annotate TEiso/CufflinksGTFToBed_Wrapper.xml @ 2:775f119b9ac2 draft

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<tool id="CufflinksGTFToBed" name="CufflinksGTFToBed" version="1.0">
    <description>CufflinksGTFToBed can convert a result GTF file of Cufflinks into a bed file.</description>
    <requirements>
        <requirement type="package" version="1.0">TEiso_Tools</requirement>
    </requirements>
    <version_command>
   CufflinksGTFToBed.py --version
    </version_command>
    <command interpreter="python">
    CufflinksGTFToBed_Wrapper.py -i $inputFile -o $outputFile
    </command>
    <inputs>
        <param name="inputFile" type="data" format="gtf" label="indicate a transcript GTF file of cufflinks."/>
    </inputs>
    <outputs>
        <data  name="outputFile" format="bed" label="${tool.name} on ${on_string} (BED)"/>
    </outputs>
    <help><![CDATA[



**CufflinksGTFToBed_wrapper converts a result GTF file of Cufflinks into a bed file.**

**what it does :**

Converts a GTF file of transcripts into a bed file. In input file, there are all the information of the transcript and their exon. CufflinksGTFToBed takes only the transcripts to convert into a bed file. 
 
It can take: Chromosome, Start, End, strand, Isoform ID, Gene ID, value of FPKM

-----

**example :**


Transcript input file: ::

    2L	cufflinks	transcript	10487	18076	372	-	.	gene_id "CUFF.1"; transcript_id "CUFF.1.1"; FPKM "1.3627628649"; frac "0.197041"; conf_lo "0.805777"; conf_hi "1.919748"; cov "1.706083";


      

----

output format: ::

    2L	10487	18076	CUFF.1.1	CUFF.1	-	1.363


]]>
    </help>
</tool>