view exseq_multi.xml @ 4:75d3df84f68a draft

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<tool id="extract_align" name="Extract sub sequence of multifasta file." version="0.1.0">
    <description>Extract sub sequence of multifasta file.</description>
    <stdio>
        <exit_code range="1:" />
    </stdio>
    <version_command>
        python3 '$__tool_directory__/exseq_multi.py -i $inputfile -s $startpos -e $endpos -o $output'
    </version_command>
    <inputs>
        <param type="data" name="inputfile" format="fasta" label="Select your multifasta file :" />
        <param type="text" name="startpos" label="Start position to cut :" /> 
        <param type="text" name="endpos" label="End position to stop the cut :" /> 
    </inputs>
    <outputs>
        <data name="output" format="fasta" />
    </outputs>
    <help>
         usage: exseq_multi.py [-h] [-i INFILE] [-s START] [-e END] [-o OUTFILE]
 
         Extract sequence of multifasta file from position start/end.

         optional arguments:
          -h, --help            show this help message and exit
          -i INFILE, --input_file INFILE
                        Multifasta file.
          -s START, --start_position START
                        Start position to extract.
          -e END, --end_position END
                        End position to extract.
          -o OUTFILE, --output_file OUTFILE
                        Output file.

    </help>
</tool>