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comparison generate_sliding_windows.xml @ 3:3dcce035dd6c draft

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author mvdbeek
date Wed, 15 Apr 2015 07:57:55 -0400
parents 22dc61eaed53
children cb2d94bb6772
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2:22dc61eaed53 3:3dcce035dd6c
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="0.1.2">
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>
7 <exit_code range="1:" /> 7 <exit_code range="1:" />
8 </stdio> 8 </stdio>
9 9
10 <command interpreter="python"><![CDATA[ 10 <command interpreter="python"><![CDATA[
11 generate_sliding_windows.py --input "$input" --output "$output1" --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 <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"/> 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."/> 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> 17 </inputs>
18 <outputs> 18 <outputs>
19 <data name="output1" format="fasta" /> 19 <data name="output" format="fasta" />
20 </outputs> 20 </outputs>
21 <tests> 21 <tests>
22 <test> 22 <test>
23 <param name="input" value="EcR_USP_224.fa"/> 23 <param name="input" value="EcR_USP_224.fa"/>
24 <param name="window" value="21"/> 24 <param name="window" value="21"/>
25 <param name="step" value="21"/> 25 <param name="step" value="21"/>
26 <output name="output1" file="output.fa"/> 26 <output name="output" file="output.fa"/>
27 </test> 27 </test>
28 </tests> 28 </tests>
29 <help><![CDATA[ 29 <help><![CDATA[
30 30
31 Generate fixed size sliding windows in fasta format from multi-fasta sequence. 31 Generate fixed size sliding windows in fasta format from multi-fasta sequence.
32
33 -----------------------------
34
35 Given an input fasta sequence
36
37 ::
38
39
40 >input
41 ATGCATGCATGCATGCATGCATGCATCGATGCATCGATCG
42
43 produces the following multi-fasta output with window size 10 and step 5:
44
45 ::
46
47
48 >input_start:1_stop:10
49 ATGCATGCAT
50 >input_start:6_stop:15
51 TGCATGCATG
52 >input_start:11_stop:20
53 GCATGCATGC
54 >input_start:16_stop:25
55 CATGCATGCA
56 >input_start:21_stop:30
57 ATGCATCGAT
58 >input_start:26_stop:35
59 TCGATGCATC
60
61 -------------------------
32 62
33 optional arguments: 63 optional arguments:
34 -h, --help show this help message and exit 64 -h, --help show this help message and exit
35 --input INPUT supply an input multi-fasta file. 65 --input INPUT supply an input multi-fasta file.
36 --output OUTPUT supply an output multi-fasta file. If not specified use 66 --output OUTPUT supply an output multi-fasta file. If not specified use