diff --git a/CHANGELOG.md b/CHANGELOG.md index 6917bc501db19acfc696713b2483b27b6bb206d7..4c80d9b2a83b6b48e23acea956974ef830d99078 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -8,6 +8,7 @@ All notable changes to Pantools will be documented in this file. ### Changed - `add_functions` can now specify a directory where functional databases are stored (!117). +- parameter `-v` is now required for `change_grouping` (!124). ### Fixed - `msa` now works correctly with 'alt_id' properties of GO nodes (!118). diff --git a/docs/source/user_guide/construct.rst b/docs/source/user_guide/construct.rst index f53096a57aa32629e94e86ecfb769292ebaa1b8c..bdbd27cb58531aef23a796ca5788d9bd750b520e 100644 --- a/docs/source/user_guide/construct.rst +++ b/docs/source/user_guide/construct.rst @@ -1461,16 +1461,15 @@ Options - Do not remove the 'is_similar' relationships between mRNA nodes. This does not influence the next grouping. * - ``--grouping-version``/``-v`` - - Select a specific grouping version to be removed. Two additional - options: 'all' to remove all groupings and 'all_inactive' to - remove all inactive groupings. + - Select a specific grouping version to be removed. Should be either a + grouping number, 'all' for all groupings or 'all_inactive' for + all inactive groupings. Example commands """""""""""""""" .. code:: bash - $ pantools remove_grouping tomato_DB $ pantools remove_grouping --version=1 tomato_DB $ pantools remove_grouping --version=all --fast tomato_DB $ pantools remove_grouping --version=all_inactive tomato_DB diff --git a/src/main/java/nl/wur/bif/pantools/cli/RemoveGrouping.java b/src/main/java/nl/wur/bif/pantools/cli/RemoveGrouping.java index 765291a923e50d90d8c7fd9d6dade11f3c03e834..3769f1add74600b39d07dbb768787388a97f86e5 100644 --- a/src/main/java/nl/wur/bif/pantools/cli/RemoveGrouping.java +++ b/src/main/java/nl/wur/bif/pantools/cli/RemoveGrouping.java @@ -26,7 +26,7 @@ public class RemoveGrouping implements Callable<Integer> { @GraphDatabase private Pantools pantools; - @Option(names = {"-v", "--grouping-version"}) + @Option(names = {"-v", "--grouping-version"}, required = true) @Pattern(regexp = "[0-9]+|all|all-inactive", flags = CASE_INSENSITIVE, message = "{pattern.grouping-version}") String groupingVersion;