|
0
|
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" size="50" type="text" value="*">
|
|
|
18 <label>Feature source to match</label>
|
|
|
19 </param>
|
|
|
20 <param name="matchtype" size="50" type="text" value="*">
|
|
|
21 <label>Feature type to match</label>
|
|
|
22 </param>
|
|
|
23 <param name="matchtag" size="50" type="text" value="*">
|
|
|
24 <label>Feature tags to match</label>
|
|
|
25 </param>
|
|
|
26 <param name="matchvalue" size="50" 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" size="50" 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" size="50" 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 </help>
|
|
|
123 </tool> |
