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

Uploaded

<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>