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comparison emboss_pepwheel.xml @ 11:0e2484b6829b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
author iuc
date Mon, 30 Jan 2017 13:27:40 -0500
parents 9b98d3d903c6
children 27c43fb015f0
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10:9b98d3d903c6 11:0e2484b6829b
1 <tool id="EMBOSS: pepwheel72" name="pepwheel" version="5.0.0"> 1 <tool id="EMBOSS: pepwheel72" name="pepwheel" version="5.0.0.1">
2 <!-- produces png file --> 2 <!-- produces png file -->
3 <description>Shows protein sequences as helices</description> 3 <description>Shows protein sequences as helices</description>
4 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> 4 <macros>
5 <command interpreter="perl">emboss_single_outputfile_wrapper.pl pepwheel -sequence $input1 -graph png -goutfile $out_file1 -squares $squares -diamonds $diamonds -octags $octags -amphipathic 5 <import>macros.xml</import>
6 </macros>
7 <expand macro="requirements" />
8 <command>perl '$__tool_directory__/emboss_single_outputfile_wrapper.pl' pepwheel -sequence '$input1' -graph png -goutfile '$out_file1' -squares '$squares' -diamonds '$diamonds' -octags '$octags' -amphipathic
6 $amphipathic -steps $steps -turns $turns -wheel $wheel -auto</command> 9 $amphipathic -steps $steps -turns $turns -wheel $wheel -auto</command>
7 <inputs> 10 <inputs>
8 <param format="data" name="input1" type="data"> 11 <param name="input1" type="data" format="data" label="Sequence" />
9 <label>Sequence</label> 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" />
10 </param> 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" />
11 <param name="steps" type="text" value="18"> 14 <param name="squares" type="text" value="ILVM" label="Residues to mark with squares" />
12 <label>Steps, the number of residues plotted per turn is this value divided by the 'turns' value</label> 15 <param name="diamonds" type="text" value="DENQST" label="Residues to mark with diamonds" />
13 </param> 16 <param name="octags" type="text" value="HKR" label="Residues to mark with octagons" />
14 <param name="turns" type="text" value="5"> 17 <param name="wheel" type="select" label="Plot the wheel">
15 <label>Turns, the number of residues plotted per turn is the 'steps' value divided by this value</label>
16 </param>
17 <param name="squares" type="text" value="ILVM">
18 <label>Residues to mark with squares</label>
19 </param>
20 <param name="diamonds" type="text" value="DENQST">
21 <label>Residues to mark with diamonds</label>
22 </param>
23 <param name="octags" type="text" value="HKR">
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> 18 <option value="yes">Yes</option>
29 <option value="no">No</option> 19 <option value="no">No</option>
30 </param> 20 </param>
31 <param name="amphipathic" type="select"> 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" >
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> 22 <option value="no">No</option>
34 <option value="yes">Yes</option> 23 <option value="yes">Yes</option>
35 </param> 24 </param>
36 </inputs> 25 </inputs>
37 <outputs> 26 <outputs>
38 <data format="png" name="out_file1" /> 27 <data name="out_file1" format="png" />
39 </outputs> 28 </outputs>
40 <help> 29 <help>
41 You can view the original documentation here_. 30 You can view the original documentation here_.
42
43 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/pepwheel.html
44 31
45 ------ 32 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/pepwheel.html
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. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
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. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
52 </help> 33 </help>
34 <expand macro="citations" />
53 </tool> 35 </tool>