root/galaxy-central/tools/emboss_5/emboss_showfeat.xml

リビジョン 2, 5.0 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central

行番号 
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>
Note: リポジトリブラウザについてのヘルプは TracBrowser を参照してください。