Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 952fdac419e9b4123c158fd088f90a9a09bc7fd3 https://github.com/galaxyproject/galaxy/commit/952fdac419e9b4123c158fd088f90... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2018-09-10 (Mon, 10 Sep 2018)

Changed paths: R tools/data_source/bed_convert.xml

Log Message: ----------- Remove unused and broken tool

Commit: f865e8359fa6c8d599011edcea61a2a728afb9ea https://github.com/galaxyproject/galaxy/commit/f865e8359fa6c8d599011edcea61a... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2018-09-10 (Mon, 10 Sep 2018)

Changed paths: M config/job_resource_params_conf.xml.sample M config/workflow_resource_params_conf.xml.sample M lib/galaxy/tools/parameters/validation.py M lib/galaxy/tools/xsd/galaxy.xsd M test/functional/tools/for_workflows/head.xml M test/unit/tools/test_wrappers.py M tools/data_source/genbank.xml M tools/data_source/upload.xml M tools/extract/liftOver_wrapper.xml M tools/filters/CreateInterval.xml M tools/filters/bed_to_bigbed.xml M tools/filters/changeCase.xml M tools/filters/fileGrep.xml M tools/filters/fixedValueColumn.xml M tools/filters/gff/gff_filter_by_attribute.xml M tools/filters/gff/gff_filter_by_feature_count.xml M tools/filters/grep.xml M tools/filters/headWrapper.xml M tools/filters/randomlines.xml M tools/filters/remove_beginning.xml M tools/filters/tailWrapper.xml M tools/filters/wig_to_bigwig.xml M tools/maf/vcf_to_maf_customtrack.xml M tools/metag_tools/blat_wrapper.xml M tools/metag_tools/shrimp_color_wrapper.xml M tools/metag_tools/shrimp_wrapper.xml M tools/plotting/bar_chart.xml M tools/plotting/boxplot.xml M tools/solid_tools/maq_cs_wrapper.xml M tools/sr_mapping/PerM.xml M tools/sr_mapping/bfast_wrapper.xml M tools/stats/filtering.xml M tools/stats/gsummary.xml M tools/stats/gsummary.xml.groups

Log Message: ----------- Deprecate `size` attribute of `<param/>` and remove it from tools

Also: - dos2unix test/functional/tools/for_workflows/head.xml - Single-quote text and data params in `<command/>` - Remove deprecated `interpreter` attribute of `<command />`

Commit: bf550da2afe94ad53aae71e3d930a49cb98558a4 https://github.com/galaxyproject/galaxy/commit/bf550da2afe94ad53aae71e3d930a... Author: John Chilton jmchilton@gmail.com Date: 2018-12-12 (Wed, 12 Dec 2018)

Changed paths: M config/job_resource_params_conf.xml.sample M config/workflow_resource_params_conf.xml.sample M lib/galaxy/tools/parameters/validation.py M lib/galaxy/tools/xsd/galaxy.xsd M test/functional/tools/for_workflows/head.xml M test/unit/tools/test_wrappers.py R tools/data_source/bed_convert.xml M tools/data_source/genbank.xml M tools/data_source/upload.xml M tools/extract/liftOver_wrapper.xml M tools/filters/CreateInterval.xml M tools/filters/bed_to_bigbed.xml M tools/filters/changeCase.xml M tools/filters/fileGrep.xml M tools/filters/fixedValueColumn.xml M tools/filters/gff/gff_filter_by_attribute.xml M tools/filters/gff/gff_filter_by_feature_count.xml M tools/filters/grep.xml M tools/filters/headWrapper.xml M tools/filters/randomlines.xml M tools/filters/remove_beginning.xml M tools/filters/tailWrapper.xml M tools/filters/wig_to_bigwig.xml M tools/maf/vcf_to_maf_customtrack.xml M tools/metag_tools/blat_wrapper.xml M tools/metag_tools/shrimp_color_wrapper.xml M tools/metag_tools/shrimp_wrapper.xml M tools/plotting/bar_chart.xml M tools/plotting/boxplot.xml M tools/solid_tools/maq_cs_wrapper.xml M tools/sr_mapping/PerM.xml M tools/sr_mapping/bfast_wrapper.xml M tools/stats/filtering.xml M tools/stats/gsummary.xml M tools/stats/gsummary.xml.groups

Log Message: ----------- Merge pull request #6684 from nsoranzo/deprecate_param_size

Deprecate `size` attribute of `<param/>` and remove it from tools

Compare: https://github.com/galaxyproject/galaxy/compare/d06718ef2420...bf550da2afe9 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/

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