comparison emboss_pepnet.xml @ 11:0e2484b6829b draft

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
comparison
equal deleted inserted replaced
10:9b98d3d903c6 11:0e2484b6829b
1 <tool id="EMBOSS: pepnet70" name="pepnet" version="5.0.0"> 1 <tool id="EMBOSS: pepnet70" name="pepnet" version="5.0.0">
2 <!-- graphical output file with path information --> 2 <!-- graphical output file with path information -->
3 <description>Displays proteins as a helical net</description> 3 <description>Displays proteins as a helical net</description>
4 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> 4 <macros>
5 <command>pepnet -sequence $input1 -graph png -goutfile $out_file1 -squares $squares -diamonds $diamonds -octags $octags -amphipathic $amphipathic -auto</command> 5 <import>macros.xml</import>
6 </macros>
7 <expand macro="requirements" />
8 <command>pepnet -sequence '$input1' -graph png -goutfile '$out_file1' -squares '$squares' -diamonds '$diamonds' -octags '$octags' -amphipathic $amphipathic -auto</command>
6 <inputs> 9 <inputs>
7 <param format="data" name="input1" type="data"> 10 <param name="input1" type="data" format="data" label="Sequence" />
8 <label>Sequence</label> 11 <param name="squares" type="text" value="ILVM" label="Residues to mark with squares" />
9 </param> 12 <param name="diamonds" type="text" value="DENQST" label="Residues to mark with diamonds" />
10 <param name="squares" type="text" value="ILVM"> 13 <param name="octags" type="text" value="HKR" label="Residues to mark with octagons" />
11 <label>Residues to mark with squares</label> 14 <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">
12 </param>
13 <param name="diamonds" type="text" value="DENQST">
14 <label>Residues to mark with diamonds</label>
15 </param>
16 <param name="octags" type="text" value="HKR ">
17 <label>Residues to mark with octagons</label>
18 </param>
19 <param name="amphipathic" type="select">
20 <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>
21 <option value="no">No</option> 15 <option value="no">No</option>
22 <option value="yes">Yes</option> 16 <option value="yes">Yes</option>
23 </param> 17 </param>
24 </inputs> 18 </inputs>
25 <outputs> 19 <outputs>
26 <data format="png" name="out_file1" /> 20 <data name="out_file1" format="png" />
27 </outputs> 21 </outputs>
28 <help> 22 <help>
29 You can view the original documentation here_. 23 You can view the original documentation here_.
30
31 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/pepnet.html
32 24
33 ------ 25 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/pepnet.html
34
35 **Citation**
36
37 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;`_
38
39 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;`_
40 </help> 26 </help>
27 <expand macro="citations" />
41 </tool> 28 </tool>