{"payload":{"feedbackUrl":"https://github.com/orgs/community/discussions/53140","repo":{"id":23992530,"defaultBranch":"main","name":"tools-iuc","ownerLogin":"galaxyproject","currentUserCanPush":false,"isFork":false,"isEmpty":false,"createdAt":"2014-09-13T11:18:49.000Z","ownerAvatar":"https://avatars.githubusercontent.com/u/7937847?v=4","public":true,"private":false,"isOrgOwned":true},"refInfo":{"name":"","listCacheKey":"v0:1720338138.0","currentOid":""},"activityList":{"items":[{"before":"b37248ea9b492c096b143272aebc79d8f04c2984","after":"fff23da3bceafb57de06af03d4c8ab4d66d4b098","ref":"refs/heads/main","pushedAt":"2024-07-18T09:31:31.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"wm75","name":"Wolfgang Maier","path":"/wm75","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4742081?s=80&v=4"},"commit":{"message":"cutadapt: replace adapter sanitizer by validator (#6161)","shortMessageHtmlLink":"cutadapt: replace adapter sanitizer by validator (<a 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tools/diffbind/diffbind.xml\r\n\r\nCo-authored-by: mtekman <20641402+mtekman@users.noreply.github.com>\r\n\r\n* put symlink back\r\n\r\n---------\r\n\r\nCo-authored-by: Björn Grüning <bjoern@gruenings.eu>\r\nCo-authored-by: mtekman <20641402+mtekman@users.noreply.github.com>","shortMessageHtmlLink":"Update DiffBind to 3.12.0 and add some requested features (<a class=\"issue-link js-issue-link\" data-error-text=\"Failed to load title\" data-id=\"2388832272\" data-permission-text=\"Title is private\" data-url=\"https://github.com/galaxyproject/tools-iuc/issues/6125\" data-hovercard-type=\"pull_request\" data-hovercard-url=\"/galaxyproject/tools-iuc/pull/6125/hovercard\" 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fastq/fastq.gz are\r\nallowd (this is a mistake IMO ...):\r\n```\r\nNotFound: cannot find 'lr'\r\n  File \"galaxy/util/template.py\", line 87, in fill_template\r\n    return unicodify(t, log_exception=False)\r\n  File \"galaxy/util/__init__.py\", line 1183, in unicodify\r\n    value = str(value)\r\n  File \"Cheetah/Template.py\", line 1053, in __unicode__\r\n    return getattr(self, mainMethName)()\r\n  File \"cheetah_DynamicallyCompiledCheetahTemplate_1720043166_6268568_19017.py\", line 172, in respond\r\nNotFound: cannot find 'lr'\r\n  File \"galaxy/util/template.py\", line 87, in fill_template\r\n    return unicodify(t, log_exception=False)\r\n  File \"galaxy/util/__init__.py\", line 1183, in unicodify\r\n    value = str(value)\r\n  File \"Cheetah/Template.py\", line 1053, in __unicode__\r\n    return getattr(self, mainMethName)()\r\n  File \"cheetah_DynamicallyCompiledCheetahTemplate_1720043166_6268568_19017.py\", line 172, in respond\r\nNotFound: cannot find 'lr'\r\n  File \"galaxy/util/template.py\", line 87, in fill_template\r\n    return unicodify(t, log_exception=False)\r\n  File \"galaxy/util/__init__.py\", line 1183, in unicodify\r\n    value = str(value)\r\n  File \"Cheetah/Template.py\", line 1053, in __unicode__\r\n    return getattr(self, mainMethName)()\r\n  File \"cheetah_DynamicallyCompiledCheetahTemplate_1720043166_6268568_19017.py\", line 172, in respond\r\nNotFound: cannot find 'lr'\r\n  File \"galaxy/util/template.py\", line 87, in fill_template\r\n    return unicodify(t, log_exception=False)\r\n  File \"galaxy/util/__init__.py\", line 1183, in unicodify\r\n    value = str(value)\r\n  File \"Cheetah/Template.py\", line 1053, in __unicode__\r\n    return getattr(self, mainMethName)()\r\n  File \"cheetah_DynamicallyCompiledCheetahTemplate_1720043166_6268568_19017.py\", line 172, in respond\r\nNotFound: cannot find 'lr'\r\n  File \"galaxy/util/template.py\", line 87, in fill_template\r\n    return unicodify(t, log_exception=False)\r\n  File \"galaxy/util/__init__.py\", line 1183, in unicodify\r\n    value = str(value)\r\n  File \"Cheetah/Template.py\", line 1053, in __unicode__\r\n    return getattr(self, mainMethName)()\r\n  File \"cheetah_DynamicallyCompiledCheetahTemplate_1720043166_6268568_19017.py\", line 172, in respond\r\nNotFound: cannot find 'lr'\r\n  File \"galaxy/util/template.py\", line 87, in fill_template\r\n    return unicodify(t, log_exception=False)\r\n  File \"galaxy/util/__init__.py\", line 1183, in unicodify\r\n    value = str(value)\r\n  File \"Cheetah/Template.py\", line 1053, in __unicode__\r\n    return getattr(self, mainMethName)()\r\n  File \"cheetah_DynamicallyCompiledCheetahTemplate_1720043166_6268568_19017.py\", line 172, in respond\r\nNotFound: cannot find 'lr'\r\n  File \"galaxy/util/template.py\", line 87, in fill_template\r\n    return unicodify(t, log_exception=False)\r\n  File \"galaxy/util/__init__.py\", line 1183, in unicodify\r\n    value = str(value)\r\n  File \"Cheetah/Template.py\", line 1053, in __unicode__\r\n    return getattr(self, mainMethName)()\r\n  File \"cheetah_DynamicallyCompiledCheetahTemplate_1720043166_6268568_19017.py\", line 172, in respond\r\nNotFound: cannot find 'lr'\r\n  File \"galaxy/util/template.py\", line 87, in fill_template\r\n    return unicodify(t, log_exception=False)\r\n  File \"galaxy/util/__init__.py\", line 1183, in unicodify\r\n    value = str(value)\r\n  File \"Cheetah/Template.py\", line 1053, in __unicode__\r\n    return getattr(self, mainMethName)()\r\n  File \"cheetah_DynamicallyCompiledCheetahTemplate_1720043166_6268568_19017.py\", line 172, in respond\r\nNotFound: cannot find 'lr'\r\n  File \"galaxy/util/template.py\", line 87, in fill_template\r\n    return unicodify(t, log_exception=False)\r\n  File \"galaxy/util/__init__.py\", line 1183, in unicodify\r\n    value = str(value)\r\n  File \"Cheetah/Template.py\", line 1053, in __unicode__\r\n    return getattr(self, mainMethName)()\r\n  File \"cheetah_DynamicallyCompiledCheetahTemplate_1720043166_6268568_19017.py\", line 172, in respond\r\nNotFound: cannot find 'lr'\r\n  File \"galaxy/util/template.py\", line 87, in fill_template\r\n    return unicodify(t, log_exception=False)\r\n  File \"galaxy/util/__init__.py\", line 1183, in unicodify\r\n    value = str(value)\r\n  File \"Cheetah/Template.py\", line 1053, in __unicode__\r\n    return getattr(self, mainMethName)()\r\n  File \"cheetah_DynamicallyCompiledCheetahTemplate_1720043166_6268568_19017.py\", line 172, in respond\r\nNotFound: cannot find 'lr'\r\n  File \"galaxy/jobs/runners/__init__.py\", line 297, in prepare_job\r\n    job_wrapper.prepare()\r\n  File \"galaxy/jobs/__init__.py\", line 1260, in prepare\r\n    ) = tool_evaluator.build()\r\n  File \"galaxy/tools/evaluation.py\", line 588, in build\r\n    global_tool_logs(self._build_command_line, config_file, \"Building Command Line\")\r\n  File \"galaxy/tools/evaluation.py\", line 98, in global_tool_logs\r\n    raise e\r\n  File \"galaxy/tools/evaluation.py\", line 94, in global_tool_logs\r\n    return func()\r\n  File \"galaxy/tools/evaluation.py\", line 611, in _build_command_line\r\n    command_line = fill_template(\r\n  File \"galaxy/util/template.py\", line 115, in fill_template\r\n    return fill_template(\r\n  File \"galaxy/util/template.py\", line 115, in fill_template\r\n    return fill_template(\r\n  File \"galaxy/util/template.py\", line 115, in fill_template\r\n    return fill_template(\r\n  File \"galaxy/util/template.py\", line 115, in fill_template\r\n    return fill_template(\r\n  File \"galaxy/util/template.py\", line 115, in fill_template\r\n    return fill_template(\r\n  File \"galaxy/util/template.py\", line 115, in fill_template\r\n    return fill_template(\r\n  File \"galaxy/util/template.py\", line 115, in fill_template\r\n    return fill_template(\r\n  File \"galaxy/util/template.py\", line 115, in fill_template\r\n    return fill_template(\r\n  File \"galaxy/util/template.py\", line 115, in fill_template\r\n    return fill_template(\r\n  File \"galaxy/util/template.py\", line 115, in fill_template\r\n    return fill_template(\r\n  File \"galaxy/util/template.py\", line 123, in fill_template\r\n    raise first_exception or e\r\n  File \"galaxy/util/template.py\", line 87, in fill_template\r\n    return unicodify(t, log_exception=False)\r\n  File \"galaxy/util/__init__.py\", line 1183, in unicodify\r\n    value = str(value)\r\n  File \"Cheetah/Template.py\", line 1053, in __unicode__\r\n    return getattr(self, mainMethName)()\r\n  File \"cheetah_DynamicallyCompiledCheetahTemplate_1720043166_6268568_19017.py\", line 172, in respond\r\n```\r\nThis is hopefully an uncontroversial fix.","shortMessageHtmlLink":"Fix unicycler datatype comparisons (<a class=\"issue-link js-issue-link\" data-error-text=\"Failed to load title\" data-id=\"2393988497\" data-permission-text=\"Title is private\" data-url=\"https://github.com/galaxyproject/tools-iuc/issues/6131\" data-hovercard-type=\"pull_request\" data-hovercard-url=\"/galaxyproject/tools-iuc/pull/6131/hovercard\" href=\"https://github.com/galaxyproject/tools-iuc/pull/6131\">#6131</a>)"}},{"before":"aad95145c89f036536b4025639bd92e626491212","after":"ff6e548e915048822d0744c1b428eab5574010c9","ref":"refs/heads/lumpy","pushedAt":"2024-07-07T11:21:49.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"bgruening","name":"Björn Grüning","path":"/bgruening","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/469983?s=80&v=4"},"commit":{"message":"fix linting, new version schema","shortMessageHtmlLink":"fix linting, new version schema"}},{"before":null,"after":"aad95145c89f036536b4025639bd92e626491212","ref":"refs/heads/lumpy","pushedAt":"2024-07-07T07:42:18.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"bgruening","name":"Björn Grüning","path":"/bgruening","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/469983?s=80&v=4"},"commit":{"message":"use TMPDIR for lumpy","shortMessageHtmlLink":"use TMPDIR for lumpy"}},{"before":"091caba3c5b066b293745ccee5cd31132fec3b4b","after":"df9c285dddde7d901823c608c8d7dab971224b5b","ref":"refs/heads/main","pushedAt":"2024-07-05T10:52:31.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"bgruening","name":"Björn Grüning","path":"/bgruening","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/469983?s=80&v=4"},"commit":{"message":"Fix SnapATAC2 gene activity matrix bug (#6109)\n\n* Fix SnapATAC2 gene activity matrix bug\r\n\r\n* bump version suffix\r\n\r\n* update test data","shortMessageHtmlLink":"Fix SnapATAC2 gene activity matrix bug (<a class=\"issue-link js-issue-link\" data-error-text=\"Failed to load title\" data-id=\"2375252625\" data-permission-text=\"Title is private\" data-url=\"https://github.com/galaxyproject/tools-iuc/issues/6109\" data-hovercard-type=\"pull_request\" data-hovercard-url=\"/galaxyproject/tools-iuc/pull/6109/hovercard\" href=\"https://github.com/galaxyproject/tools-iuc/pull/6109\">#6109</a>)"}},{"before":"d7cada7ddf775e946e218fdc839e6e4c8aac6d80","after":"091caba3c5b066b293745ccee5cd31132fec3b4b","ref":"refs/heads/main","pushedAt":"2024-07-05T05:51:21.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"bgruening","name":"Björn Grüning","path":"/bgruening","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/469983?s=80&v=4"},"commit":{"message":"Make bed features from nonparametric continuous extreme bigwig value regions.  (#6121)\n\n* adding new tool bigwig_outlier_bed\r\n\r\n* remove redundant script\r\n\r\n* replace test.bw with test-data/1.bigwig to decrease test outputs below 1MB maximum for linter.\r\n\r\n* added bigtools to bio.tools for this new entry\r\nadded edam\r\n\r\n* Add a proper version command by importing pybedtools\r\n\r\n* fix doi for pybigtools\r\n\r\n* Incorporate Bjoern's ideas.\r\n\r\nSingle select to configure 3 possible outputs.\r\n\r\nUpper quantile now required. Chide if no low quantile and no output because low not in the choice.\r\n\r\nHelp vastly expanded.\r\n\r\n* Added the bigwig metadata name as the label for bed feature name so no need for the user to supply one.\r\n\r\n* Clearing out old test data. Passes tests here but diffs in CI. Something odd.\r\n\r\n* readding fixed test outputs again again.\r\n\r\n* Ah. was overwriting a bed with the two bigwig test.\r\n\r\n* remove print leftovers\r\n\r\n* Separated python script to enable access for linting in CI\r\n\r\n* fix flake8 complaints with black on the new separate python script\r\n\r\n* fix imports\r\n\r\n* Do not make the output contig statistics table if there's no table output needed.\r\n\r\n* make the table calculations optional and mostly as a separate function since they may not be needed.\r\n\r\n* Clean up some comments.\r\nmakeTableRow renamed\r\n\r\n* Update tools/bigwig_outlier_bed/.shed.yml\r\n\r\nCo-authored-by: Björn Grüning <bjoern@gruenings.eu>\r\n\r\n* Update tools/bigwig_outlier_bed/.shed.yml\r\n\r\nCo-authored-by: Björn Grüning <bjoern@gruenings.eu>\r\n\r\n* Clean up all field prompt text and consolidate the help text into chunks.\r\n\r\n* remove test for both qhi/qlo because qhi is not optional\r\n\r\n---------\r\n\r\nCo-authored-by: Björn Grüning <bjoern@gruenings.eu>","shortMessageHtmlLink":"Make bed features from nonparametric continuous extreme bigwig value …"}},{"before":"e7eed8294ff51dbbd819ace7184b2a555677d770","after":"d7cada7ddf775e946e218fdc839e6e4c8aac6d80","ref":"refs/heads/main","pushedAt":"2024-07-03T11:43:22.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"bgruening","name":"Björn Grüning","path":"/bgruening","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/469983?s=80&v=4"},"commit":{"message":"Added features for ToolDistillator v0.9 (#6124)","shortMessageHtmlLink":"Added features for ToolDistillator v0.9 (<a class=\"issue-link js-issue-link\" data-error-text=\"Failed to load title\" data-id=\"2388201319\" data-permission-text=\"Title is private\" data-url=\"https://github.com/galaxyproject/tools-iuc/issues/6124\" data-hovercard-type=\"pull_request\" data-hovercard-url=\"/galaxyproject/tools-iuc/pull/6124/hovercard\" href=\"https://github.com/galaxyproject/tools-iuc/pull/6124\">#6124</a>)"}},{"before":"8586409c5f329eaf75902eedc3d29a6e82560788","after":"e7eed8294ff51dbbd819ace7184b2a555677d770","ref":"refs/heads/main","pushedAt":"2024-07-01T18:21:08.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"bgruening","name":"Björn Grüning","path":"/bgruening","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/469983?s=80&v=4"},"commit":{"message":"Updating tools/pbmm2 from version 1.13.1 to 1.14.99 (#6092)\n\nCo-authored-by: planemo-autoupdate <planemo-autoupdate@users.noreply.github.com>","shortMessageHtmlLink":"Updating tools/pbmm2 from version 1.13.1 to 1.14.99 (<a class=\"issue-link js-issue-link\" data-error-text=\"Failed to load title\" data-id=\"2356336409\" data-permission-text=\"Title is private\" data-url=\"https://github.com/galaxyproject/tools-iuc/issues/6092\" data-hovercard-type=\"pull_request\" data-hovercard-url=\"/galaxyproject/tools-iuc/pull/6092/hovercard\" href=\"https://github.com/galaxyproject/tools-iuc/pull/6092\">#6092</a>)"}},{"before":"e1af25e42839c772b023f700210013658e42dc15","after":"8586409c5f329eaf75902eedc3d29a6e82560788","ref":"refs/heads/main","pushedAt":"2024-07-01T18:12:28.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"bgruening","name":"Björn Grüning","path":"/bgruening","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/469983?s=80&v=4"},"commit":{"message":"Update HiCExplorer to 3.7.5 (#6112)\n\n* add dbkey to build matrix. Tests failed because of prepareqc upstream?\r\n\r\n* fails - upstream module error.\r\n\r\n* update label help\r\n\r\n* bump version just for hicbuildmatrix\r\n\r\n* bump hicexplorer version to fix pandas and other dependency issues\r\n\r\n* remove redundant fake version suffix - already bumped to 3.7.3\r\n\r\n* Update tools/hicexplorer/hicBuildMatrix.xml\r\n\r\nCo-authored-by: Björn Grüning <bjoern@gruenings.eu>\r\n\r\n* add profile version\r\n\r\n* upgrade samtools and a few test datasets\r\n\r\n* more fixes for tests\r\n\r\n* update plotmatrix test outputs and passing hicbuildmatrix outputs are here - will see where they got to.\r\n\r\n* adding the fixed output for hicbuildmatrix\r\n\r\n* updating hicbuildmatrix test outputs again again.\r\n\r\n* bump hicexplorer version\r\n\r\n* fix wrappers that modify input dataset\r\n\r\n* change space to tabs in bed file\r\n\r\n* fix input matrix and update output\r\n\r\n* remove hicTADClassifier and hicTrainTADClassifier\r\n\r\n* use 3.7.5\r\n\r\n* fix version number\r\n\r\n* update filetype input + diff test\r\n\r\n---------\r\n\r\nCo-authored-by: fubar2 <ross.lazarus@gmail.com>\r\nCo-authored-by: Ross Lazarus <fubar2@users.noreply.github.com>\r\nCo-authored-by: Björn Grüning <bjoern@gruenings.eu>\r\nCo-authored-by: Bjoern Gruening <bjoern.gruening@gmail.com>","shortMessageHtmlLink":"Update HiCExplorer to 3.7.5 (<a class=\"issue-link js-issue-link\" data-error-text=\"Failed to load title\" data-id=\"2379986969\" data-permission-text=\"Title is private\" data-url=\"https://github.com/galaxyproject/tools-iuc/issues/6112\" data-hovercard-type=\"pull_request\" data-hovercard-url=\"/galaxyproject/tools-iuc/pull/6112/hovercard\" href=\"https://github.com/galaxyproject/tools-iuc/pull/6112\">#6112</a>)"}},{"before":"dd35055c76d86fe98985b5825c1751efb8208242","after":"e1af25e42839c772b023f700210013658e42dc15","ref":"refs/heads/main","pushedAt":"2024-06-30T11:17:21.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"bgruening","name":"Björn Grüning","path":"/bgruening","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/469983?s=80&v=4"},"commit":{"message":"Improve the Falco wrapper (#6116)\n\n* Improve the Falco wrapper\r\n\r\n- Mention FastQC in the description to make the tool findable when\r\n  searching for the original\r\n- Add information about advantages and current limitations compared to\r\n  FastQC to help section\r\n- Do not produce the results summary file by default, but only on demand\r\n- Simplify symlinking\r\n\r\n* Fix wrongly negated output filter","shortMessageHtmlLink":"Improve the Falco wrapper (<a class=\"issue-link js-issue-link\" data-error-text=\"Failed to load title\" data-id=\"2382190355\" data-permission-text=\"Title is private\" data-url=\"https://github.com/galaxyproject/tools-iuc/issues/6116\" data-hovercard-type=\"pull_request\" data-hovercard-url=\"/galaxyproject/tools-iuc/pull/6116/hovercard\" href=\"https://github.com/galaxyproject/tools-iuc/pull/6116\">#6116</a>)"}},{"before":"934f4b672e4f21e211a530281a973b61c20035c5","after":"dd35055c76d86fe98985b5825c1751efb8208242","ref":"refs/heads/main","pushedAt":"2024-06-27T17:10:03.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"bernt-matthias","name":"M Bernt","path":"/bernt-matthias","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/25689525?s=80&v=4"},"commit":{"message":"Fix filter_tabular tool if ``skip_lines`` is left unset (#6108)\n\n* Fix filter_tabular tool if ``skip_lines`` is left unset\r\n\r\nFixes\r\nhttps://sentry.galaxyproject.org/share/issue/2fdb36e276fd4e21889ced01da9683da/:\r\n```\r\nNotFound: cannot find 'tbl'\r\n  File \"galaxy/jobs/runners/__init__.py\", line 297, in prepare_job\r\n    job_wrapper.prepare()\r\n  File \"galaxy/jobs/__init__.py\", line 1260, in prepare\r\n    ) = tool_evaluator.build()\r\n  File \"galaxy/tools/evaluation.py\", line 586, in build\r\n    global_tool_logs(self._build_config_files, config_file, \"Building Config Files\")\r\n  File \"galaxy/tools/evaluation.py\", line 98, in global_tool_logs\r\n    raise e\r\n  File \"galaxy/tools/evaluation.py\", line 94, in global_tool_logs\r\n    return func()\r\n  File \"galaxy/tools/evaluation.py\", line 658, in _build_config_files\r\n    self.__write_workdir_file(config_filename, config_text, param_dict, is_template=is_template)\r\n  File \"galaxy/tools/evaluation.py\", line 791, in __write_workdir_file\r\n    value = fill_template(content, context=context, python_template_version=self.tool.python_template_version)\r\n  File \"galaxy/util/template.py\", line 115, in fill_template\r\n    return fill_template(\r\n  File \"galaxy/util/template.py\", line 115, in fill_template\r\n    return fill_template(\r\n  File \"galaxy/util/template.py\", line 115, in fill_template\r\n    return fill_template(\r\n  File \"galaxy/util/template.py\", line 115, in fill_template\r\n    return fill_template(\r\n  File \"galaxy/util/template.py\", line 115, in fill_template\r\n    return fill_template(\r\n  File \"galaxy/util/template.py\", line 115, in fill_template\r\n    return fill_template(\r\n  File \"galaxy/util/template.py\", line 115, in fill_template\r\n    return fill_template(\r\n  File \"galaxy/util/template.py\", line 115, in fill_template\r\n    return fill_template(\r\n  File \"galaxy/util/template.py\", line 115, in fill_template\r\n    return fill_template(\r\n  File \"galaxy/util/template.py\", line 115, in fill_template\r\n    return fill_template(\r\n  File \"galaxy/util/template.py\", line 123, in fill_template\r\n    raise first_exception or e\r\n  File \"galaxy/util/template.py\", line 87, in fill_template\r\n    return unicodify(t, log_exception=False)\r\n  File \"galaxy/util/__init__.py\", line 1183, in unicodify\r\n    value = str(value)\r\n  File \"Cheetah/Template.py\", line 1053, in __unicode__\r\n    return getattr(self, mainMethName)()\r\n  File \"cheetah_DynamicallyCompiledCheetahTemplate_1719172856_827265_49661.py\", line 100, in respond\r\n```\r\n\r\n* Add homepage_url and expect_num_outputs\r\n\r\n* Fix flake8\r\n\r\n* fix regular expressions\r\n\r\n* improve regexes\r\n\r\nthe colnames enclosed in `\"` should not contain `\"`\r\n\r\n* Bump other tools\r\n\r\n---------\r\n\r\nCo-authored-by: Matthias Bernt <m.bernt@ufz.de>","shortMessageHtmlLink":"Fix filter_tabular tool if <code>skip_lines</code> is left unset (<a class=\"issue-link js-issue-link\" data-error-text=\"Failed to load title\" data-id=\"2374794380\" data-permission-text=\"Title is private\" data-url=\"https://github.com/galaxyproject/tools-iuc/issues/6108\" data-hovercard-type=\"pull_request\" 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href=\"https://github.com/galaxyproject/tools-iuc/pull/6110\">#6110</a>)"}},{"before":"9e3708d04faea0f1be4ea8918e859d6f2c7eb31d","after":"62a738f626aee9c8e1f1c5cbd63a59b3390d4ed5","ref":"refs/heads/main","pushedAt":"2024-06-26T09:27:43.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"bernt-matthias","name":"M Bernt","path":"/bernt-matthias","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/25689525?s=80&v=4"},"commit":{"message":"maaslin2 version update to 1.16.0 (#5999)\n\n* maaslin2 version update to 1.16.0\r\n\r\n* removing test cases with fixed_effect=NULL\r\n\r\n* use of reference in test cases : maaslin2\r\n\r\n* working residuals, zip output\r\n\r\n* test cases updated\r\n\r\n* Update tools/maaslin2/macros.xml\r\n\r\nCo-authored-by: paulzierep <paul.zierep@googlemail.com>\r\n\r\n* setting --core to 1\r\n\r\n---------\r\n\r\nCo-authored-by: paulzierep <paul.zierep@googlemail.com>","shortMessageHtmlLink":"maaslin2 version update to 1.16.0 (<a class=\"issue-link js-issue-link\" data-error-text=\"Failed to load title\" data-id=\"2284398059\" data-permission-text=\"Title is private\" data-url=\"https://github.com/galaxyproject/tools-iuc/issues/5999\" data-hovercard-type=\"pull_request\" data-hovercard-url=\"/galaxyproject/tools-iuc/pull/5999/hovercard\" href=\"https://github.com/galaxyproject/tools-iuc/pull/5999\">#5999</a>)"}},{"before":"3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5","after":"9e3708d04faea0f1be4ea8918e859d6f2c7eb31d","ref":"refs/heads/main","pushedAt":"2024-06-26T09:13:04.000Z","pushType":"pr_merge","commitsCount":3,"pusher":{"login":"mvdbeek","name":"Marius van den Beek","path":"/mvdbeek","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/6804901?s=80&v=4"},"commit":{"message":"Merge pull request #6107 from abretaud/funannotate_ro_tmp\n\nFunannotate: use better tmpdir","shortMessageHtmlLink":"Merge pull request <a class=\"issue-link js-issue-link\" data-error-text=\"Failed to load title\" data-id=\"2370536991\" data-permission-text=\"Title is private\" data-url=\"https://github.com/galaxyproject/tools-iuc/issues/6107\" data-hovercard-type=\"pull_request\" data-hovercard-url=\"/galaxyproject/tools-iuc/pull/6107/hovercard\" href=\"https://github.com/galaxyproject/tools-iuc/pull/6107\">#6107</a> from abretaud/funannotate_ro_tmp"}},{"before":"d28dc08cee5d18601ba09f7e4aba4647ce2193c1","after":"3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5","ref":"refs/heads/main","pushedAt":"2024-06-21T18:31:00.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"bernt-matthias","name":"M Bernt","path":"/bernt-matthias","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/25689525?s=80&v=4"},"commit":{"message":"rename all config dirs to avoid conflicts when running parallel tasks… (#6041)\n\n* rename all config dirs to avoid conflicts when running parallel tasks in galaxy workflow\r\n\r\n* upgrade tool version suffix\r\n\r\n* Update macros.xml\r\n\r\n* Update dimet_timecourse_analysis.xml\r\n\r\n* Update dimet_pca_plot.xml\r\n\r\n* Update dimet_pca_analysis.xml\r\n\r\n* Update dimet_pca_analysis.xml\r\n\r\n* Update dimet_metabologram.xml\r\n\r\n* Update dimet_metabologram.xml\r\n\r\n* Update dimet_isotopologues_plot.xml\r\n\r\n* Update dimet_isotopologues_plot.xml\r\n\r\n* Update dimet_enrichment_plot.xml\r\n\r\n* Update dimet_differential_multigroup_analysis.xml\r\n\r\n* Update dimet_differential_multigroup_analysis.xml\r\n\r\n* Update dimet_differential_analysis.xml\r\n\r\n* Update dimet_bivariate_analysis.xml\r\n\r\n* Update dimet_abundance_plot.xml\r\n\r\n* replace __new_file_path__ by temp directory in job working directory\r\n\r\n* replace back temp by __new_file_path__ directory in job working directory\r\n\r\n* replace back temp by __new_file_path__ directory in job working directory\r\n\r\n* put back the ./config dir in macros.xml, remoce -cp option in hydra args and replace ++hydra.run.dir=XXXXX by ++hydra.run.dir=.\r\n\r\n---------\r\n\r\nCo-authored-by: M Bernt <m.bernt@ufz.de>","shortMessageHtmlLink":"rename all config dirs to avoid conflicts when running parallel tasks… ("}},{"before":"32fbe8a14173afe0b39f1483afaba958dc6cd027","after":"d28dc08cee5d18601ba09f7e4aba4647ce2193c1","ref":"refs/heads/main","pushedAt":"2024-06-21T15:32:05.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"bgruening","name":"Björn Grüning","path":"/bgruening","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/469983?s=80&v=4"},"commit":{"message":"Update Scanpy filter (new function) (#6086)\n\n* Adding new function to scanpy filter\r\n\r\n* adjusting macros for new function in scanoy filter\r\n\r\n* adding test data for new function of scanpy filter\r\n\r\n* adding new test data for scanpy filter new function\r\n\r\n* review changes to filter.xml","shortMessageHtmlLink":"Update Scanpy filter (new function) (<a class=\"issue-link js-issue-link\" data-error-text=\"Failed to load 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