Mercurial > repos > mvdbeek > generate_sliding_windows

comparison generate_sliding_windows.xml @ 4:cb2d94bb6772 draft

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author mvdbeek
date Wed, 15 Apr 2015 09:08:37 -0400
parents 3dcce035dd6c
children 79e43a3b0883
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3:3dcce035dd6c 4:cb2d94bb6772
1 <tool id="generate_sliding_windows" name="generate_sliding_windows" version="0.1.2"> 1 <tool id="generate_sliding_windows" name="generate_sliding_windows" version="0.1.3">
2 <description>Split fasta sequence in nucleotide windows</description> 2 <description>Split fasta sequence in nucleotide windows</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.65">biopython</requirement> 4 <requirement type="package" version="1.65">biopython</requirement>
5 </requirements> 5 </requirements>
6 <stdio> 6 <stdio>
9 9
10 <command interpreter="python"><![CDATA[ 10 <command interpreter="python"><![CDATA[
11 generate_sliding_windows.py --input "$input" --output "$output" --window $window --step $step 11 generate_sliding_windows.py --input "$input" --output "$output" --window $window --step $step
12 ]]></command> 12 ]]></command>
13 <inputs> 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" /> 14 <conditional name="refFastaSource">
15 <param help="" label="Will you select a fasta sequence from your history or use a pre-installed sequence?" name="fastaSource" type="select">
16 <option value="history">Use one from the history</option>
17 <option value="pre-installed">Use a pre-installed fasta sequence</option>
18 </param>
19 <when value="pre-installed">
20 <param help="if you wish to have your fasta sequence listed contact instance administrator" label="Select a fasta sequence" name="input" type="select">
21 <options from_data_table="all_fasta">
22 </options>
23 </param>
24 </when>
25 <when value="history">
26 <param format="fasta" label="Select a fasta file for which you wish to generate a multi-fasta file in a sliding window fashion" name="input" type="data" />
27 </when>
28 </conditional>
15 <param type="integer" name="window" value="21" min="1" label="window size" help="Specifiy the size of the windows that should be generated"/> 29 <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."/> 30 <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> 31 </inputs>
18 <outputs> 32 <outputs>
19 <data name="output" format="fasta" /> 33 <data name="output" format="fasta" />