<tool id="generate_sliding_windows" name="generate_sliding_windows"  version="0.1.1">
<description>"Split fasta sequence in nucleotide windows"</description>
    <requirements>
        <requirement type="package" version="1.65">biopython</requirement>
    </requirements>
    <stdio>
        <exit_code range="1:" />
    </stdio>

    <command interpreter="python"><![CDATA[
        generate_sliding_windows.py --input "$input1" --output "$output1" --window $window --step $step
    ]]></command>
    <inputs>
        <param type="data" name="input" label="input fasta file" help="select fasta file for which you wish to generate a multi-fasta file in a sliding window fashion" format="fasta" />
        <param type="integer" name="window" value="21" min="1" label="window size" help="Specifiy the size of the windows that should be generated"/>
        <param type="integer" name="step" value="21" min="1" label="step size" help="Specify the distance with which windows should be spaced apart."/>
    </inputs>
    <outputs>
        <data name="output1" format="fasta" />
    </outputs>
    <tests>
        <test>
            <param name="input1" value="EcR_USP_224.fa"/>
            <param name="window" value="21"/>
            <param name="step" value="21"/>
            <output name="output1" file="output.fa"/>
        </test>
    </tests>
    <help><![CDATA[

Generate fixed size sliding windows in fasta format from multi-fasta sequence.

optional arguments:
  -h, --help       show this help message and exit
  --input INPUT    supply an input multi-fasta file.
  --output OUTPUT  supply an output multi-fasta file. If not specified use
                   stdout.
  --window WINDOW  Set the size of the generated windows
  --step STEP      Set distance between the windows

    ]]></help>
</tool>