* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
---!>
-<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. (automatically disables questionnaire, version and usage stats checks)</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">-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">-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">-nousagestats</div>
- <td>
- <div align="left">Turn off google analytics usage tracking</div>
- </td>
- </tr>
- <tr><td>
- <div align="center">-[no]sortbytree</div>
- <td>
- <div align="left">Enable or disable automatic sorting of associated view when a new tree is displayed</div>
- </td>
- </tr>
- <tr>
- <td>
- <div align="center">-dasserver nickname=URL</div>
- <td>
- <div align="left">Add and enable a <a href="dassettings.html">DAS server</a> with given
- nickname (alphanumeric or underscores only) for retrieval of features
- for all alignments<br>
- Sources that also support the sequence command may be specified by prepending the URL with 'sequence:'<br>
- <em>e.g.</em> sequence:http://localdas.somewhere.org/das/source</div>
- </td>
- </tr>
- <tr>
- <td>
- <div align="center">-fetchfrom nickname</div>
- <td>
- <div align="left">Query a <a href="dassettings.html">DAS source</a> called 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">-vdoc VAMSAS DOCUMENT FILE or URL</div>
- <td>
- <div align="left">Import the given vamsas document into a new session.<br><em>New in 2.5</em></div>
- </td>
- </tr>
- <tr>
- <td>
- <div align="center">-vsess VAMSAS SESSION URL</div>
- <td>
- <div align="left">Join the given vamsas session<br>If a document was also specified, this will be imported first and then committed as new data from Jalview to the specified session (Experimental - not yet enabled!).<em>New in 2.5</em></div></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>
+-->
git://source.jalview.org / jalview.git / blobdiff