annotate TEiso/GFFToBed_Wrapper.xml @ 11:782306d67e39 draft

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<tool id="GFFToBed" name="GFFToBed" version="1.0">
    <description>GFFToBed can convert a result GTF file 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">
    GFFToBed_Wrapper.py -i $inputFile -o $outputFile
    </command>
    <inputs>
        <param name="inputFile" type="data" format="gff" label="indicate a transcript GFF file of cufflinks."/>
    </inputs>
    <outputs>
        <data  name="outputFile" format="bed" label="${tool.name} on ${on_string} (BED)"/>
    </outputs>
    <help><![CDATA[


**GFFToBed_wrapper converts a result GTF file into a bed file.**

**what it does :**

converts a result GFF3 file into a bed file
 
it can take: Chromosome, Start, End, ID, Target, strand.

-----

**example :**

a GFF3 file of the Transposable elements as input file: ::

    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   
    2L	DmelCaf1_2_2_REPET_TEs	match	16205	16490	0.0	+	.	ID=ms2_dmel_chr2L_RXX-LARD_DmelCaf1_2_2-L-B578-Map1;Target=RXX-LARD_DmelCaf1_2_2-L-B578-Map1 2551 2828;Identity=97.5
    2R	DmelCaf1_2_2_REPET_TEs	match	24134   24428   0.0	-	.	ID=ms4350_dmel_chr2R_RXX-LARD-chim_DmelCaf1_2_2-L-B414-Map1;Target=RXX-LARD-chim_DmelCaf1_2_2-L-B414-Map1 2894 3273

-----

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	+
    2L	16205	16490	ms2_dmel_chr2L_RXX-LARD_DmelCaf1_2_2-L-B578-Map1		RXX-LARD_DmelCaf1_2_2-L-B578-Map1 2551 2828	+
    2R	24134	24428	ms4350_dmel_chr2R_RXX-LARD-chim_DmelCaf1_2_2-L-B414-Map1	RXX-LARD-chim_DmelCaf1_2_2-L-B414-Map1 2894	3273	-



]]>
    </help>
</tool>