|
0
|
1 <tool id="anomaly_wrapper" name="Anomaly" version="0.2">
|
|
|
2 <description></description>
|
|
|
3 <requirements>
|
|
|
4 <requirement type="package" version="3.02">glimmer</requirement>
|
|
|
5 </requirements>
|
|
|
6 <command interpreter="python">
|
|
|
7 anomaly_wrapper.py --anSequence $anSequence --anCoords $anCoords
|
|
|
8 #if $anStartCodons
|
|
|
9 --anStartCodons="$anStartCodons"
|
|
|
10 #end if
|
|
|
11 #if $anCheckFirstCodon
|
|
|
12 --anCheckFirstCodon
|
|
|
13 #end if
|
|
|
14 #if $anCheckStopCodon
|
|
|
15 --anCheckStopCodon
|
|
|
16 #end if
|
|
|
17 #if $anStopCodons
|
|
|
18 --anStopCodons="$anStopCodons"
|
|
|
19 #end if
|
|
|
20 --anOutput $anOutput --logfile $logfile
|
|
|
21 </command>
|
|
|
22
|
|
|
23 <inputs>
|
|
|
24 <param name="anSequence" type="data" format="fasta" label="DNA sequence to be analyzed" help="FASTA format" />
|
|
|
25
|
|
|
26 <param name="anCoords" type="data" format="glimmer_coords" label="Region coordinates" />
|
|
|
27
|
|
|
28 <param name="anStartCodons" type="text" value="" optional="true" label="Specify allowable start codons as a comma-separated list (-A)" help="Sample format: 'atg,gtg' . The default start codons are atg, gtg and ttg." />
|
|
|
29
|
|
|
30 <param name="anCheckFirstCodon" type="boolean" checked="false" label="Omit the check that the first codon is a start codon (-s)" help="" />
|
|
|
31
|
|
|
32 <param name="anCheckStopCodon" type="boolean" checked="false" label="Check whether the codon preceding the start coordinate position is a stop codon (-t)" help="This is useful if the coordinates represent the entire region between stop codons." />
|
|
|
33
|
|
|
34 <param name="anStopCodons" type="text" value="" optional="true" label="Specify allowable stop codons as a comma-separated list (-Z)" help="Sample format: 'tag,tga'. The default stop codons are tag, tga and taa." />
|
|
|
35 </inputs>
|
|
|
36
|
|
|
37 <outputs>
|
|
|
38 <data name="logfile" format="txt" label="${tool.name} on ${on_string}: log" />
|
|
|
39 <data name="anOutput" format="txt" label="${tool.name} on ${on_string}: output" />
|
|
|
40 </outputs>
|
|
|
41
|
|
|
42 <tests>
|
|
|
43
|
|
|
44 </tests>
|
|
|
45 <help>
|
|
|
46 **What it does**
|
|
|
47
|
|
|
48 Read DNA sequence in "sequence-file" and for each region specified by the coordinates in "coord-file", check whether the region represents a normal gene, i.e., it begins with a start codon, ends with a stop codon, and has no frame shifts.
|
|
|
49
|
|
|
50 **License and citation**
|
|
|
51
|
|
|
52 This Galaxy tool is Copyright © 2013 `CRS4 Srl.`_ and is released under the `MIT license`_.
|
|
|
53
|
|
|
54 .. _CRS4 Srl.: http://www.crs4.it/
|
|
|
55 .. _MIT license: http://opensource.org/licenses/MIT
|
|
|
56
|
|
|
57 If you use this tool in Galaxy, please cite |Cuccuru2013|_.
|
|
|
58
|
|
|
59 .. |Cuccuru2013| replace:: Cuccuru, G., Orsini, M., Pinna, A., Sbardellati, A., Soranzo, N., Travaglione, A., Uva, P., Zanetti, G., Fotia, G. (2013) Orione, a web-based framework for NGS analysis in microbiology. *Submitted*
|
|
|
60 .. _Cuccuru2013: http://orione.crs4.it/
|
|
|
61
|
|
|
62 This tool uses `Glimmer`_, which is licensed separately. Please cite |Delcher2007|_.
|
|
|
63
|
|
|
64 .. _Glimmer: http://ccb.jhu.edu/software/glimmer/index.shtml
|
|
|
65 .. |Delcher2007| replace:: Delcher, A. L., Bratke, K. A., Powers, E. C., Salzberg, S. L. (2007) Identifying bacterial genes and endosymbiont DNA with Glimmer. *Bioinformatics* 23(6), 673-679
|
|
|
66 .. _Delcher2007: http://bioinformatics.oxfordjournals.org/content/23/6/673
|
|
|
67 </help>
|
|
|
68 </tool>
|
