X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fclarguments.html;h=8d6a4d893e2ed87043a8b9831e53b5303a6e98c0;hb=86e85aa5eaf27310d84ad693fe38adcdf8a87ca9;hp=45dfab51ece7082389bdb766649bcc93b8705456;hpb=713c09ec2d6f35d74ba2c6ed114bb3a29f3f5cf5;p=jalview.git
diff --git a/help/html/features/clarguments.html b/help/html/features/clarguments.html
index 45dfab5..8d6a4d8 100644
--- a/help/html/features/clarguments.html
+++ b/help/html/features/clarguments.html
@@ -26,17 +26,102 @@
-
- -annotations FILE |
- Add precalculated annotations to the alignment. See Annotation
- File description. |
-
-
- -fasta FILE |
+
+
+ -annotations FILE
+ |
+ Add precalculated annotations to the alignment. See Annotation File
+ description. |
+
+
+
+
+ |
+
+ |
+
+
+
+ -nodisplay
+ |
+ Run Jalview without User Interface
+ |
+
+
+
+ -props FILE
+ |
+ Use the given Jalview properties file instead
+ of users default
+ |
+
+
+
+ -tree FILE
+ |
+ Load the given newick format tree file onto
+ the alignment
+ |
+
+
+
+ -features FILE
+ |
+ Use the given file to mark features on the
+ alignment
+ |
+
+
+
+ -questionnaire URL
+ |
+ Queries the given URL for information about
+ any Jalview user questionnaires
+ |
+
+
+
+ -noquestionnaire
+ |
+ Turn off questionnaire check
+ |
+
+
+
+ -dasserver nickname=URL
+ |
+ Add and enable a das server with given
+ nickname (alphanumeric or underscores only) for retrieval of features
+ for all alignments
+ |
+
+
+
+ -fetchfrom nickname
+ |
+ Query nickname for features for the alignments
+ and display them
+ |
+
+
+
+ -groovy FILE
+ |
+ Execute groovy script in FILE (where FILE may be 'STDIN' to read from the standard input) after all other
+ arguments have been processed
+ |
+
+
+
+ -fasta FILE
+ |
- Create alignment file FILE in Fasta format. |
-
-
+
+ Create alignment file FILE in Fasta format.
+ |
+
+
-clustal FILE |
Create alignment file FILE in Clustal format. |
@@ -55,6 +140,10 @@
Create alignment file FILE in PIR format. |
+ -pfam FILE |
+ Create alignment file FILE in PFAM format. |
+
+
-blc FILE |
Create alignment file FILE in BLC format. |