Mercurial > repos > mvdbeek > generate_sliding_windows
comparison generate_sliding_windows.xml @ 0:559cf4ca1f2d draft
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| author | mvdbeek |
|---|---|
| date | Wed, 15 Apr 2015 06:34:23 -0400 |
| parents | |
| children | 10a0153b74d1 |
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| -1:000000000000 | 0:559cf4ca1f2d |
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| 1 <tool id="generate_sliding_windows" name="generate_sliding_windows" version="0.1.1"> | |
| 2 <description>"Split fasta sequence in nucleotide windows"</description> | |
| 3 <requirements> | |
| 4 <requirement type="package" version="1.65">biopython</requirement> | |
| 5 </requirements> | |
| 6 <stdio> | |
| 7 <exit_code range="1:" /> | |
| 8 </stdio> | |
| 9 | |
| 10 <command interpreter="python"><![CDATA[ | |
| 11 generate_sliding_windows.py --input "$input1" --output "$output1" --window $window --step $step | |
| 12 ]]></command> | |
| 13 <inputs> | |
| 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" /> | |
| 15 <param type="integer" name="window" value="21" min="1" label="window size" help="Specifiy the size of the windows that should be generated"/> | |
| 16 <param type="integer" name="step" value="21" min="1" label="step size" help="Specify the distance with which windows should be spaced apart."/> | |
| 17 </inputs> | |
| 18 <outputs> | |
| 19 <data name="output1" format="fasta" /> | |
| 20 </outputs> | |
| 21 <tests> | |
| 22 <test> | |
| 23 <param name="input1" value="EcR_USP_224.fa"/> | |
| 24 <param name="window" value="21"/> | |
| 25 <param name="step" value="21"/> | |
| 26 <output name="output1" file="output.fa"/> | |
| 27 </test> | |
| 28 </tests> | |
| 29 <help><![CDATA[ | |
| 30 | |
| 31 Generate fixed size sliding windows in fasta format from multi-fasta sequence. | |
| 32 | |
| 33 optional arguments: | |
| 34 -h, --help show this help message and exit | |
| 35 --input INPUT supply an input multi-fasta file. | |
| 36 --output OUTPUT supply an output multi-fasta file. If not specified use | |
| 37 stdout. | |
| 38 --window WINDOW Set the size of the generated windows | |
| 39 --step STEP Set distance between the windows | |
| 40 | |
| 41 ]]></help> | |
| 42 </tool> |