Jeremy,
Thanks. The horizontal rule is working for me now.
An example of the second item is attached in XML file. The last list at the
bottom doesn't render a blank line after the last list item, but used to.
Rgds,
Greg
On Tue, Mar 27, 2012 at 11:51 PM, Jeremy Goecks wrote:
> Greg,
>
> 1. The horizontal rule dividers specified by a "-" in the text have
> disappeared.
>
>
> Fixed in galaxy-central changeset cb5ff5b1bd67
>
> 2. Also I spotted a change where this ..
>
> *- line 1 of some bullets*
> *- line 2 of some bullets*
> *
> *
> *Following line*.
>
> .. lost the blank line after the "line 2" line.
>
>
> Where exactly is this occurring?
>
> Thanks for the feedback,
> J.
>
>
--
Greg Edwards,
Port Jackson Bioinformatics
gedwar...@gmail.com
in a peptide set
reportSites.pl
-galaxy 1
-galaxydebug 0
-pep val=$pepfile
-columns val=$columns
-dbval=$dbfile
-dbtypeval=$dbtype
-progressemailidval=$progressemailid
-progressemailmins val=$progressemailmins
-pidprefix val=$pidprefix
-htmlout val=$htmlout
-guihelp $guihelp
-rundescription "$rundescription"
$extra_args
-galaxy__new_file_path__$__new_file_path__
-galaxy__tool_data_path__ $__tool_data_path__
-galaxy__root_dir__ $__root_dir__
-galaxy__datatypes_config__ $__datatypes_config__
-galaxy__user_id__ $__user_id__
-galaxy__user_email__ $__user_email__
-galaxy__app__ $__app__
Automatically Detect
IPI . . . . . . . . . . . . . . Style >IPI:IPI00187591.3|...
NCBI . . . . . . . . . . . . Style >gi|359493355|...
UniProt SwissProt . . Style >sp|Q6GZX4|...
UniProt Trembl . . . . Style >tr|A0A171|...
None
Basic help on options
Longer help on options
Examples of usage
Brief program documentation
If the above file inputs offer no files to choose from, there are no files of
suitable type in the data file list (ie. History, see right). Upload data files
(protein database, and peptide csv) from your local machine with Get Data / Upload File
from the Tools list. File type can be sensed by the upload, or set in the
upload form, or changed later in the History with the ? or Pencil icon.
To view your results, click on the eye . To download results, click on the floppy disk.
In the downloaded zip file, open Report_phospho_sites_on_data_nn_and_data_nn.html.
-
**What it does**
This tool runs the reportSites Perl program, reporting on phosphorylation sites in a peptide set.
A paper is in publication on the code. Please cite the following if needed:
"ReportSites - a computational method to extract positional and physico-chemical
information from large-scale proteomic post-translational modification datasets",
Journal of Proteomics and Bioinformatics (accepted).
- Alistair V.G. Edwards
- Gregory J. Edwards
- Martin R. Larsen
- Stuart J. Cordwell
Also see the information under menu item Help / How To Cite Galaxy.
Interface version: 26mar12 (ie. the above input and control form).
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