vamsas 0.2 client capabilities

[jalview.git] / help / html / features / clarguments.html

diff --git a/help/html/features/clarguments.html b/help/html/features/clarguments.html
index 10917b4..e571b12 100644 (file)
--- a/help/html/features/clarguments.html
+++ b/help/html/features/clarguments.html
@@ -9,7 +9,7 @@
  <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>
+ <td width="73%"><div align="left">Run Jalview without User Interface. (automatically disables questionnaire, version and usage stats checks)</div></td>
  </tr>
 
  <tr> 
@@ -36,79 +36,85 @@
        </tr>
        <tr>
                <td>
-               <div align="center"></div>
+               <div align="center">-tree FILE</div>
                <td>
-               <div align="left"></div>
+               <div align="left">Load the given newick format tree file onto
+               the alignment</div>
                </td>
        </tr>
        <tr>
                <td>
-               <div align="center">-nodisplay</div>
+               <div align="center">-questionnaire URL</div>
                <td>
-               <div align="left">Run Jalview without User Interface</div>
+               <div align="left">Queries the given URL for information about
+               any Jalview user questionnaires</div>
                </td>
        </tr>
        <tr>
                <td>
-               <div align="center">-props FILE</div>
+               <div align="center">-noquestionnaire</div>
                <td>
-               <div align="left">Use the given Jalview properties file instead
-               of users default</div>
+               <div align="left">Turn off questionnaire check</div>
                </td>
        </tr>
-       <tr>
+       <tr><td>
+               <div align="center">-nousagestats</div>
                <td>
-               <div align="center">-tree FILE</div>
+               <div align="left">Turn off google analytics usage tracking</div>
+               </td>
+       </tr>
+       <tr><td>
+       <div align="center">-[no]sortbytree</div>
                <td>
-               <div align="left">Load the given newick format tree file onto
-               the alignment</div>
+               <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">-features FILE</div>
+               <div align="center">-dasserver nickname=URL</div>
                <td>
-               <div align="left">Use the given file to mark features on the
-               alignment</div>
+               <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">-questionnaire URL</div>
+               <div align="center">-fetchfrom nickname</div>
                <td>
-               <div align="left">Queries the given URL for information about
-               any Jalview user questionnaires</div>
+               <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">-noquestionnaire</div>
+               <div align="center">-groovy FILE</div>
                <td>
-               <div align="left">Turn off questionnaire check</div>
+               <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="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>
+               <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">-fetchfrom nickname</div>
+               <div align="center">-vsess VAMSAS SESSION URL</div>
                <td>
-               <div align="left">Query nickname for features for the alignments
-               and display them</div>
+               <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, after all other
+               <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>