X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fclarguments.html;h=8d6a4d893e2ed87043a8b9831e53b5303a6e98c0;hb=56ad3ae1c8b2fefd7af371049e344acfc1f23944;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.