Mercurial > repos > peterjc > venn_list

changeset 12:e13206029a72 draft default tip

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v0.1.1, removed legacy tool_dependencies.xml - use conda for dependencies
author peterjc
date Wed, 29 May 2019 06:03:59 -0400
parents 679b6323db03
children
files tools/venn_list/README.rst tools/venn_list/tool_dependencies.xml tools/venn_list/venn_list.xml
diffstat 3 files changed, 26 insertions(+), 40 deletions(-) [+]
line wrap: on
line diff
--- 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
@@ -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.
 ======= ======================================================================
 
 
--- 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
@@ -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
--- 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
@@ -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>