Mercurial > repos > peterjc > predictnls
changeset 5:1a1446972dec draft
README.rst markup
| author | peterjc |
|---|---|
| date | Wed, 05 Aug 2015 12:24:56 -0400 |
| parents | ff3221dc06a7 |
| children | 0b6a51c7e008 |
| files | tools/predictnls/README.rst |
| diffstat | 1 files changed, 9 insertions(+), 13 deletions(-) [+] |
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--- a/tools/predictnls/README.rst Thu May 21 10:58:04 2015 -0400 +++ b/tools/predictnls/README.rst Wed Aug 05 12:24:56 2015 -0400 @@ -5,8 +5,8 @@ (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved. See the licence text below. -The tool consists of a Galaxy interface definition (predictnls.xml), and a Python -script (predictnls.py) which re-implements the command line tool predictNLS. This +The tool consists of a Galaxy interface definition (``predictnls.xml``), and a Python +script (``predictnls.py``) which re-implements the command line tool predictNLS. This should match the behaviour of predictNLS v1.0.20 (July 2011), the current latest release from the Rost Lab, see http://rostlab.org and their paper: @@ -30,12 +30,12 @@ =================== There are just four files which should be moved under the Galaxy tools folder, -e.g. in a tools/protein_analysis filter: +e.g. in a ``tools/protein_analysis`` filter: -* predictlns.xml (the Galaxy tool definition) -* predictlns.py (the Python script) -* predictlns.txt (this README file) -* My_NLS_list (the default set of NLS motifs from the Rost Lab) +* ``predictlns.xml`` (the Galaxy tool definition) +* ``predictlns.py`` (the Python script) +* ``predictlns.txt`` (this README file) +* ``My_NLS_list`` (the default set of NLS motifs from the Rost Lab) You will also need to modify the tools_conf.xml file to tell Galaxy to offer the tool. If you are using other protein analysis tools like TMHMM or SignalP, put @@ -75,10 +75,6 @@ This script and related tools were initially developed on the following hg branch: http://bitbucket.org/peterjc/galaxy-central/src/tools -For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use -the following command from the Galaxy root folder:: - - For pushing a release to the test or main "Galaxy Tool Shed", use the following Planemo commands (which requires you have set your Tool Shed access details in ``~/.planemo.yml`` and that you have access rights on the Tool Shed):: @@ -114,7 +110,7 @@ the Rost Lab, which was released under the GPL v3. Therefore, as I consider this to be a derivative work, this too is released under the GPL v3. -Please note that the My_NLS_list should be an exact copy of the file of the -same name included with predictnls-1.0.7.tar.gz to predictnls-1.0.20.tar.gz +Please note that the ``My_NLS_list`` file should be an exact copy of the file of the +same name included with ``predictnls-1.0.7.tar.gz`` to ``predictnls-1.0.20.tar.gz`` inclusive (the list was extended in v1.0.7 in August 2010, see the change log included in those tar-balls), available from ftp://rostlab.org/predictnls/