Mercurial > repos > devteam > emboss_5
annotate emboss_5/emboss_pepwheel.xml @ 8:b810c96613ee draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
author | devteam |
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date | Wed, 11 Nov 2015 12:12:41 -0500 |
parents | b94ca591877b |
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rev | line source |
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0 | 1 <tool id="EMBOSS: pepwheel72" name="pepwheel" version="5.0.0"> |
2 <!-- produces png file --> | |
3 <description>Shows protein sequences as helices</description> | |
4 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> | |
5 <command interpreter="perl">emboss_single_outputfile_wrapper.pl pepwheel -sequence $input1 -graph png -goutfile $out_file1 -squares $squares -diamonds $diamonds -octags $octags -amphipathic | |
6 $amphipathic -steps $steps -turns $turns -wheel $wheel -auto</command> | |
7 <inputs> | |
8 <param format="data" name="input1" type="data"> | |
9 <label>Sequence</label> | |
10 </param> | |
8
b810c96613ee
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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11 <param name="steps" type="text" value="18"> |
0 | 12 <label>Steps, the number of residues plotted per turn is this value divided by the 'turns' value</label> |
13 </param> | |
8
b810c96613ee
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
0
diff
changeset
|
14 <param name="turns" type="text" value="5"> |
0 | 15 <label>Turns, the number of residues plotted per turn is the 'steps' value divided by this value</label> |
16 </param> | |
8
b810c96613ee
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
0
diff
changeset
|
17 <param name="squares" type="text" value="ILVM"> |
0 | 18 <label>Residues to mark with squares</label> |
19 </param> | |
8
b810c96613ee
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
0
diff
changeset
|
20 <param name="diamonds" type="text" value="DENQST"> |
0 | 21 <label>Residues to mark with diamonds</label> |
22 </param> | |
8
b810c96613ee
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
0
diff
changeset
|
23 <param name="octags" type="text" value="HKR"> |
0 | 24 <label>Residues to mark with octagons</label> |
25 </param> | |
26 <param name="wheel" type="select"> | |
27 <label>Plot the wheel</label> | |
28 <option value="yes">Yes</option> | |
29 <option value="no">No</option> | |
30 </param> | |
31 <param name="amphipathic" type="select"> | |
32 <label>If this is true then the residues ACFGILMVWY are marked as squares and all other residues are unmarked. This overrides any other markup that you may have specified</label> | |
33 <option value="no">No</option> | |
34 <option value="yes">Yes</option> | |
35 </param> | |
36 </inputs> | |
37 <outputs> | |
38 <data format="png" name="out_file1" /> | |
39 </outputs> | |
40 <help> | |
41 You can view the original documentation here_. | |
42 | |
43 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/pepwheel.html | |
44 | |
45 ------ | |
46 | |
47 **Citation** | |
48 | |
49 For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ | |
50 | |
51 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ | |
52 </help> | |
53 </tool> |