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comparison nucleosome_prediction.xml @ 0:2c42bb973ac3 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nucleosome_prediction commit b309226826df04a53a14b1867547ce6c4810648f
author bgruening
date Tue, 27 Sep 2016 10:02:29 -0400
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1 <tool id="Nucleosome" name="Nucleosome Predictions" version="3.0">
2 <requirements>
3 <requirement type="package" version="3.0">nucleosome_prediction</requirement>
4 </requirements>
5 <command detect_errors="exit_code"><![CDATA[
6 nucleosome_prediction.pl
7 -t Example
8 -s '$input'
9 -p predition_output
10 -tab
11 -c $c
12 -temp $temp
13 $raw_binding
14 ]]></command>
15
16 <inputs>
17 <param type="data" name="input" label="Input sequence file (.fasta format)" format="fasta" />
18 <param argument="-c" type="float" value="0.1"
19 label="Nucleosomes Concentration" help="Nucleosomes concentration: the default value = 0.1"/>
20 <param argument="-temp" type="integer" value="1"
21 label="Temperature Scaling" help="Temperature scaling: the default value = 1"/>
22 <param argument="-raw_binding" type="boolean" truevalue="-raw_binding" falsevalue=""
23 label="Raw Binding" help="Raw Binding: When 'No' (default), then the output will be the default average occupancy probabilities. When 'yes', then the output will be the raw nucleosome binding log-ratio per basepair"/>
24 </inputs>
25
26 <outputs>
27 <data name="output" format="tabular" from_work_dir="predition_output.tab" />
28 </outputs>
29
30 <tests>
31 <test>
32 <param name="input" value="input.fa" ftype="fasta"/>
33 <param name="raw_binding" value="True"/>
34 <output name="output" file="npresults.tab" ftype="tabular"/>
35 </test>
36 <test>
37 <param name="input" value="input.fa" ftype="fasta"/>
38 <param name="c" value="0.1"/>
39 <param name="temp" value="1"/>
40 <output name="output" file="npresultsf.tab" ftype="tabular"/>
41 </test>
42 </tests>
43
44 <help><![CDATA[
45
46 **What it does**
47 This tool allows you to submit a genomic sequence and to recieve a prediction of the nucleosomes positions on it, based on the nucleosome-DNA interaction model that we developed in these papers:
48 This version (version 3) is applicable to all species.
49
50 The tool takes a sequence .fasta file and finds all positions of the matrices above the background
51
52 ]]></help>
53
54 <citations>
55
56 <citation type="bibtex">
57 @MISC{10.1038/nature07667,
58 DOI = {10.1038/nature07667},
59 note = {The DNA-encoded nucleosome organization of a eukaryotic genome}
60 year = "2009"
61 }
62 </citation>
63 </citations>
64
65 </tool>