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comparison anomaly_wrapper.xml @ 0:9c8ffce71f7c draft default tip

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author crs4
date Mon, 09 Sep 2013 12:16:17 -0400
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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>