diff tools/seq_select_by_id/README.rst @ 6:91f55ee8fea5 draft

v0.0.11; more tests and assorting minor changes
author peterjc
date Wed, 13 May 2015 10:56:29 -0400
parents 1a83f5ab9e95
children a5602454b0ad
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line diff
--- a/tools/seq_select_by_id/README.rst	Thu Nov 21 04:54:59 2013 -0500
+++ b/tools/seq_select_by_id/README.rst	Wed May 13 10:56:29 2015 -0400
@@ -1,7 +1,7 @@
 Galaxy tool to select FASTA, QUAL, FASTQ or SFF sequences by ID
-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.
@@ -36,20 +36,20 @@
 There are just two files to install to use this tool from within Galaxy:
-* seq_select_by_id.py (the Python script)
-* seq_select_by_id.xml (the Galaxy tool definition)
+* ``seq_select_by_id.py`` (the Python script)
+* ``seq_select_by_id.xml`` (the Galaxy tool definition)
-The suggested location is a dedicated tools/seq_select_by_id folder.
+The suggested location is a dedicated ``tools/seq_select_by_id`` 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="seq_select_by_id/seq_select_by_id.xml" />
-If you wish to run the unit tests, also add this to tools_conf.xml.sample
-and move/copy the test-data files under Galaxy's test-data folder. Then::
+If you wish to run the unit tests, also move/copy the ``test-data/`` files
+under Galaxy's ``test-data/`` folder. Then::
-    $ ./run_functional_tests.sh -id seq_select_by_id
+    $ ./run_tests.sh -id seq_select_by_id
 You will also need to install Biopython 1.54 or later. That's it.
@@ -73,7 +73,18 @@
         - Fixed Biopython dependency setup.
         - Development moved to GitHub, https://github.com/peterjc/pico_galaxy
         - Renamed folder and adopted README.rst naming.
-v0.0.8  - Corrected automated dependency definition
+v0.0.8  - Corrected automated dependency definition.
+v0.0.9  - Simplified XML to apply input format to output data.
+        - Tool definition now embeds citation information.
+        - Include input dataset name in output dataset names.
+        - If white space is found in the requested tabular field then only
+          the first word is used as the identifier (with a warning to stderr).
+v0.0.10 - Includes testing of stdout messages.
+        - Includes testing of failure modes.
+v0.0.11 - Use the ``format_source=...`` tag.
+        - Reorder XML elements (internal change only).
+        - Planemo for Tool Shed upload (``.shed.yml``, internal change only).
+        - Quote filenames in case of spaces (internal change only).
 ======= ======================================================================
@@ -86,21 +97,31 @@
 Development has now moved to a dedicated GitHub repository:
-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)::
+    $ planemo shed_upload --shed_target testtoolshed --check_diff ~/repositories/pico_galaxy/tools/seq_select_by_id/
+    ...
-    $ tar -czf seq_select_by_id.tar.gz tools/seq_select_by_id/README.rst tools/seq_select_by_id/seq_select_by_id.* tools/seq_select_by_id/tool_dependencies.xml test-data/k12_ten_proteins.fasta test-data/k12_hypothetical.fasta test-data/k12_hypothetical.tabular
+    $ planemo shed_upload --shed_target toolshed --check_diff ~/repositories/pico_galaxy/tools/seq_select_by_id/
+    ...
+To just build and check the tar ball, use::
-Check this worked::
-    $ tar -tzf seq_select_by_id.tar.gz
+    $ planemo shed_upload --tar_only  ~/repositories/pico_galaxy/tools/seq_select_by_id/
+    ...
+    $ tar -tzf shed_upload.tar.gz 
+    test-data/k12_hypothetical.fasta
+    test-data/k12_hypothetical.tabular
+    test-data/k12_hypothetical_alt.tabular
+    test-data/k12_ten_proteins.fasta
-    test-data/k12_ten_proteins.fasta
-    test-data/k12_hypothetical.fasta
-    test-data/k12_hypothetical.tabular
 Licence (MIT)