X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp%2Fhtml%2Ffeatures%2Fclarguments.html;h=6df40b525556a8817b8c3acd7ab712114003f481;hb=893f21fe8df6a9d47ced8140e3ba75f03407be00;hp=7c2e9d5bc9f0a5c2a98ac89f136ac2ea3cf572cf;hpb=3778008766299b5db71d77e8530a9c0fe9b6916d;p=jalview.git diff --git a/help/help/html/features/clarguments.html b/help/help/html/features/clarguments.html index 7c2e9d5..6df40b5 100644 --- a/help/help/html/features/clarguments.html +++ b/help/help/html/features/clarguments.html @@ -44,7 +44,7 @@
- These new arguments are all accessed with a --doubledash
form of
+ These new arguments are all accessed with a ‑‑doubledash
form of
command line argument (with the one exception where simply opening one or more
files can be performed without any arguments other than the filenames).
However, you cannot mix old and new style arguments, so if you use any
-singledash
arguments (with the exception of -help
or -h
), they will all be interpreted as
- old style arguments with the new --doubledash
+ old style arguments with the new ‑‑doubledash
arguments being ignored. If you have a script
that uses the old arguments without any dashes, and uses the bare-word
open
then these will also be interpreted as old style arguments.
@@ -97,52 +97,52 @@
--arg value
+ ‑‑arg value
--arg=value
+ ‑‑arg=value
--arg file1.fa otherfile.stk
+ ‑‑arg file1.fa otherfile.stk
--arg filename*.fa
(filenames expanded by shell)
+ ‑‑arg filename*.fa
(filenames expanded by shell)
--arg=filename*.fa
(filenames expanded by Jalview)
+ ‑‑arg=filename*.fa
(filenames expanded by Jalview)
no
.
--switch
+ ‑‑switch
--noswitch
+ ‑‑noswitch
--image
output can be modified with a --scale=number
factor, or a --structure
can refer to a sequence with a --seqid=ID
). This additional information can be added in a number of different ways.
+ Some values can be modified, or may need additional information (for instance an ‑‑image
output can be modified with a ‑‑scale=number
factor, or a ‑‑structure
can refer to a sequence with a ‑‑seqid=ID
). This additional information can be added in a number of different ways.
--image output.png --scale 2.5
+ ‑‑image output.png --scale 2.5
--open=[nowrap,colour=gecos-blossom]uniref50.fa
+ ‑‑open=[nowrap,colour=gecos-blossom]uniref50.fa
no
to negate the value, as with the argument name.
--image[MYID]=output.png --other --args --scale[MYID]=2.5
+ ‑‑image[MYID]=output.png --other --args --scale[MYID]=2.5
--image=output.png --other --args --all --scale=2.5
+ ‑‑image=output.png --other --args --all --scale=2.5
--image=output.png --other --args --scale[*]=2.5
+ ‑‑image=output.png --other --args --scale[*]=2.5
- Jalview can be run in headless mode, i.e. without the usual graphical user interface (GUI), by specifying the --headless
argument. With command line arguments you can specify operations for Jalview to perform on one or more files and then stop running. Most likely you will want to output another file, either an alignment for image file.
+ Jalview can be run in headless mode, i.e. without the usual graphical user interface (GUI), by specifying the ‑‑headless
argument. With command line arguments you can specify operations for Jalview to perform on one or more files and then stop running. Most likely you will want to output another file, either an alignment for image file.
- If you specify an argument for an output file (one or more of --output
, --image
or --structureimage
) then it will be assumed that you wish to run in headless mode.
+ If you specify an argument for an output file (one or more of ‑‑output
, ‑‑image
or ‑‑structureimage
) then it will be assumed that you wish to run in headless mode.
- You can force Jalview to run in graphical mode using the --gui
argument.
+ You can force Jalview to run in graphical mode using the ‑‑gui
argument.