root/galaxy-central/tools/emboss_5/emboss_prettyplot.xml @ 3

リビジョン 2, 5.2 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central

行番号 
1<tool id="EMBOSS: prettyplot79" name="prettyplot" version="5.0.0">
2  <!-- produces png output with file name -->
3  <description>Displays aligned sequences, with colouring and boxing</description>
4  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
5  <command>prettyplot -sequences $input1 -graph png -goutfile $out_file1 -residuesperline $residuesperline -resbreak $resbreak -ccolours $ccolours -cidentity $cidentity -csimilarity $csimilarity
6  -cother $cother -docolour $docolour -gtitle $title -pair $pair -identity $identity -box $box -boxcol $boxcol -boxcolval $boxcolval -name $name -maxnamelen $maxnamelen -number $number -listoptions
7  $listoptions -consensus $consensus -collision $collision -alternative $alternative -showscore $showscore -portrait $portrait -auto</command>
8  <inputs>
9    <param format="data" name="input1" type="data">
10      <label>Sequence</label>
11    </param>
12    <param name="residuesperline" size="10" type="text" value="50">
13      <label>The number of residues to be displayed on each line</label>
14    </param>
15    <param name="resbreak" size="10" type="text" value="50">
16      <label>Residues before a space</label>
17    </param>
18    <param name="ccolours" type="select">
19      <label>Colour residues by their consensus value</label>
20      <option value="yes">Yes</option>
21      <option value="no">No</option>
22    </param>
23    <param name="cidentity" size="10" type="text" value="RED">
24      <label>Colour to display identical residues</label>
25    </param>
26    <param name="csimilarity" size="10" type="text" value="GREEN">
27      <label>Colour to display similar residues</label>
28    </param>
29    <param name="cother" size="10" type="text" value="BLACK">
30      <label>Colour to display other residues</label>
31    </param>
32    <param name="docolour" type="select">
33      <label>Colour residues by table oily, amide etc.</label>
34      <option value="no">No</option>
35      <option value="yes">Yes</option>
36    </param>
37    <param name="title" type="select">
38      <label>Display the title</label>
39      <option value="yes">Yes</option>
40      <option value="no">No</option>
41    </param>
42    <param name="pair" size="10" type="text" value="1.5,1.0,0.5">
43      <label>Values to represent identical similar related</label>
44    </param>
45    <param name="identity" size="10" type="text" value="0">
46      <label>Only match those which are identical in all sequences</label>
47    </param>
48    <param name="box" type="select">
49      <label>Display prettyboxes</label>
50      <option value="yes">Yes</option>
51      <option value="no">No</option>
52    </param>
53    <param name="boxcol" type="select">
54      <label>Colour the background in the boxes</label>
55      <option value="no">No</option>
56      <option value="yes">Yes</option>
57    </param>
58    <param name="boxcolval" size="10" type="text" value="GREY">
59      <label>Colour to be used for background</label>
60    </param>
61    <param name="name" type="select">
62      <label>Display the sequence names</label>
63      <option value="yes">Yes</option>
64      <option value="no">No</option>
65    </param>
66    <param name="maxnamelen" size="10" type="text" value="10">
67      <label>Margin size for the sequence name</label>
68    </param>
69    <param name="number" type="select">
70      <label>Display the residue number</label>
71      <option value="yes">Yes</option>
72      <option value="no">No</option>
73    </param>
74    <param name="listoptions" type="select">
75      <label>Display the date and options used</label>
76      <option value="yes">Yes</option>
77      <option value="no">No</option>
78    </param>
79    <param name="consensus" type="select">
80      <label>Display the consensus</label>
81      <option value="no">No</option>
82      <option value="yes">Yes</option>
83    </param>
84    <param name="collision" type="select">
85      <label>Allow collisions in calculating consensus</label>
86      <option value="yes">Yes</option>
87      <option value="no">No</option>
88    </param>
89    <param name="alternative" type="select">
90      <label>Use alternative collisions routine</label>
91      <option value="0">Normal collision check</option>
92      <option value="1">Checks identical scores with the max score found. So if any other residue matches the identical score then a collision has occurred</option>
93      <option value="2">If another residue has a greater than or equal to matching score and these do not match then a collision has occurred</option>
94      <option value="3">Checks all those not in the current consensus.If any of these give a top score for matching or identical scores then a collision has occured</option>
95    </param>
96    <param name="showscore" size="10" type="text" value="-1">
97      <label>Print residue scores</label>
98    </param>
99    <param name="portrait" type="select">
100      <label>Set page to Portrait</label>
101      <option value="no">No</option>
102      <option value="yes">Yes</option>
103    </param>
104  </inputs>
105  <outputs>
106    <data format="png" name="out_file1" />
107  </outputs>
108  <help>
109    You can view the original documentation here_.
110   
111    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/prettyplot.html
112  </help>
113</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。