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

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<tool id="GFFToBed" name="GFFToBed" version="1.0">
    <description>GFFToBed 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>
   GFFToBed.py --version
    </version_command>
    <command interpreter="python">
    GFFToBedWrapper_Wrapper.py -i $inputFile -o $outputFile
    </command>
    <inputs>
        <param name="inputFile" type="data" format="gff" label="indicate a transcript GTF file of cufflinks."/>
    </inputs>
    <outputs>
        <data  name="outputFile" format="bed" label="${tool.name} on ${on_string} (BED)"/>
    </outputs>
    <help><![CDATA[
      
**GFFToBed_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, ID, Target, strand

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**input format :**

.. class:: infomark

2L	DmelCaf1_2_2_REPET_TEs	match	47519	52563	0.0	+	.	ID=ms1_dmel_chr2L_RIX-comp_DmelCaf1_2_2-B-P58.20-Map11;Target=RIX-comp_DmelCaf1_2_2-B-P58.20-Map11 6 5050;Identity=99.8


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**output format :**

2L	47519	52563	ms1_dmel_chr2L_RIX-comp_DmelCaf1_2_2-B-P58.20-Map11		RIX-comp_DmelCaf1_2_2-B-P58.20-Map11 6 5050		+

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**reference :**

]]>
    </help>
</tool>