3 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
4 * Copyright (C) 2015 The Jalview Authors
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3
11 * of the License, or (at your option) any later version.
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14 * WITHOUT ANY WARRANTY; without even the implied warranty
15 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
16 * PURPOSE. See the GNU General Public License for more details.
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19 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 * The Jalview Authors are detailed in the 'AUTHORS' file.
22 <title>Jalview Command Line Arguments</title>
25 <strong>The Jalview Executable's Command Line Arguments</strong>
28 <a href="commandline.html">running Jalview from the command line</a>
31 <table width="100%" border="1" cellspacing="0" cellpadding="0">
33 <td width="27%"><div align="center">-nodisplay</div></td>
34 <td width="73%"><div align="left">Run Jalview without
35 User Interface. (automatically disables questionnaire, version
36 and usage stats checks)</div></td>
40 <td><div align="center">-props FILE/URL</div></td>
41 <td><div align="left">Use the given Jalview properties
42 file instead of users default.</div></td>
45 <td><div align="center">-features FILE/URL</div></td>
46 <td><div align="left">
48 Use the given file to add sequence features to an alignment.
49 See <a href="featuresFormat.html" target="NEW">Features
50 File</a> (Known as Groups file prior to 2.08) description.
57 <div align="center">-colour COLOURSCHEME</div>
59 <td>Set the colourscheme for the alignment. This can be any
60 of the built-in colourschemes, a name of a predefined
61 colourscheme (defined in the Jalview properties file), or an
62 'inline' colourscheme (see the applet's colour parameter for
63 more information).</td>
67 <div align="center">-annotations FILE/URL</div>
69 <td>Add precalculated annotations to the alignment. See <a
70 href="annotationsFormat.html" target="NEW"
71 >Annotation File</a> description.
76 <div align="center">-tree FILE/URL</div>
78 <div align="left">Load the given newick format tree file
79 onto the alignment</div>
84 <div align="center">-questionnaire URL</div>
86 <div align="left">Queries the given URL for information
87 about any Jalview user questionnaires</div>
92 <div align="center">-noquestionnaire</div>
94 <div align="left">Turn off questionnaire check</div>
99 <div align="center">-nousagestats</div>
101 <div align="left">Turn off google analytics usage tracking</div>
106 <div align="center">-[no]sortbytree</div>
108 <div align="left">Enable or disable automatic sorting of
109 associated view when a new tree is displayed</div>
114 <div align="center">-dasserver nickname=URL</div>
117 Add and enable a <a href="dassettings.html">DAS server</a>
118 with given nickname (alphanumeric or underscores only) for
119 retrieval of features for all alignments<br> Sources that
120 also support the sequence command may be specified by
121 prepending the URL with 'sequence:'<br> <em>e.g.</em>
122 sequence:http://localdas.somewhere.org/das/source
128 <div align="center">-fetchfrom nickname</div>
131 Query a <a href="dassettings.html">DAS source</a> called
132 nickname for features for the alignments and display them
138 <div align="center">-groovy FILE/URL</div>
140 <div align="left">Execute groovy script in FILE (where
141 FILE may be 'STDIN' to read from the standard input) after all
142 other arguments have been processed</div>
147 <div align="center">-jabaws URL</div>
149 <div align="left">Specify the URL of the preferred JABAWS
155 <div align="center">-vdoc VAMSAS DOCUMENT FILE/URL</div>
158 Import the given vamsas document into a new session.<br>
165 <div align="center">-vsess VAMSAS SESSION URL</div>
168 Join the given vamsas session<br>If a document was also
169 specified, this will be imported first and then committed as
170 new data from Jalview to the specified session (Experimental -
171 not yet enabled!).<em>New in 2.5</em>
178 <div align="center">-fasta FILE</div>
182 <div align="left">Create alignment file FILE in Fasta
187 <td><div align="center">-clustal FILE</div></td>
188 <td><div align="left">Create alignment file FILE in
189 Clustal format.</div></td>
192 <td><div align="center">-msf FILE</div></td>
194 <td><div align="left">Create alignment file FILE in MSF
198 <td><div align="center">-pileup FILE</div></td>
199 <td><div align="left">Create alignment file FILE in
200 Pileup format.</div></td>
203 <td><div align="center">-pir FILE</div></td>
205 <td><div align="left">Create alignment file FILE in PIR
209 <td><div align="center">-pfam FILE</div></td>
210 <td><div align="left">Create alignment file FILE in
211 PFAM format.</div></td>
214 <td><div align="center">-blc FILE</div></td>
215 <td><div align="left">Create alignment file FILE in BLC
219 <td><div align="center">-json FILE</div></td>
220 <td><div align="left">Create alignment file FILE in
221 JSON format.</div></td>
224 <td><div align="center">-jalview FILE</div></td>
226 <td><div align="left">Create alignment file FILE in
227 Jalview format.</div></td>
230 <td><div align="center">-png FILE</div></td>
231 <td><div align="left">Create PNG image FILE from
232 alignment.</div></td>
235 <td><div align="center">-imgMap FILE</div></td>
237 <td><div align="left">Create HTML file FILE with image
238 map of PNG image.</div></td>
241 <td><div align="center">-eps FILE</div></td>
242 <td><div align="left">Create EPS file FILE from
243 alignment.</div></td>
246 <td><div align="center">-svg FILE</div></td>
247 <td><div align="left">Create Scalable Vector Graphics
248 file FILE from alignment.</div></td>