view TEiso/ClosestToStartSite_Wrapper.xml @ 1:15d6811e6bf5 draft

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<tool id="ClosestToStartSite" name="ClosestToStartSite" version="1.0">
    <description>ClosestToStartSite parses a bed file and generate a report about positions of features A to features B. It can also add the class code of features A.</description>
    <requirements>
        <requirement type="package" version="1.0">TEiso_Tools</requirement>
    </requirements>
    <version_command>
   ClosestToStartSite.py --version
    </version_command>
   <command interpreter="python">
    #if $ClassCode.get_class_code
    	ClosestToStartSite_Wrapper.py -i $inputFile -c $cuffcom_tmap -o $outputFile
    #else
    	ClosestToStartSite_Wrapper.py -i $inputFile -o $outputFile
     #end if
    </command>
    <inputs>
        <param name="inputFile" type="data" format="bed" label="indicate a bed file."/>
        <conditional name="ClassCode">
            <param name="get_class_code" type="boolean" label="get information of class code from cuff_in.tmap" truevalue="yes" falsevalue="no" checked="off" />
            <when value="no"/>
            <when value="yes">
                <param name="cuffcom_tmap" type="data" format="tabular" label="indicate cuff_in.tmap" help="default = 1"/>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data  name="outputFile" format="bed" label="${tool.name} on ${on_string} (BED)"/>
    </outputs>
    <help><![CDATA[
      



**ClosestToStartSite parses a bed file and generate a report about positions of features A (according to its TSS) to features B. It can also add the class code of features A.**

**what it does :**

generate a report about positions of features B to features A (according to its TSS). In input file, there are the information of the two features. ClosestToStartSite reports only the cases that features Bis near to TSS or has overlap with TSS of features A. it can be also run cuffcopare to features A, and add the class code information to output file.


-----

**example :**


Bed input file: ::

    2L  239751  240346  CUFF.36.1       CUFF.36 -       2L      239932  241306  RXX     +       415     TE_overlap_TSS
    2L  113233  113411  CUFF.14.1       CUFF.14 -       2L      113496  113509  RLX     -       -854    TE_near_TSS


----

output format: ::


    2L	239751	240346	CUFF.36.1	CUFF.36	-	2L	239932	241306	RXX	+	415	TE_overlap_TSS
    2L	113233	113411	CUFF.14.1	CUFF.14	-	2L	113496	113509	RLX	-	-854	TE_near_TSS


output format with calss code: ::
 

    2L	239751	240346	CUFF.36.1	CUFF.36	-	2L	239932	241306	RXX	+	415	TE_overlap_TSS	c	gene-id-1
    2L	113233	113411	CUFF.14.1	CUFF.14	-	2L	113496	113509	RLX	-	-854	TE_near_TSS	=	gene-id-2


]]>
    </help>
</tool>