Mercurial > repos > drosofff > msp_cap3

annotate cap3.xml @ 7:858e4f25ec2d draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_cap3 commit 91a0ccc6289f607b16e9ed2482e256c10704f034
author drosofff
date Wed, 28 Oct 2015 13:27:05 -0400
parents e29f3d1124e4
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
5
dd02d02ca305 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_cap3 commit 4d8b548f6c04c81e335187589749ec6bf91ce24e
drosofff
parents: 4
diff changeset
1 <tool id="cap3" name="cap3" version="1.2.0">
0
118834adb4ce planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
2 <description>Sequence Assembly tool</description>
118834adb4ce planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
3 <requirements>
118834adb4ce planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
4 <requirement type="package" version="3">cap3</requirement>
118834adb4ce planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
5 </requirements>
118834adb4ce planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
6 <command>
7
858e4f25ec2d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_cap3 commit 91a0ccc6289f607b16e9ed2482e256c10704f034
drosofff
parents: 6
diff changeset
7 cap3 "$inputSequences" -o $overlaplength -p $overlapidentity > "$cap3stdout";
0
118834adb4ce planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
8 mv "$inputSequences".cap.contigs $contigs;
118834adb4ce planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
9 mv "$inputSequences".cap.contigs.qual $contigsqual;
118834adb4ce planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
10 mv "$inputSequences".cap.contigs.links $contigslink;
118834adb4ce planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
11 mv "$inputSequences".cap.ace $ace;
118834adb4ce planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
12 mv "$inputSequences".cap.info $info;
118834adb4ce planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
13 mv "$inputSequences".cap.singlets $singlets;
3
83716d69ef81 planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents: 2
diff changeset
14 cat $contigs $singlets > $contigsandsinglets
0
118834adb4ce planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
15
118834adb4ce planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
16 </command>
118834adb4ce planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
17
118834adb4ce planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
18 <inputs>
118834adb4ce planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
19 <param label="Input sequences to assemble" name="inputSequences" type="data" format="fasta" help="Input sequences to assemble" />
5
dd02d02ca305 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_cap3 commit 4d8b548f6c04c81e335187589749ec6bf91ce24e
drosofff
parents: 4
diff changeset
20 <param label="specify overlap length cutoff > 15 (40)" name="overlaplength" type="integer" size="3" value="40" help="-o option. must be > 15. 40 by default" />
dd02d02ca305 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_cap3 commit 4d8b548f6c04c81e335187589749ec6bf91ce24e
drosofff
parents: 4
diff changeset
21 <param label="specify overlap percent identity cutoff N > 65 (90)" name="overlapidentity" type="integer" size="3" value="90" help="-p option. must be > 65. 90 by default" />
0
118834adb4ce planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
22 </inputs>
118834adb4ce planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
23
118834adb4ce planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
24 <outputs>
1
8fe1c798372d planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents: 0
diff changeset
25 <data format="fasta" name="contigsandsinglets" label="${tool.name} on ${on_string}: Contigs and singlets" from_work_dir="${inputSequences}.cap.contigs" />
8fe1c798372d planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents: 0
diff changeset
26 <data format="txt" name="cap3stdout" label="${tool.name} on ${on_string}: Standard Output" hidden="true"/>
0
118834adb4ce planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
27 <data format="fasta" name="contigs" label="${tool.name} on ${on_string}: Contigs" from_work_dir="${inputSequences}.cap.contigs" />
1
8fe1c798372d planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents: 0
diff changeset
28 <data format="txt" name="contigsqual" label="${tool.name} on ${on_string}: Contigs Qual" from_work_dir="${inputSequences}.cap.contigs.qual" hidden="true" />
8fe1c798372d planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents: 0
diff changeset
29 <data format="txt" name="contigslink" label="${tool.name} on ${on_string}: Contigs Link" from_work_dir="${inputSequences}.cap.contigs.links" hidden="true" />
8fe1c798372d planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents: 0
diff changeset
30 <data format="txt" name="ace" label="${tool.name} on ${on_string}: Ace" from_work_dir="${inputSequences}.cap.ace" hidden="true" />
8fe1c798372d planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents: 0
diff changeset
31 <data format="txt" name="info" label="${tool.name} on ${on_string}: Info" from_work_dir="${inputSequences}.cap.info" hidden="true" />
8fe1c798372d planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents: 0
diff changeset
32 <data format="txt" name="singlets" label="${tool.name} on ${on_string}: Singlets" from_work_dir="${inputSequences}.cap.singlets" />
0
118834adb4ce planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
33 </outputs>
118834adb4ce planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
34
1
8fe1c798372d planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents: 0
diff changeset
35 <tests>
8fe1c798372d planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents: 0
diff changeset
36 <test>
8fe1c798372d planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents: 0
diff changeset
37 <param name="inputSequences" value="input.fa" ftype="fasta"/>
5
dd02d02ca305 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_cap3 commit 4d8b548f6c04c81e335187589749ec6bf91ce24e
drosofff
parents: 4
diff changeset
38 <param name="overlaplength" value="40" />
dd02d02ca305 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_cap3 commit 4d8b548f6c04c81e335187589749ec6bf91ce24e
drosofff
parents: 4
diff changeset
39 <param name="overlapidentity" value="90" />
1
8fe1c798372d planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents: 0
diff changeset
40 <output name="contigsandsinglets" file="contigsandsinglets.fa"/>
8fe1c798372d planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents: 0
diff changeset
41 <output name="cap3stdout" file="cap3stdout.txt"/>
8fe1c798372d planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents: 0
diff changeset
42 <output name="contigs" file="contigs.fa"/>
8fe1c798372d planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents: 0
diff changeset
43 <output name="contigsqual" file="contigsqual.txt"/>
8fe1c798372d planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents: 0
diff changeset
44 <output name="contigslink" file="contigslink.txt"/>
8fe1c798372d planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents: 0
diff changeset
45 <output name="ace" file="ace.txt"/>
4
4cf7201615f5 planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents: 3
diff changeset
46 <output name="info" file="info.txt"/>
1
8fe1c798372d planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents: 0
diff changeset
47 <output name="singlets" file="singlets.fa"/>
8fe1c798372d planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents: 0
diff changeset
48 </test>
8fe1c798372d planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents: 0
diff changeset
49 </tests>
8fe1c798372d planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents: 0
diff changeset
50
8fe1c798372d planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents: 0
diff changeset
51
0
118834adb4ce planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
52 <help>
1
8fe1c798372d planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents: 0
diff changeset
53 **What it does**
8fe1c798372d planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents: 0
diff changeset
54
8fe1c798372d planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents: 0
diff changeset
55 This tool is a CAP3 wrapper developed for the visitor2 set of worflows
8fe1c798372d planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents: 0
diff changeset
56
8fe1c798372d planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents: 0
diff changeset
57 Under this conditions, it takes as input a set of blast hits in fasta format and performs CAP3 assembly on these sequences
8fe1c798372d planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents: 0
diff changeset
58
8fe1c798372d planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents: 0
diff changeset
59 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).
8fe1c798372d planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents: 0
diff changeset
60
8fe1c798372d planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents: 0
diff changeset
61 Standard CAP3 outputs Contigs and Singlets are returned in the history, as well as a merge of these two datasets (Contigs and singlets)
8fe1c798372d planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents: 0
diff changeset
62
8fe1c798372d planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents: 0
diff changeset
63 **Acknowledgments**
8fe1c798372d planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents: 0
diff changeset
64
2
d33e0baca778 planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents: 1
diff changeset
65 This Galaxy tool makes use of the `package_cap3_3`_ Galaxy package developed by jjohnson.
1
8fe1c798372d planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents: 0
diff changeset
66
8fe1c798372d planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents: 0
diff changeset
67 It is Copyright © 2014-2015 `CNRS and University Pierre et Marie Curie`_ and is released under the `MIT license`_.
8fe1c798372d planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents: 0
diff changeset
68
8fe1c798372d planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents: 0
diff changeset
69 .. _package_cap3_3: https://testtoolshed.g2.bx.psu.edu/view/jjohnson/package_cap3_3
8fe1c798372d planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents: 0
diff changeset
70 .. _CNRS and University Pierre et Marie Curie: http://www.ibps.upmc.fr/en
8fe1c798372d planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents: 0
diff changeset
71 .. _MIT license: http://opensource.org/licenses/MIT
8fe1c798372d planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents: 0
diff changeset
72
0
118834adb4ce planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
73
118834adb4ce planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
74 </help>
1
8fe1c798372d planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents: 0
diff changeset
75 <citations>
8fe1c798372d planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents: 0
diff changeset
76 <citation type="bibtex">@article{Huang:1999wb,
8fe1c798372d planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents: 0
diff changeset
77 author = {Huang, X and Madan, A},
8fe1c798372d planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents: 0
diff changeset
78 title = {{CAP3: A DNA sequence assembly program.}},
8fe1c798372d planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents: 0
diff changeset
79 journal = {Genome research},
8fe1c798372d planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents: 0
diff changeset
80 year = {1999},
8fe1c798372d planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents: 0
diff changeset
81 volume = {9},
8fe1c798372d planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents: 0
diff changeset
82 number = {9},
8fe1c798372d planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents: 0
diff changeset
83 pages = {868--877},
8fe1c798372d planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents: 0
diff changeset
84 month = sep
8fe1c798372d planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents: 0
diff changeset
85 }
8fe1c798372d planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents: 0
diff changeset
86 </citation>
8fe1c798372d planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents: 0
diff changeset
87 </citations>
8fe1c798372d planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents: 0
diff changeset
88
0
118834adb4ce planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
89 </tool>