Mercurial > repos > devteam > emboss_5
comparison emboss_pepwheel.xml @ 10:d49956b87f7e draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
author | iuc |
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date | Wed, 08 Feb 2017 12:42:22 -0500 |
parents | |
children | 8992d258e42f |
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9:511429456d3c | 10:d49956b87f7e |
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1 <tool id="EMBOSS: pepwheel72" name="pepwheel" version="5.0.0.1"> | |
2 <!-- produces png file --> | |
3 <description>Shows protein sequences as helices</description> | |
4 <macros> | |
5 <import>macros.xml</import> | |
6 </macros> | |
7 <expand macro="requirements" /> | |
8 <command>perl '$__tool_directory__/emboss_single_outputfile_wrapper.pl' pepwheel -sequence '$input1' -graph png -goutfile '$out_file1' -squares '$squares' -diamonds '$diamonds' -octags '$octags' -amphipathic | |
9 $amphipathic -steps $steps -turns $turns -wheel $wheel -auto</command> | |
10 <inputs> | |
11 <param name="input1" type="data" format="data" label="Sequence" /> | |
12 <param name="steps" type="integer" value="18" label="Steps, the number of residues plotted per turn is this value divided by the 'turns' value" /> | |
13 <param name="turns" type="integer" value="5" label="Turns, the number of residues plotted per turn is the 'steps' value divided by this value" /> | |
14 <param name="squares" type="text" value="ILVM" label="Residues to mark with squares" /> | |
15 <param name="diamonds" type="text" value="DENQST" label="Residues to mark with diamonds" /> | |
16 <param name="octags" type="text" value="HKR" label="Residues to mark with octagons" /> | |
17 <param name="wheel" type="select" label="Plot the wheel"> | |
18 <option value="yes">Yes</option> | |
19 <option value="no">No</option> | |
20 </param> | |
21 <param name="amphipathic" type="select" label="Amphipathic?" help="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" > | |
22 <option value="no">No</option> | |
23 <option value="yes">Yes</option> | |
24 </param> | |
25 </inputs> | |
26 <outputs> | |
27 <data name="out_file1" format="png" /> | |
28 </outputs> | |
29 <help> | |
30 You can view the original documentation here_. | |
31 | |
32 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/pepwheel.html | |
33 </help> | |
34 <expand macro="citations" /> | |
35 </tool> |