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

Uploaded

<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 result GTF file of Cufflinks into a bed file. 

It can take: Chromosome, Start, End, strand, Isoform ID, Gene ID, value of FPKM

-----

**input format :**

.. class:: infomark

fake	Cufflinks	transcript	140	532	1000	+	.	gene_id "CUFF.1"; 
transcript_id "CUFF.1.1"; FPKM "26875.6073354154"; frac "1.000000"; conf_lo "24989.806681"; conf_hi "28761.407990"; cov "752.375132";
-----

**output format :**

fake	140	532	CUFF.1.1	CUFF.1	+	26875.607

-----


-----

**reference :**

]]>
    </help>
</tool>