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planemo upload for repository https://bitbucket.org/drosofff/gedtools/
author drosofff
date Sun, 21 Jun 2015 14:30:20 -0400
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1 <tool id="cap3" name="cap3" version="1.1.0">
2 <description>Sequence Assembly tool</description>
3 <requirements>
4 <requirement type="package" version="3">cap3</requirement>
5 </requirements>
6 <command>
7 cap3 "$inputSequences" > "$cap3stdout";
8 mv "$inputSequences".cap.contigs $contigs;
9 mv "$inputSequences".cap.contigs.qual $contigsqual;
10 mv "$inputSequences".cap.contigs.links $contigslink;
11 mv "$inputSequences".cap.ace $ace;
12 mv "$inputSequences".cap.info $info;
13 mv "$inputSequences".cap.singlets $singlets;
14 cat $contigs $singlets > $contigsandsinglets
15
16 </command>
17
18 <inputs>
19 <param label="Input sequences to assemble" name="inputSequences" type="data" format="fasta" help="Input sequences to assemble" />
20 </inputs>
21
22 <outputs>
23 <data format="fasta" name="contigsandsinglets" label="${tool.name} on ${on_string}: Contigs and singlets" from_work_dir="${inputSequences}.cap.contigs" />
24 <data format="txt" name="cap3stdout" label="${tool.name} on ${on_string}: Standard Output" hidden="true"/>
25 <data format="fasta" name="contigs" label="${tool.name} on ${on_string}: Contigs" from_work_dir="${inputSequences}.cap.contigs" />
26 <data format="txt" name="contigsqual" label="${tool.name} on ${on_string}: Contigs Qual" from_work_dir="${inputSequences}.cap.contigs.qual" hidden="true" />
27 <data format="txt" name="contigslink" label="${tool.name} on ${on_string}: Contigs Link" from_work_dir="${inputSequences}.cap.contigs.links" hidden="true" />
28 <data format="txt" name="ace" label="${tool.name} on ${on_string}: Ace" from_work_dir="${inputSequences}.cap.ace" hidden="true" />
29 <data format="txt" name="info" label="${tool.name} on ${on_string}: Info" from_work_dir="${inputSequences}.cap.info" hidden="true" />
30 <data format="txt" name="singlets" label="${tool.name} on ${on_string}: Singlets" from_work_dir="${inputSequences}.cap.singlets" />
31 </outputs>
32
33 <tests>
34 <test>
35 <param name="inputSequences" value="input.fa" ftype="fasta"/>
36 <output name="contigsandsinglets" file="contigsandsinglets.fa"/>
37 <output name="cap3stdout" file="cap3stdout.txt"/>
38 <output name="contigs" file="contigs.fa"/>
39 <output name="contigsqual" file="contigsqual.txt"/>
40 <output name="contigslink" file="contigslink.txt"/>
41 <output name="ace" file="ace.txt"/>
42 <output name="info" file="info.txt"/>
43 <output name="singlets" file="singlets.fa"/>
44 </test>
45 </tests>
46
47
48 <help>
49 **What it does**
50
51 This tool is a CAP3 wrapper developed for the visitor2 set of worflows
52
53 Under this conditions, it takes as input a set of blast hits in fasta format and performs CAP3 assembly on these sequences
54
55 Standard CAP3 outputs (Standard Output, Contigs Qual, Contigs Link, Ace and Info) are kept hidden in the Galaxy history (feel free to reveal these hidden datasets).
56
57 Standard CAP3 outputs Contigs and Singlets are returned in the history, as well as a merge of these two datasets (Contigs and singlets)
58
59 **Acknowledgments**
60
61 This Galaxy tool makes use of the `package_cap3_3`_ Galaxy package developed by jjohnson.
62
63 It is Copyright © 2014-2015 `CNRS and University Pierre et Marie Curie`_ and is released under the `MIT license`_.
64
65 .. _package_cap3_3: https://testtoolshed.g2.bx.psu.edu/view/jjohnson/package_cap3_3
66 .. _CNRS and University Pierre et Marie Curie: http://www.ibps.upmc.fr/en
67 .. _MIT license: http://opensource.org/licenses/MIT
68
69
70 </help>
71 <citations>
72 <citation type="bibtex">@article{Huang:1999wb,
73 author = {Huang, X and Madan, A},
74 title = {{CAP3: A DNA sequence assembly program.}},
75 journal = {Genome research},
76 year = {1999},
77 volume = {9},
78 number = {9},
79 pages = {868--877},
80 month = sep
81 }
82 </citation>
83 </citations>
84
85 </tool>