help/html/features/clarguments.html

   1 #-------------------------------------------------------------------------------
   2 # Jalview - A Sequence Alignment Editor and Viewer (Version 2.5.1)
   3 # Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
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   5 # This file is part of Jalview.
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   9 # as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
  10 #
  11 # Jalview is distributed in the hope that it will be useful, but
  12 # WITHOUT ANY WARRANTY; without even the implied warranty
  13 # of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  14 # PURPOSE.  See the GNU General Public License for more details.
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  20  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
  21  * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  22  *
  23  * This file is part of Jalview.
  24  *
  25  * Jalview is free software: you can redistribute it and/or
  26  * modify it under the terms of the GNU General Public License
  27  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
  28  *
  29  * Jalview is distributed in the hope that it will be useful, but
  30  * WITHOUT ANY WARRANTY; without even the implied warranty
  31  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  32  * PURPOSE.  See the GNU General Public License for more details.
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  35 -->
  36 <title>Jalview Command Line Arguments</title>
  37 <body>
  38 <p><strong>The Jalview Executable's Command Line Arguments</strong></p>
  39 See
  40 <a href="commandline.html">running Jalview from the command line</a>
  41 for more information.
  42 <br>
  43 <table width="100%" border="1" cellspacing="0" cellpadding="0">
  44         <tr>
  45                 <td width="27%">
  46                 <div align="center">-nodisplay</div>
  47                 </td>
  48                 <td width="73%">
  49                 <div align="left">Run Jalview without User Interface.
  50                 (automatically disables questionnaire, version and usage stats checks)</div>
  51                 </td>
  52         </tr>
  53
  54         <tr>
  55                 <td>
  56                 <div align="center">-props FILE</div>
  57                 </td>
  58                 <td>
  59                 <div align="left">Use the given Jalview properties file instead
  60                 of users default.</div>
  61                 </td>
  62         </tr>
  63         <tr>
  64                 <td>
  65                 <div align="center">-features FILE</div>
  66                 </td>
  67                 <td>
  68                 <div align="left">
  69                 <p>Use the given file to add sequence features to an alignment.
  70                 See <a href="featuresFormat.html" target="NEW">Features File</a>
  71                 (Known as Groups file prior to 2.08) description.</p>
  72
  73                 </div>
  74                 </td>
  75         </tr>
  76         <tr>
  77                 <td>
  78                 <div align="center">-colour COLOURSCHEME</div>
  79                 </td>
  80                 <td>Set the colourscheme for the alignment. This can be any of
  81                 the built-in colourschemes, a name of a predefined colourscheme
  82                 (defined in the jalview properties file), or an 'inline' colourscheme
  83                 (see the applet's colour parameter for more information).</td>
  84         </tr>
  85         <tr>
  86                 <td>
  87                 <div align="center">-annotations FILE</div>
  88                 </td>
  89                 <td>Add precalculated annotations to the alignment. See <a
  90                         href="annotationsFormat.html" target="NEW">Annotation File</a>
  91                 description.</td>
  92         </tr>
  93         <tr>
  94                 <td>
  95                 <div align="center">-tree FILE</div>
  96                 <td>
  97                 <div align="left">Load the given newick format tree file onto
  98                 the alignment</div>
  99                 </td>
 100         </tr>
 101         <tr>
 102                 <td>
 103                 <div align="center">-questionnaire URL</div>
 104                 <td>
 105                 <div align="left">Queries the given URL for information about
 106                 any Jalview user questionnaires</div>
 107                 </td>
 108         </tr>
 109         <tr>
 110                 <td>
 111                 <div align="center">-noquestionnaire</div>
 112                 <td>
 113                 <div align="left">Turn off questionnaire check</div>
 114                 </td>
 115         </tr>
 116         <tr>
 117                 <td>
 118                 <div align="center">-nousagestats</div>
 119                 <td>
 120                 <div align="left">Turn off google analytics usage tracking</div>
 121                 </td>
 122         </tr>
 123         <tr>
 124                 <td>
 125                 <div align="center">-[no]sortbytree</div>
 126                 <td>
 127                 <div align="left">Enable or disable automatic sorting of
 128                 associated view when a new tree is displayed</div>
 129                 </td>
 130         </tr>
 131         <tr>
 132                 <td>
 133                 <div align="center">-dasserver nickname=URL</div>
 134                 <td>
 135                 <div align="left">Add and enable a <a href="dassettings.html">DAS
 136                 server</a> with given nickname (alphanumeric or underscores only) for
 137                 retrieval of features for all alignments<br>
 138                 Sources that also support the sequence command may be specified by
 139                 prepending the URL with 'sequence:'<br>
 140                 <em>e.g.</em> sequence:http://localdas.somewhere.org/das/source</div>
 141                 </td>
 142         </tr>
 143         <tr>
 144                 <td>
 145                 <div align="center">-fetchfrom nickname</div>
 146                 <td>
 147                 <div align="left">Query a <a href="dassettings.html">DAS
 148                 source</a> called nickname for features for the alignments and display
 149                 them</div>
 150                 </td>
 151         </tr>
 152         <tr>
 153                 <td>
 154                 <div align="center">-groovy FILE</div>
 155                 <td>
 156                 <div align="left">Execute groovy script in FILE (where FILE may
 157                 be 'STDIN' to read from the standard input) after all other arguments
 158                 have been processed</div>
 159                 </td>
 160         </tr>
 161         <tr>
 162                 <td>
 163                 <div align="center">-vdoc VAMSAS DOCUMENT FILE or URL</div>
 164                 <td>
 165                 <div align="left">Import the given vamsas document into a new
 166                 session.<br>
 167                 <em>New in 2.5</em></div>
 168                 </td>
 169         </tr>
 170         <tr>
 171                 <td>
 172                 <div align="center">-vsess VAMSAS SESSION URL</div>
 173                 <td>
 174                 <div align="left">Join the given vamsas session<br>
 175                 If a document was also specified, this will be imported first and then
 176                 committed as new data from Jalview to the specified session
 177                 (Experimental - not yet enabled!).<em>New in 2.5</em></div>
 178                 </div>
 179                 </td>
 180         </tr>
 181         <tr>
 182                 <td>
 183                 <div align="center">-groovy FILE</div>
 184                 <td>
 185                 <div align="left">Execute groovy script in FILE (where FILE may
 186                 be 'STDIN' to read from the standard input) after all other arguments
 187                 have been processed</div>
 188                 </td>
 189         </tr>
 190         <tr>
 191                 <td>
 192                 <div align="center">-fasta FILE</div>
 193                 </td>
 194
 195                 <td>
 196                 <div align="left">Create alignment file FILE in Fasta format.</div>
 197                 </td>
 198         </tr>
 199         <tr>
 200                 <td>
 201                 <div align="center">-clustal FILE</div>
 202                 </td>
 203                 <td>
 204                 <div align="left">Create alignment file FILE in Clustal format.</div>
 205                 </td>
 206         </tr>
 207         <tr>
 208                 <td>
 209                 <div align="center">-msf FILE</div>
 210                 </td>
 211
 212                 <td>
 213                 <div align="left">Create alignment file FILE in MSF format.</div>
 214                 </td>
 215         </tr>
 216         <tr>
 217                 <td>
 218                 <div align="center">-pileup FILE</div>
 219                 </td>
 220                 <td>
 221                 <div align="left">Create alignment file FILE in Pileup format.</div>
 222                 </td>
 223         </tr>
 224         <tr>
 225                 <td>
 226                 <div align="center">-pir FILE</div>
 227                 </td>
 228
 229                 <td>
 230                 <div align="left">Create alignment file FILE in PIR format.</div>
 231                 </td>
 232         </tr>
 233         <tr>
 234                 <td>
 235                 <div align="center">-pfam FILE</div>
 236                 </td>
 237                 <td>
 238                 <div align="left">Create alignment file FILE in PFAM format.</div>
 239                 </td>
 240         </tr>
 241         <tr>
 242                 <td>
 243                 <div align="center">-blc FILE</div>
 244                 </td>
 245                 <td>
 246                 <div align="left">Create alignment file FILE in BLC format.</div>
 247                 </td>
 248         </tr>
 249         <tr>
 250                 <td>
 251                 <div align="center">-jalview FILE</div>
 252                 </td>
 253
 254                 <td>
 255                 <div align="left">Create alignment file FILE in Jalview format.</div>
 256                 </td>
 257         </tr>
 258         <tr>
 259                 <td>
 260                 <div align="center">-png FILE</div>
 261                 </td>
 262                 <td>
 263                 <div align="left">Create PNG image FILE from alignment.</div>
 264                 </td>
 265         </tr>
 266         <tr>
 267                 <td>
 268                 <div align="center">-imgMap FILE</div>
 269                 </td>
 270
 271                 <td>
 272                 <div align="left">Create HTML file FILE with image map of PNG
 273                 image.</div>
 274                 </td>
 275         </tr>
 276         <tr>
 277                 <td>
 278                 <div align="center">-eps FILE</div>
 279                 </td>
 280                 <td>
 281                 <div align="left">Create EPS file FILE from alignment.</div>
 282                 </td>
 283         </tr>
 284 </table>
 285 </body>
 286 </html>