diff tools/get_orfs_or_cdss/README.rst @ 7:705a2e2df7fb draft

v0.1.1 fix typo; v0.1.0 BED output (Eric Rasche), NCBI genetic code 24; v0.0.7 embeds citation

--- a/tools/get_orfs_or_cdss/README.rst	Thu Nov 21 10:47:53 2013 -0500
+++ b/tools/get_orfs_or_cdss/README.rst	Thu Jul 30 12:35:31 2015 -0400
@@ -1,7 +1,7 @@
 Galaxy tool to find ORFs or simple CDSs
 =======================================
 
-This tool is copyright 2011-2013 by Peter Cock, The James Hutton Institute
+This tool is copyright 2011-2015 by Peter Cock, The James Hutton Institute
 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
 See the licence text below (MIT licence).
 
@@ -31,21 +31,23 @@
 
 There are just two files to install to use this tool from within Galaxy:
 
-* get_orfs_or_cdss.py (the Python script)
-* get_orfs_or_cdss.xml (the Galaxy tool definition)
+* ``get_orfs_or_cdss.py`` (the Python script)
+* ``get_orfs_or_cdss.xml`` (the Galaxy tool definition)
 
-The suggested location is in a dedicated tools/get_orfs_or_cdss folder.
+The suggested location is in a dedicated ``tools/get_orfs_or_cdss`` folder.
 
-You will also need to modify the tools_conf.xml file to tell Galaxy to offer the
+You will also need to modify the ``tools_conf.xml`` file to tell Galaxy to offer the
 tool. One suggested location is in the filters section. Simply add the line::
 
     <tool file="get_orfs_or_cdss/get_orfs_or_cdss.xml" />
 
-You will also need to install Biopython 1.54 or later. If you want to run
-the unit tests, include this line in tools_conf.xml.sample and the sample
-FASTA files under the test-data directory. Then::
+You will also need to install Biopython 1.65 or later (slightly older versions
+should be fine, but will not have the latest NCBI genetic code tables).
 
-    ./run_functional_tests.sh -id get_orfs_or_cdss
+If you wish to run the unit tests, also	move/copy the ``test-data/`` files
+under Galaxy's ``test-data/`` folder. Then::
+
+    ./run_tests.sh -id get_orfs_or_cdss
 
 That's it.
 
@@ -68,6 +70,11 @@
         - Updated citation information (Cock et al. 2013).
         - Renamed folder and adopted README.rst naming.
 v0.0.6  - Corrected automated dependency defintion.
+v0.0.7  - Tool definition now embeds citation information.
+v0.1.0  - Tool now outputs BED formatted calls (by @erasche, Eric Rasche).
+        - Using ``optparse`` for the Python command line API (Eric Rasche).
+        - Added NCBI genetic code table 24, Pterobranchia Mitochondrial.
+v0.1.1  - Reorder XML elements (internal change only).
 ======= ======================================================================
 
 
@@ -80,28 +87,41 @@
 Development has now moved to a dedicated GitHub repository:
 https://github.com/peterjc/pico_galaxy/tree/master/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)::
 
-    $ tar -czf get_orfs_or_cdss.tar.gz tools/get_orfs_or_cdss/README.rst tools/get_orfs_or_cdss/get_orfs_or_cdss.* tools/get_orfs_or_cdss/tool_dependencies.xml test-data/get_orf_input*.fasta test-data/Ssuis.fasta
+    $ planemo shed_update --shed_target testtoolshed --check_diff ~/repositories/pico_galaxy/tools/get_orfs_or_cdss/
+    ...
 
-Check this worked::
+or::
 
-    $ tar -tzf get_orfs_or_cdss.tar.gz
-    tools/get_orfs_or_cdss/README.rst
-    tools/get_orfs_or_cdss/get_orfs_or_cdss.py
-    tools/get_orfs_or_cdss/get_orfs_or_cdss.xml
-    tools/get_orfs_or_cdss/tool_dependencies.xml
-    test-data/get_orf_input.fasta
+    $ planemo shed_update --shed_target toolshed --check_diff ~/repositories/pico_galaxy/tools/get_orfs_or_cdss/
+    ...
+
+To just build and check the tar ball, use::
+
+    $ planemo shed_upload --tar_only  ~/repositories/pico_galaxy/tools/get_orfs_or_cdss/
+    ...
+    $ tar -tzf shed_upload.tar.gz
+    test-data/Ssuis.fasta
+    test-data/get_orf_input.Suis_ORF.bed
     test-data/get_orf_input.Suis_ORF.nuc.fasta
     test-data/get_orf_input.Suis_ORF.prot.fasta
+    test-data/get_orf_input.fasta
+    test-data/get_orf_input.t11_bed_out.bed
     test-data/get_orf_input.t11_nuc_out.fasta
+    test-data/get_orf_input.t11_open_bed_out.bed
     test-data/get_orf_input.t11_open_nuc_out.fasta
     test-data/get_orf_input.t11_open_prot_out.fasta
     test-data/get_orf_input.t11_prot_out.fasta
+    test-data/get_orf_input.t1_bed_out.bed
     test-data/get_orf_input.t1_nuc_out.fasta
     test-data/get_orf_input.t1_prot_out.fasta
-    test-data/Ssuis.fasta
+    tools/get_orfs_or_cdss/get_orfs_or_cdss.py
+    tools/get_orfs_or_cdss/get_orfs_or_cdss.xml
+    tools/get_orfs_or_cdss/README.rst
+    tools/get_orfs_or_cdss/tool_dependencies.xml
 
 
 Licence (MIT)