3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
4 * Copyright (C) $$Year-Rel$$ The Jalview Authors
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
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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">Annotation
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">-nonews</div>
102 Disable check for <a href="../webServices/newsreader.html">Jalview
103 news</a> on startup (not recommended other than for classroom /
110 <div align="center">-nousagestats</div>
112 <div align="left">Turn off google analytics usage tracking</div>
117 <div align="center">-[no]sortbytree</div>
119 <div align="left">Enable or disable automatic sorting of
120 associated view when a new tree is displayed</div>
125 <div align="center">-groovy FILE/URL</div>
127 <div align="left">Execute groovy script in FILE (where
128 FILE may be 'STDIN' to read from the standard input) after all
129 other arguments have been processed</div>
134 <div align="center">-jabaws URL</div>
136 <div align="left">Specify the URL of the preferred JABAWS
142 <div align="center">-vdoc VAMSAS DOCUMENT FILE/URL</div>
145 Import the given vamsas document into a new session.<br>
152 <div align="center">-vsess VAMSAS SESSION URL</div>
155 Join the given vamsas session<br>If a document was also
156 specified, this will be imported first and then committed as
157 new data from Jalview to the specified session (Experimental -
158 not yet enabled!).<em>New in 2.5</em>
165 <div align="center">-fasta FILE</div>
169 <div align="left">Create alignment file FILE in Fasta
174 <td><div align="center">-clustal FILE</div></td>
175 <td><div align="left">Create alignment file FILE in
176 Clustal format.</div></td>
179 <td><div align="center">-msf FILE</div></td>
181 <td><div align="left">Create alignment file FILE in MSF
185 <td><div align="center">-pileup FILE</div></td>
186 <td><div align="left">Create alignment file FILE in
187 Pileup format.</div></td>
190 <td><div align="center">-pir FILE</div></td>
192 <td><div align="left">Create alignment file FILE in PIR
196 <td><div align="center">-pfam FILE</div></td>
197 <td><div align="left">Create alignment file FILE in
198 PFAM format.</div></td>
201 <td><div align="center">-blc FILE</div></td>
202 <td><div align="left">Create alignment file FILE in BLC
206 <td><div align="center">-json FILE</div></td>
207 <td><div align="left">Create alignment file FILE in
208 JSON format.</div></td>
211 <td><div align="center">-jalview FILE</div></td>
213 <td><div align="left">Create alignment file FILE in
214 Jalview format.</div></td>
217 <td><div align="center">-png FILE</div></td>
218 <td><div align="left">Create PNG image FILE from
219 alignment.</div></td>
222 <td><div align="center">-imgMap FILE</div></td>
224 <td><div align="left">Create HTML file FILE with image
225 map of PNG image.</div></td>
228 <td><div align="center">-eps FILE</div></td>
229 <td><div align="left">Create EPS file FILE from
230 alignment.</div></td>
233 <td><div align="center">-svg FILE</div></td>
234 <td><div align="left">Create Scalable Vector Graphics
235 file FILE from alignment.</div></td>
238 <td><div align="center">-biojsMSA FILE</div></td>
239 <td><div align="left">Write an HTML page to display
240 the alignment with the <a href="biojsmsa.html">
241 BioJS MSAviewer MSA</a>