Mercurial > repos > drosofff > msp_cap3

comparison cap3.xml @ 1:8fe1c798372d draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
author drosofff
date Sat, 20 Jun 2015 05:34:21 -0400
parents 118834adb4ce
children d33e0baca778
comparison
equal deleted inserted replaced
0:118834adb4ce 1:8fe1c798372d
1 <tool id="cap3" name="cap3" version="1.0.1"> 1 <tool id="cap3" name="cap3" version="1.1.0">
2 <description>Sequence Assembly tool</description> 2 <description>Sequence Assembly tool</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="3">cap3</requirement> 4 <requirement type="package" version="3">cap3</requirement>
5 </requirements> 5 </requirements>
6 <command> 6 <command>
7 cap3 "$inputSequences" > "$cap3stdout"; 7 cap3 "$inputSequences" > "$cap3stdout";
8 cat "$inputSequences".cap.contigs "$inputSequences".cap.singlets > $contigsandsinglets
8 mv "$inputSequences".cap.contigs $contigs; 9 mv "$inputSequences".cap.contigs $contigs;
9 mv "$inputSequences".cap.contigs.qual $contigsqual; 10 mv "$inputSequences".cap.contigs.qual $contigsqual;
10 mv "$inputSequences".cap.contigs.links $contigslink; 11 mv "$inputSequences".cap.contigs.links $contigslink;
11 mv "$inputSequences".cap.ace $ace; 12 mv "$inputSequences".cap.ace $ace;
12 mv "$inputSequences".cap.info $info; 13 mv "$inputSequences".cap.info $info;
17 <inputs> 18 <inputs>
18 <param label="Input sequences to assemble" name="inputSequences" type="data" format="fasta" help="Input sequences to assemble" /> 19 <param label="Input sequences to assemble" name="inputSequences" type="data" format="fasta" help="Input sequences to assemble" />
19 </inputs> 20 </inputs>
20 21
21 <outputs> 22 <outputs>
22 <data format="txt" name="cap3stdout" label="${tool.name} on ${on_string}: Standard Output"/> 23 <data format="fasta" name="contigsandsinglets" label="${tool.name} on ${on_string}: Contigs and singlets" from_work_dir="${inputSequences}.cap.contigs" />
24 <data format="txt" name="cap3stdout" label="${tool.name} on ${on_string}: Standard Output" hidden="true"/>
23 <data format="fasta" name="contigs" label="${tool.name} on ${on_string}: Contigs" from_work_dir="${inputSequences}.cap.contigs" /> 25 <data format="fasta" name="contigs" label="${tool.name} on ${on_string}: Contigs" from_work_dir="${inputSequences}.cap.contigs" />
24 <data format="txt" name="contigsqual" label="${tool.name} on ${on_string}: Contigs Qual" from_work_dir="${inputSequences}.cap.contigs.qual" hidden="True" /> 26 <data format="txt" name="contigsqual" label="${tool.name} on ${on_string}: Contigs Qual" from_work_dir="${inputSequences}.cap.contigs.qual" hidden="true" />
25 <data format="txt" name="contigslink" label="${tool.name} on ${on_string}: Contigs Link" from_work_dir="${inputSequences}.cap.contigs.links" 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" />
26 <data format="txt" name="ace" label="${tool.name} on ${on_string}: Ace" from_work_dir="${inputSequences}.cap.ace" hidden="True" /> 28 <data format="txt" name="ace" label="${tool.name} on ${on_string}: Ace" from_work_dir="${inputSequences}.cap.ace" hidden="true" />
27 <data format="txt" name="info" label="${tool.name} on ${on_string}: Info" from_work_dir="${inputSequences}.cap.info" hidden="True" /> 29 <data format="txt" name="info" label="${tool.name} on ${on_string}: Info" from_work_dir="${inputSequences}.cap.info" hidden="true" />
28 <data format="txt" name="singlets" label="${tool.name} on ${on_string}: Singlets" from_work_dir="${inputSequences}.cap.singlets" hidden="True" /> 30 <data format="txt" name="singlets" label="${tool.name} on ${on_string}: Singlets" from_work_dir="${inputSequences}.cap.singlets" />
29 </outputs> 31 </outputs>
30 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="singlets" file="singlets.fa"/>
43 </test>
44 </tests>
45
46
31 <help> 47 <help>
48 **What it does**
49
50 This tool is a CAP3 wrapper developed for the visitor2 set of worflows
51
52 Under this conditions, it takes as input a set of blast hits in fasta format and performs CAP3 assembly on these sequences
53
54 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).
55
56 Standard CAP3 outputs Contigs and Singlets are returned in the history, as well as a merge of these two datasets (Contigs and singlets)
57
58 **Acknowledgments**
59
60 This Galaxy tool makes use of the `package_cap3_3`_ Galaxy package developed by jjohnson the galaxy tool `get_fasta_from_taxon`_.
61
62 It is Copyright © 2014-2015 `CNRS and University Pierre et Marie Curie`_ and is released under the `MIT license`_.
63
64 .. _package_cap3_3: https://testtoolshed.g2.bx.psu.edu/view/jjohnson/package_cap3_3
65 .. _CNRS and University Pierre et Marie Curie: http://www.ibps.upmc.fr/en
66 .. _MIT license: http://opensource.org/licenses/MIT
67
32 68
33 </help> 69 </help>
70 <citations>
71 <citation type="bibtex">@article{Huang:1999wb,
72 author = {Huang, X and Madan, A},
73 title = {{CAP3: A DNA sequence assembly program.}},
74 journal = {Genome research},
75 year = {1999},
76 volume = {9},
77 number = {9},
78 pages = {868--877},
79 month = sep
80 }
81 </citation>
82 </citations>
83
34 </tool> 84 </tool>