Mercurial > repos > mvdbeek > generate_sliding_windows
view generate_sliding_windows.xml @ 3:3dcce035dd6c draft
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author | mvdbeek |
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date | Wed, 15 Apr 2015 07:57:55 -0400 |
parents | 22dc61eaed53 |
children | cb2d94bb6772 |
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<tool id="generate_sliding_windows" name="generate_sliding_windows" version="0.1.2"> <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 "$input" --output "$output" --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="output" format="fasta" /> </outputs> <tests> <test> <param name="input" value="EcR_USP_224.fa"/> <param name="window" value="21"/> <param name="step" value="21"/> <output name="output" file="output.fa"/> </test> </tests> <help><![CDATA[ Generate fixed size sliding windows in fasta format from multi-fasta sequence. ----------------------------- Given an input fasta sequence :: >input ATGCATGCATGCATGCATGCATGCATCGATGCATCGATCG produces the following multi-fasta output with window size 10 and step 5: :: >input_start:1_stop:10 ATGCATGCAT >input_start:6_stop:15 TGCATGCATG >input_start:11_stop:20 GCATGCATGC >input_start:16_stop:25 CATGCATGCA >input_start:21_stop:30 ATGCATCGAT >input_start:26_stop:35 TCGATGCATC ------------------------- 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>