groovy and das fetching stuff in command line argument list

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

diff --git a/help/html/features/clarguments.html b/help/html/features/clarguments.html
index 45dfab5..10917b4 100644 (file)
--- a/help/html/features/clarguments.html
+++ b/help/html/features/clarguments.html
@@ -26,17 +26,102 @@
 
  </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">-fasta FILE</div></td>
+       <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, 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="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>
@@ -55,6 +140,10 @@
  <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>