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1 <tool id="generate_sliding_windows" name="generate_sliding_windows" version="0.1.1">
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2 <description>"Split fasta sequence in nucleotide windows"</description>
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3 <requirements>
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4 <requirement type="package" version="1.65">biopython</requirement>
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5 </requirements>
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6 <stdio>
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7 <exit_code range="1:" />
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8 </stdio>
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9
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10 <command interpreter="python"><![CDATA[
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11 generate_sliding_windows.py --input "$input1" --output "$output1" --window $window --step $step
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12 ]]></command>
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13 <inputs>
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14 <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" />
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15 <param type="integer" name="window" value="21" min="1" label="window size" help="Specifiy the size of the windows that should be generated"/>
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16 <param type="integer" name="step" value="21" min="1" label="step size" help="Specify the distance with which windows should be spaced apart."/>
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17 </inputs>
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18 <outputs>
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19 <data name="output1" format="fasta" />
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20 </outputs>
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21 <tests>
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22 <test>
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23 <param name="input1" value="EcR_USP_224.fa"/>
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24 <param name="window" value="21"/>
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25 <param name="step" value="21"/>
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26 <output name="output1" file="output.fa"/>
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27 </test>
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28 </tests>
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29 <help><![CDATA[
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30
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31 Generate fixed size sliding windows in fasta format from multi-fasta sequence.
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32
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33 optional arguments:
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34 -h, --help show this help message and exit
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35 --input INPUT supply an input multi-fasta file.
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36 --output OUTPUT supply an output multi-fasta file. If not specified use
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37 stdout.
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38 --window WINDOW Set the size of the generated windows
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39 --step STEP Set distance between the windows
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40
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41 ]]></help>
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42 </tool>
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