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Merge branch 'releases/Release_2_11_3_Branch'
[jalview.git] / help / html / features / clarguments.html
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-<html>
-<title>Jalview Command Line Arguments
-</title>
-<body>
- <p><strong>The Jalview Executable's Command Line
- Arguments</strong></p>
- See <a href="commandline.html">running Jalview from the command
- line</a> for more information.<br>
- <table width="100%" border="1" cellspacing="0" cellpadding="0">
- <tr > 
- <td width="27%"><div align="center">-nodisplay</div></td>
- <td width="73%"><div align="left">Run Jalview without User Interface.</div></td>
- </tr>
-
- <tr> 
- <td><div align="center">-props FILE</div></td>
- <td><div align="left">Use the given Jalview properties file instead 
- of users default.</div></td>
- </tr>
- <tr> 
- <td><div align="center">-features FILE</div></td>
- <td><div align="left"> 
- <p>Use the given file to add sequence features to an alignment. 
- See <a href="featuresFormat.html" target="NEW">Features 
- File</a> (Known as Groups file prior to 2.08) description. </p>
-
- </div></td>
- </tr>
-       <tr>
-               <td>
-               <div align="center">-annotations FILE</div>
-               </td>
-               <td>Add precalculated annotations to the alignment. See <a
-                       href="annotationsFormat.html" target="NEW">Annotation File</a>
-               description.</td>
-       </tr>
-       <tr>
-               <td>
-               <div align="center"></div>
-               <td>
-               <div align="left"></div>
-               </td>
-       </tr>
-       <tr>
-               <td>
-               <div align="center">-nodisplay</div>
-               <td>
-               <div align="left">Run Jalview without User Interface</div>
-               </td>
-       </tr>
-       <tr>
-               <td>
-               <div align="center">-props FILE</div>
-               <td>
-               <div align="left">Use the given Jalview properties file instead
-               of users default</div>
-               </td>
-       </tr>
-       <tr>
-               <td>
-               <div align="center">-tree FILE</div>
-               <td>
-               <div align="left">Load the given newick format tree file onto
-               the alignment</div>
-               </td>
-       </tr>
-       <tr>
-               <td>
-               <div align="center">-features FILE</div>
-               <td>
-               <div align="left">Use the given file to mark features on the
-               alignment</div>
-               </td>
-       </tr>
-       <tr>
-               <td>
-               <div align="center">-questionnaire URL</div>
-               <td>
-               <div align="left">Queries the given URL for information about
-               any Jalview user questionnaires</div>
-               </td>
-       </tr>
-       <tr>
-               <td>
-               <div align="center">-noquestionnaire</div>
-               <td>
-               <div align="left">Turn off questionnaire check</div>
-               </td>
-       </tr>
-       <tr>
-               <td>
-               <div align="center">-dasserver nickname=URL</div>
-               <td>
-               <div align="left">Add and enable a das server with given
-               nickname (alphanumeric or underscores only) for retrieval of features
-               for all alignments</div>
-               </td>
-       </tr>
-       <tr>
-               <td>
-               <div align="center">-fetchfrom nickname</div>
-               <td>
-               <div align="left">Query nickname for features for the alignments
-               and display them</div>
-               </td>
-       </tr>
-       <tr>
-               <td>
-               <div align="center">-groovy FILE</div>
-               <td>
-               <div align="left">Execute groovy script in FILE (where FILE may be 'STDIN' to read from the standard input) after all other
-               arguments have been processed</div>
-               </td>
-       </tr>
-       <tr>
-               <td>
-               <div align="center">-fasta FILE</div>
-               </td>
-
-               <td>
-               <div align="left">Create alignment file FILE in Fasta format.</div>
-               </td>
-       </tr>
-       <tr> 
- <td><div align="center">-clustal FILE</div></td>
- <td><div align="left">Create alignment file FILE in Clustal format.</div></td>
- </tr>
- <tr> 
- <td><div align="center">-msf FILE</div></td>
-
- <td><div align="left">Create alignment file FILE in MSF format.</div></td>
- </tr>
- <tr> 
- <td><div align="center">-pileup FILE</div></td>
- <td><div align="left">Create alignment file FILE in Pileup format.</div></td>
- </tr>
- <tr> 
- <td><div align="center">-pir FILE</div></td>
-
- <td><div align="left">Create alignment file FILE in PIR format.</div></td>
- </tr>
- <tr> 
- <td><div align="center">-pfam FILE</div></td>
- <td><div align="left">Create alignment file FILE in PFAM format.</div></td>
- </tr>
- <tr> 
- <td><div align="center">-blc FILE</div></td>
- <td><div align="left">Create alignment file FILE in BLC format.</div></td>
- </tr>
- <tr> 
- <td><div align="center">-jalview FILE</div></td>
-
- <td><div align="left">Create alignment file FILE in Jalview format.</div></td>
- </tr>
- <tr> 
- <td><div align="center">-png FILE</div></td>
- <td><div align="left">Create PNG image FILE from alignment.</div></td>
- </tr>
- <tr> 
- <td><div align="center">-imgMap FILE</div></td>
-
- <td><div align="left">Create HTML file FILE with image map of PNG 
- image.</div></td>
- </tr>
- <tr> 
- <td><div align="center">-eps FILE</div></td>
- <td><div align="left">Create EPS file FILE from alignment.</div></td>
- </tr>
- </table>
-</body>
-</html>