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

リビジョン 2, 4.8 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central

行番号 
1<tool id="EMBOSS: lindna48" name="lindna" version="5.0.0">
2  <!-- tool produces memory error in ajmem.c -->
3  <description>Draws linear maps of DNA constructs</description>
4  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
5  <command>lindna -infile $input1 -graphout png -goutfile $out_file1 -ruler $ruler -blocktype $blocktype -maxgroups $maxgroups -maxlabels $maxlabels -intersymbol $intersymbol -intercolour $intercolour
6  -interticks $interticks -gapsize $gapsize -ticklines $ticklines -textheight $textheight -textlength $textlength -margin $margin -tickheight $tickheight -blockheight $blockheight -rangeheight
7  $rangeheight -gapgroup $gapgroup -postext $postext -auto</command>
8  <inputs>
9    <param format="data" name="input1" type="data">
10      <label>Sequences</label>
11    </param>
12    <param name="ruler" type="select">
13      <label>Draw a ruler</label>
14      <option value="yes">Yes</option>
15      <option value="no">No</option>
16    </param>
17    <param name="blocktype" type="select">
18      <label>Type of blocks</label>
19      <option value="Filled">Filled blocks</option>
20      <option value="Open">Open blocks</option>
21      <option value="Outline">Black border</option>
22    </param>
23    <param name="maxgroups" size="4" type="text" value="20">
24      <label>Maximum number of groups</label>
25    </param>
26    <param name="maxlabels" size="6" type="text" value="10000">
27      <label>Maximum number of labels</label>
28    </param>
29    <param name="intersymbol" type="select">
30      <label>Type of blocks</label>
31      <option value="Straight">Straight</option>
32    </param>
33    <param name="intercolour" type="select">
34      <label>Colour of junctions between blocks</label>
35      <option value="1">Red</option>
36      <option value="0">Black</option>
37      <option value="2">Yellow</option>
38      <option value="3">Green</option>
39      <option value="4">Aquamarine</option>
40      <option value="5">Pink</option>
41      <option value="6">Wheat</option>
42      <option value="7">Grey</option>
43      <option value="8">Brown</option>
44      <option value="9">Blue</option>
45      <option value="10">Blue-violet</option>
46      <option value="11">Cyan</option>
47      <option value="12">Turquoise</option>
48      <option value="13">Magenta</option>
49      <option value="14">Salmon</option>
50      <option value="15">White</option>
51    </param>
52    <param name="interticks" type="select">
53      <label>Horizontal junctions between ticks</label>
54      <option value="no">No</option>
55      <option value="yes">Yes</option>
56    </param>
57    <param name="gapsize" size="6" type="text" value="500">
58      <label>Interval between ticks in the ruler</label>
59    </param>
60    <param name="ticklines" type="select">
61      <label>Vertical lines at the ruler's ticks</label>
62      <option value="no">No</option>
63      <option value="yes">Yes</option>
64    </param>
65    <param name="textheight" size="4" type="text" value="1.0">
66      <label>Height of text. Enter a number &lt;1.0 or &gt;1.0 to decrease or increase the size, respectively</label>
67    </param>
68    <param name="textlength" size="4" type="text" value="1.0">
69      <label>Length of text. Enter a number &lt;1.0 or &gt;1.0 to decrease or increase the size, respectively</label>
70    </param>
71    <param name="margin" size="4" type="text" value="1.0">
72      <label>Width of left margin. This is the region left to the groups where the names of the groups are displayed. Enter a number &lt;1.0 or &gt;1.0 to decrease or increase the size,
73      respectively</label>
74    </param>
75    <param name="tickheight" size="4" type="text" value="1.0">
76      <label>Height of ticks. Enter a number &lt;1.0 or &gt;1.0 to decrease or increase the size, respectively</label>
77    </param>
78    <param name="blockheight" size="4" type="text" value="1.0">
79      <label>Height of blocks. Enter a number &lt;1.0 or &gt;1.0 to decrease or increase the size, respectively</label>
80    </param>
81    <param name="rangeheight" size="4" type="text" value="1.0">
82      <label>Height of range ends. Enter a number &lt;1.0 or &gt;1.0 to decrease or increase the size, respectively</label>
83    </param>
84    <param name="gapgroup" size="4" type="text" value="1.0">
85      <label>Space between groups. Enter a number &lt;1.0 or &gt;1.0 to decrease or increase the size, respectively</label>
86    </param>
87    <param name="postext" size="4" type="text" value="1.0">
88      <label>Space between text and ticks, blocks, and ranges. Enter a number &lt;1.0 or &gt;1.0 to decrease or increase the size, respectively</label>
89    </param>
90  </inputs>
91  <outputs>
92    <data format="png" name="out_file1" />
93  </outputs>
94  <help>
95    You can view the original documentation here_.
96   
97    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/lindna.html
98  </help>
99</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。