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annotate emboss_5/emboss_epestfind.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: epestfind29" name="epestfind" version="5.0.0"> |
2 <description>Finds PEST motifs as potential proteolytic cleavage sites</description> | |
3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> | |
4 <command interpreter="perl">emboss_single_outputfile_wrapper.pl epestfind -sequence $input1 -goutfile $ofile2 -outfile $ofile1 -window $window -order $order -potential $potential -poor $poor | |
5 -invalid $invalid -map $map -graph png -auto</command> | |
6 <inputs> | |
7 <param format="data" name="input1" type="data"> | |
8 <label>Sequence</label> | |
9 </param> | |
8
b810c96613ee
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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10 <param name="window" type="text" value="10"> |
0 | 11 <label>Minimal distance between positively charged amino acids</label> |
12 </param> | |
13 <param name="order" type="select"> | |
14 <label>Sort by</label> | |
15 <option value="3">Score</option> | |
16 <option value="1">Length</option> | |
17 <option value="2">Position</option> | |
18 </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
|
19 <param name="threshold" type="text" value="5.0"> |
0 | 20 <label>Threshold value to discriminate weak from potential PEST motifs.</label> |
21 </param> | |
22 <param name="potential" type="select"> | |
23 <label>Decide whether potential PEST motifs should be printed</label> | |
24 <option value="yes">Yes</option> | |
25 <option value="no">No</option> | |
26 </param> | |
27 <param name="poor" type="select"> | |
28 <label>Decide whether poor PEST motifs should be printed</label> | |
29 <option value="yes">Yes</option> | |
30 <option value="no">No</option> | |
31 </param> | |
32 <param name="invalid" type="select"> | |
33 <label>Decide whether invalid PEST motifs should be printed</label> | |
34 <option value="no">No</option> | |
35 <option value="yes">Yes</option> | |
36 </param> | |
37 <param name="map" type="select"> | |
38 <label>Decide whether PEST motifs should be mapped to sequence</label> | |
39 <option value="yes">Yes</option> | |
40 <option value="no">No</option> | |
41 </param> | |
42 </inputs> | |
43 <outputs> | |
44 <data format="png" name="ofile2" /> | |
45 <data format="epestfind" name="ofile1" /> | |
46 </outputs> | |
47 <!-- <tests> | |
48 <test> | |
49 <param name="input1" value="2.fasta"/> | |
50 <param name="window" value="10"/> | |
51 <param name="order" value="3"/> | |
52 <param name="threshold" value="5.0"/> | |
53 <param name="potential" value="yes"/> | |
54 <param name="poor" value="yes"/> | |
55 <param name="invalid" value="no"/> | |
56 <param name="map" value="yes"/> | |
57 <output name="ofile1" file="emboss_epestfind_out.epestfind"/> | |
58 </test> | |
59 </tests> output file contains file location info --> | |
60 <help> | |
61 You can view the original documentation here_. | |
62 | |
63 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/epestfind.html | |
64 | |
65 ------ | |
66 | |
67 **Citation** | |
68 | |
69 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>`_ | |
70 | |
71 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>`_ | |
72 </help> | |
73 </tool> |