help/html/features/clarguments.html

   1 <html>
   2 <title>Jalview Command Line Arguments
   3 </title>
   4 <body>
   5  <p><strong>The Jalview Executable's Command Line
   6  Arguments</strong></p>
   7  See <a href="commandline.html">running Jalview from the command
   8  line</a> for more information.<br>
   9  <table width="100%" border="1" cellspacing="0" cellpadding="0">
  10  <tr >
  11  <td width="27%"><div align="center">-nodisplay</div></td>
  12  <td width="73%"><div align="left">Run Jalview without User Interface.</div></td>
  13  </tr>
  14
  15  <tr>
  16  <td><div align="center">-props FILE</div></td>
  17  <td><div align="left">Use the given Jalview properties file instead
  18  of users default.</div></td>
  19  </tr>
  20  <tr>
  21  <td><div align="center">-features FILE</div></td>
  22  <td><div align="left">
  23  <p>Use the given file to add sequence features to an alignment.
  24  See <a href="featuresFormat.html" target="NEW">Features
  25  File</a> (Known as Groups file prior to 2.08) description. </p>
  26
  27  </div></td>
  28  </tr>
  29         <tr>
  30                 <td>
  31                 <div align="center">-annotations FILE</div>
  32                 </td>
  33                 <td>Add precalculated annotations to the alignment. See <a
  34                         href="annotationsFormat.html" target="NEW">Annotation File</a>
  35                 description.</td>
  36         </tr>
  37         <tr>
  38                 <td>
  39                 <div align="center"></div>
  40                 <td>
  41                 <div align="left"></div>
  42                 </td>
  43         </tr>
  44         <tr>
  45                 <td>
  46                 <div align="center">-nodisplay</div>
  47                 <td>
  48                 <div align="left">Run Jalview without User Interface</div>
  49                 </td>
  50         </tr>
  51         <tr>
  52                 <td>
  53                 <div align="center">-props FILE</div>
  54                 <td>
  55                 <div align="left">Use the given Jalview properties file instead
  56                 of users default</div>
  57                 </td>
  58         </tr>
  59         <tr>
  60                 <td>
  61                 <div align="center">-tree FILE</div>
  62                 <td>
  63                 <div align="left">Load the given newick format tree file onto
  64                 the alignment</div>
  65                 </td>
  66         </tr>
  67         <tr>
  68                 <td>
  69                 <div align="center">-features FILE</div>
  70                 <td>
  71                 <div align="left">Use the given file to mark features on the
  72                 alignment</div>
  73                 </td>
  74         </tr>
  75         <tr>
  76                 <td>
  77                 <div align="center">-questionnaire URL</div>
  78                 <td>
  79                 <div align="left">Queries the given URL for information about
  80                 any Jalview user questionnaires</div>
  81                 </td>
  82         </tr>
  83         <tr>
  84                 <td>
  85                 <div align="center">-noquestionnaire</div>
  86                 <td>
  87                 <div align="left">Turn off questionnaire check</div>
  88                 </td>
  89         </tr>
  90         <tr>
  91                 <td>
  92                 <div align="center">-dasserver nickname=URL</div>
  93                 <td>
  94                 <div align="left">Add and enable a <a href="dassettings.html">DAS server</a> with given
  95                 nickname (alphanumeric or underscores only) for retrieval of features
  96                 for all alignments<br>
  97                 Sources that also support the sequence command may be specified by prepending the URL with 'sequence:'<br>
  98                 <em>e.g.</em> sequence:http://localdas.somewhere.org/das/source</div>
  99                 </td>
 100         </tr>
 101         <tr>
 102                 <td>
 103                 <div align="center">-fetchfrom nickname</div>
 104                 <td>
 105                 <div align="left">Query a <a href="dassettings.html">DAS source</a> called nickname for features for the alignments
 106                 and display them</div>
 107                 </td>
 108         </tr>
 109         <tr>
 110                 <td>
 111                 <div align="center">-groovy FILE</div>
 112                 <td>
 113                 <div align="left">Execute groovy script in FILE (where FILE may be 'STDIN' to read from the standard input) after all other
 114                 arguments have been processed</div>
 115                 </td>
 116         </tr>
 117         <tr>
 118                 <td>
 119                 <div align="center">-fasta FILE</div>
 120                 </td>
 121
 122                 <td>
 123                 <div align="left">Create alignment file FILE in Fasta format.</div>
 124                 </td>
 125         </tr>
 126         <tr>
 127  <td><div align="center">-clustal FILE</div></td>
 128  <td><div align="left">Create alignment file FILE in Clustal format.</div></td>
 129  </tr>
 130  <tr>
 131  <td><div align="center">-msf FILE</div></td>
 132
 133  <td><div align="left">Create alignment file FILE in MSF format.</div></td>
 134  </tr>
 135  <tr>
 136  <td><div align="center">-pileup FILE</div></td>
 137  <td><div align="left">Create alignment file FILE in Pileup format.</div></td>
 138  </tr>
 139  <tr>
 140  <td><div align="center">-pir FILE</div></td>
 141
 142  <td><div align="left">Create alignment file FILE in PIR format.</div></td>
 143  </tr>
 144  <tr>
 145  <td><div align="center">-pfam FILE</div></td>
 146  <td><div align="left">Create alignment file FILE in PFAM format.</div></td>
 147  </tr>
 148  <tr>
 149  <td><div align="center">-blc FILE</div></td>
 150  <td><div align="left">Create alignment file FILE in BLC format.</div></td>
 151  </tr>
 152  <tr>
 153  <td><div align="center">-jalview FILE</div></td>
 154
 155  <td><div align="left">Create alignment file FILE in Jalview format.</div></td>
 156  </tr>
 157  <tr>
 158  <td><div align="center">-png FILE</div></td>
 159  <td><div align="left">Create PNG image FILE from alignment.</div></td>
 160  </tr>
 161  <tr>
 162  <td><div align="center">-imgMap FILE</div></td>
 163
 164  <td><div align="left">Create HTML file FILE with image map of PNG
 165  image.</div></td>
 166  </tr>
 167  <tr>
 168  <td><div align="center">-eps FILE</div></td>
 169  <td><div align="left">Create EPS file FILE from alignment.</div></td>
 170  </tr>
 171  </table>
 172 </body>
 173 </html>