| Previous changeset 11:679b6323db03 (2019-05-29) |
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Commit message:
v0.1.1, removed legacy tool_dependencies.xml - use conda for dependencies |
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modified:
tools/venn_list/README.rst tools/venn_list/venn_list.xml |
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removed:
tools/venn_list/tool_dependencies.xml |
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| diff -r 679b6323db03 -r e13206029a72 tools/venn_list/README.rst --- a/tools/venn_list/README.rst Wed May 29 04:45:19 2019 -0400 +++ b/tools/venn_list/README.rst Wed May 29 06:03:59 2019 -0400 |
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| @@ -54,35 +54,36 @@ ======= ====================================================================== Version Changes ------- ---------------------------------------------------------------------- -v0.0.3 - Initial public release. -v0.0.4 - Ignore blank lines when loading IDs from tabular files -v0.0.5 - Explicit Galaxy error handling of return codes +v0.1.1 - Removed legacy ``tool_dependencies.xml`` file (the legacy Galaxy + packages did not cover matplotlib_venn anyway). +v0.1.0 - Now uses Python library matplotlib_venn to draw the diagram + instead of R's limma via rpy). Contribution from Frederic Sapet. +v0.0.12 - Internal Python style change. + - Python 3 compatible exception handling. +v0.0.11 - Use ``<command detect_errors="aggressive">`` (internal change only). + - Single quote command line arguments (internal change only) + - Python 3 compatible print function. + - Capture python script version when run from Galaxy. +v0.0.10 - Updated to point at Biopython 1.67 (latest version in Tool Shed). + - Explicit dependency on ``galaxy_sequence_utils``. + - Python style updates (internal change only). +v0.0.9 - Test with three-way Venn diagram. + - Includes testing of failure mode. + - Planemo for Tool Shed upload (``.shed.yml``, internal change only). +v0.0.8 - Reorder XML elements (internal change only). + - Fixed and improved error handling when rpy is not available. + - Test output relaxed to cope with more variation in PDF output. + - Declare Biopython dependency via the Tool Shed. +v0.0.7 - Renamed folder and README file. + - Tool definition now embeds citation information. v0.0.6 - Added unit tests. - Use reStructuredText for this README file. - Adopt standard MIT licence. - Updated citation information (Cock et al. 2013). - Development moved to GitHub, https://github.com/peterjc/pico_galaxy -v0.0.7 - Renamed folder and README file. - - Tool definition now embeds citation information. -v0.0.8 - Reorder XML elements (internal change only). - - Fixed and improved error handling when rpy is not available. - - Test output relaxed to cope with more variation in PDF output. - - Declare Biopython dependency via the Tool Shed. -v0.0.9 - Test with three-way Venn diagram. - - Includes testing of failure mode. - - Planemo for Tool Shed upload (``.shed.yml``, internal change only). - - Tool Shed dependency for rpy and limma (thanks to Björn Grüning). -v0.0.10 - Updated to point at Biopython 1.67 (latest version in Tool Shed). - - Explicit dependency on ``galaxy_sequence_utils``. - - Python style updates (internal change only). -v0.0.11 - Use ``<command detect_errors="aggressive">`` (internal change only). - - Single quote command line arguments (internal change only) - - Python 3 compatible print function. - - Capture python script version when run from Galaxy. -v0.0.12 - Internal Python style change. - - Python 3 compatible exception handling. -v0.1.0 - Now uses Python library matplotlib_venn to draw the diagram - instead of R's limma via rpy). Contribution from Frederic Sapet. +v0.0.5 - Explicit Galaxy error handling of return codes +v0.0.4 - Ignore blank lines when loading IDs from tabular files +v0.0.3 - Initial public release. ======= ====================================================================== |
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| diff -r 679b6323db03 -r e13206029a72 tools/venn_list/tool_dependencies.xml --- a/tools/venn_list/tool_dependencies.xml Wed May 29 04:45:19 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,15 +0,0 @@ -<?xml version="1.0" ?> -<tool_dependency> - <package name="galaxy_sequence_utils" version="1.0.1"> - <repository changeset_revision="c1ab450748ba" name="package_galaxy_sequence_utils_1_0_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"/> - </package> - <package name="limma" version="3.25.3"> - <repository changeset_revision="b19c06e97bce" name="package_r2_limma_3_25_3" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"/> - </package> - <package name="rpy" version="1.0.3"> - <repository changeset_revision="82170c94ca7c" name="package_rpy_1_0_3" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu"/> - </package> - <package name="biopython" version="1.67"> - <repository changeset_revision="a12f73c3b116" name="package_biopython_1_67" owner="biopython" toolshed="https://toolshed.g2.bx.psu.edu"/> - </package> -</tool_dependency> \ No newline at end of file |
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| diff -r 679b6323db03 -r e13206029a72 tools/venn_list/venn_list.xml --- a/tools/venn_list/venn_list.xml Wed May 29 04:45:19 2019 -0400 +++ b/tools/venn_list/venn_list.xml Wed May 29 06:03:59 2019 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="venn_list" name="Venn Diagram" version="0.1.0"> +<tool id="venn_list" name="Venn Diagram" version="0.1.1"> <description>from lists</description> <requirements> <requirement type="package" version="1.1.3">galaxy_sequence_utils</requirement> |