help/html/features/clarguments.html

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