Mercurial > repos > devteam > emboss_5
comparison emboss_showfeat.xml @ 10:9b98d3d903c6 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba
author | devteam |
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date | Fri, 12 Aug 2016 19:17:10 -0400 |
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children | 0e2484b6829b |
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9:18a63c800a4d | 10:9b98d3d903c6 |
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1 <tool id="EMBOSS: showfeat85" name="showfeat" version="5.0.0"> | |
2 <!-- tool gives memory errors --> | |
3 <description>Show features of a sequence</description> | |
4 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> | |
5 <command>showfeat -sequence $input1 -outfile $out_file1 -matchsource "$matchsource" -matchtype "$matchtype" -matchtag "$matchtag" -matchvalue "$matchvalue" -sort $sort -annotation "$annotation" -id | |
6 $id -description "$description" -scale "$scale" -width "$width" -collapse $collapse -forward $forward -reverse $reverse -unknown $unknown -strand $strand -source $source -position $position -type | |
7 $type -tags $tags -values $values -stricttags $stricttags -html $html_out1 -auto</command> | |
8 <inputs> | |
9 <param format="data" name="input1" type="data"> | |
10 <label>Sequences</label> | |
11 </param> | |
12 <param name="html_out1" type="select"> | |
13 <label>Format output as an HTML table</label> | |
14 <option value="no">No</option> | |
15 <option value="yes">Yes</option> | |
16 </param> | |
17 <param name="matchsource" type="text" value="*"> | |
18 <label>Feature source to match</label> | |
19 </param> | |
20 <param name="matchtype" type="text" value="*"> | |
21 <label>Feature type to match</label> | |
22 </param> | |
23 <param name="matchtag" type="text" value="*"> | |
24 <label>Feature tags to match</label> | |
25 </param> | |
26 <param name="matchvalue" type="text" value="*"> | |
27 <label>Tag values to match</label> | |
28 </param> | |
29 <param name="sort" type="select"> | |
30 <label>Sort by</label> | |
31 <option value="start">Start position</option> | |
32 <option value="source">Source</option> | |
33 <option value="type">Type</option> | |
34 <option value="nosort">No sorting done</option> | |
35 <option value="join">Join coding regions together</option> | |
36 </param> | |
37 <param name="annotation" type="text" value=""> | |
38 <label>Regions to annotate by marking</label> | |
39 </param> | |
40 <param name="id" type="select"> | |
41 <label>Display the ID name of the sequence</label> | |
42 <option value="yes">Yes</option> | |
43 <option value="no">No</option> | |
44 </param> | |
45 <param name="description" type="select"> | |
46 <label>Display the description of the sequence</label> | |
47 <option value="yes">Yes</option> | |
48 <option value="no">No</option> | |
49 </param> | |
50 <param name="scale" type="select"> | |
51 <label>Display the scale line</label> | |
52 <option value="yes">Yes</option> | |
53 <option value="no">No</option> | |
54 </param> | |
55 <param name="width" type="text" value="60"> | |
56 <label>Screen width</label> | |
57 </param> | |
58 <param name="collapse" type="select"> | |
59 <label>Collapse features</label> | |
60 <option value="no">No</option> | |
61 <option value="yes">Yes</option> | |
62 </param> | |
63 <param name="forward" type="select"> | |
64 <label>Display forward sense features</label> | |
65 <option value="yes">Yes</option> | |
66 <option value="no">No</option> | |
67 </param> | |
68 <param name="reverse" type="select"> | |
69 <label>Display reverse sense features</label> | |
70 <option value="yes">Yes</option> | |
71 <option value="no">No</option> | |
72 </param> | |
73 <param name="unknown" type="select"> | |
74 <label>Display unknown sense features</label> | |
75 <option value="yes">Yes</option> | |
76 <option value="no">No</option> | |
77 </param> | |
78 <param name="strand" type="select"> | |
79 <label>Display the strand of the features</label> | |
80 <option value="no">No</option> | |
81 <option value="yes">Yes</option> | |
82 </param> | |
83 <param name="source" type="select"> | |
84 <label>Display the source of the features</label> | |
85 <option value="no">No</option> | |
86 <option value="yes">Yes</option> | |
87 </param> | |
88 <param name="position" type="select"> | |
89 <label>SDisplay the start and end position of the features</label> | |
90 <option value="no">No</option> | |
91 <option value="yes">Yes</option> | |
92 </param> | |
93 <param name="type" type="select"> | |
94 <label>Display the type of the features</label> | |
95 <option value="yes">Yes</option> | |
96 <option value="no">No</option> | |
97 </param> | |
98 <param name="tags" type="select"> | |
99 <label>Display the tags and values of the features</label> | |
100 <option value="no">No</option> | |
101 <option value="yes">Yes</option> | |
102 </param> | |
103 <param name="values" type="select"> | |
104 <label>Display the tag values of the features</label> | |
105 <option value="yes">Yes</option> | |
106 <option value="no">No</option> | |
107 </param> | |
108 <param name="stricttags" type="select"> | |
109 <label>Display only those tag/value pairs in a feature that match the specified tag and value</label> | |
110 <option value="no">No</option> | |
111 <option value="yes">Yes</option> | |
112 </param> | |
113 </inputs> | |
114 <outputs> | |
115 <data format="showfeat" name="out_file1" /> | |
116 </outputs> | |
117 <code file="emboss_format_corrector.py" /> | |
118 <help> | |
119 You can view the original documentation here_. | |
120 | |
121 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/showfeat.html | |
122 | |
123 ------ | |
124 | |
125 **Citation** | |
126 | |
127 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>`_ | |
128 | |
129 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>`_ | |
130 </help> | |
131 </tool> |