2]
+                                    =========================>
+                             -------------
+                            F[8]        F[9]
+            
+                                                     gene
+                 					F[1]=========================>F[2]
+            
+      								F[8]---------------F[9]
+            
+               
+            
+                                   F[1]=============================>F[2]
+                F[8]---------------F[9]
+            
+            
+                                    F[1]<=============================F[2]
+                                                       ---------------------------
+                                                    F[8]           F[9]
+            
+            
+                                F[1]<=============================F[2]
+                                               F[8]---------------F[9]
+            
+                  
+                                                            F[1]<=============================F[2]
+                                                                                            F[8]---------------F[9]
+
+******  "B-inclus-A"
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+            
+                    
+            
+                                    F[1]            gene          F[2]
+                                    ==============================
+                                            -------------
+                                            F[8]        F[9]
+            
+******  "A-inclus-B"
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~            
+            
+                        
+                                    F[1]======================F[2]
+                    F[8]----------------------------------------------------F[9]
+            
+            
+            
+            
+         					         F[1]==================================>F[2]
+             F[8]----------------------------------------------------------F[9]
+             
+             
+             
+                 					F[1]<==================================F[2]
+                    F[8]----------------------------------------------------------F[9]
+             
+             
+            
+******  "A-inclus-B-inTSS"
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~           
+                    
+ 											 F[1]<==================================F[2]
+                       [8]----------------------------------------------------------F[9]
+            
+                  
+ 												F[1]==================================>F[2]
+                                   					F[8]----------------------------------------------------------F[9]
+            
+    
+-----
+
+**reference :**
+
+]]>
+    </help>
+</tool>