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‎HISTORY.rst

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History
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-------
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.. to_doc
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---------------------
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0.75.27 (2025-03-03)
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---------------------
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* Remove usage of `defaults` conda channel (thanks to `@bernt-matthias`_).
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`Pull Request 1487`_
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* Add category "Geo Science" (thanks to `@bernt-matthias`_). `Pull Request 1483`_
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* Bump requirements for galaxy packages to 24.2 (thanks to `@jdavcs`_). `Pull
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Request 1491`_
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* Use python 3.13 for deploymen (thanks to `@bernt-matthias`_). `Pull Request 1488`_
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* Fix repository category update (thanks to `@mvdbeek`_). `Pull Request 1481`_
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---------------------
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0.75.26 (2024-09-24)
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tools - and more experimental features involving Docker and Homebrew. 7d07782_
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.. github_links
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.. _Pull Request 1487: https://github.com/galaxyproject/planemo/pull/1487
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.. _Pull Request 1483: https://github.com/galaxyproject/planemo/pull/1483
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.. _Pull Request 1491: https://github.com/galaxyproject/planemo/pull/1491
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.. _Pull Request 1488: https://github.com/galaxyproject/planemo/pull/1488
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.. _Pull Request 1481: https://github.com/galaxyproject/planemo/pull/1481
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.. _Pull Request 1474: https://github.com/galaxyproject/planemo/pull/1474
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.. _Pull Request 1452: https://github.com/galaxyproject/planemo/pull/1452
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.. _Pull Request 1473: https://github.com/galaxyproject/planemo/pull/1473
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.. _@Delphine-L: https://github.com/Delphine-L
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.. _@elichad: https://github.com/elichad
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.. _@pavanvidem: https://github.com/pavanvidem
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.. _@jdavcs: https://github.com/jdavcs

‎docs/commands/autoupdate.rst

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@@ -143,7 +143,7 @@ Auto-update tool requirements by checking against Conda and updating if newer ve
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packages.
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--conda_auto_init / --no_conda_auto_init
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Conda dependency resolution for Galaxy will
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auto install conda itself using miniconda if
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auto install conda itself using miniforge if
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not availabe on conda_prefix.
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--simultaneous_uploads / --no_simultaneous_uploads
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When uploading files to Galaxy for tool or

‎docs/commands/conda_install.rst

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and debugging.
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--conda_auto_init / --no_conda_auto_init
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Conda dependency resolution for Galaxy will
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auto install conda itself using miniconda if
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auto install conda itself using miniforge if
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not availabe on conda_prefix.
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--help Show this message and exit.
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‎docs/commands/mull.rst

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subdirectories.
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--mulled_conda_version TEXT Install a specific version of Conda before
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running the command, by default the version
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that comes with the continuumio miniconda3
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that comes with the continuumio miniforge
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image will be used under Linux and under Mac
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OS X Conda will be upgraded to to work around
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a bug in 4.2.

‎docs/commands/mulled_init.rst

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--mulled_conda_version TEXT Install a specific version of Conda before
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running the command, by default the version that
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comes with the continuumio miniconda3 image will
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comes with the continuumio miniforge image will
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be used under Linux and under Mac OS X Conda will
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be upgraded to to work around a bug in 4.2.
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--mulled_namespace TEXT Build a mulled image with the specified namespace

‎docs/commands/run.rst

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packages.
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--conda_auto_init / --no_conda_auto_init
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Conda dependency resolution for Galaxy will
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auto install conda itself using miniconda if
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auto install conda itself using miniforge if
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not availabe on conda_prefix.
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--simultaneous_uploads / --no_simultaneous_uploads
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When uploading files to Galaxy for tool or

‎docs/commands/serve.rst

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packages.
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--conda_auto_init / --no_conda_auto_init
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Conda dependency resolution for Galaxy will
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auto install conda itself using miniconda if
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auto install conda itself using miniforge if
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not availabe on conda_prefix.
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--simultaneous_uploads / --no_simultaneous_uploads
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When uploading files to Galaxy for tool or

‎docs/commands/shed_init.rst

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--remote_repository_url TEXT Specify repository remote_repository_url for
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.shed.yml.
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--homepage_url TEXT Specify repository homepage_url for .shed.yml.
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--category [Assembly|Astronomy|ChIP-seq|Climate Analysis|CLIP-seq|Combinatorial Selections|Computational chemistry|Constructive Solid Geometry|Convert Formats|Data Export|Data Managers|Data Source|Ecology|Entomology|Epigenetics|Fasta Manipulation|Fastq Manipulation|Flow Cytometry Analysis|Genome annotation|Genome editing|Genome-Wide Association Study|Genomic Interval Operations|GIS|Graphics|Imaging|InteractiveTools|Machine Learning|Materials science|Metabolomics|Metagenomics|Micro-array Analysis|Molecular Dynamics|Muon spectroscopy|Nanopore|Next Gen Mappers|NLP|Ontology Manipulation|Phylogenetics|Proteomics|RNA|SAM|Sequence Analysis|Single Cell|Spatial Omics|Statistics|Structural Materials Analysis|Synthetic Biology|Systems Biology|Text Manipulation|Tool Dependency Packages|Tool Generators|Transcriptomics|Variant Analysis|Visualization|Web Services]
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--category [Assembly|Astronomy|ChIP-seq|Climate Analysis|CLIP-seq|Combinatorial Selections|Computational chemistry|Constructive Solid Geometry|Convert Formats|Data Export|Data Managers|Data Source|Ecology|Entomology|Epigenetics|Fasta Manipulation|Fastq Manipulation|Flow Cytometry Analysis|Genome annotation|Genome editing|Genome-Wide Association Study|Genomic Interval Operations|Geo Science|GIS|Graphics|Imaging|InteractiveTools|Machine Learning|Materials science|Metabolomics|Metagenomics|Micro-array Analysis|Molecular Dynamics|Muon spectroscopy|Nanopore|Next Gen Mappers|NLP|Ontology Manipulation|Phylogenetics|Proteomics|RNA|SAM|Sequence Analysis|Single Cell|Spatial Omics|Statistics|Structural Materials Analysis|Synthetic Biology|Systems Biology|Text Manipulation|Tool Dependency Packages|Tool Generators|Transcriptomics|Variant Analysis|Visualization|Web Services]
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Specify repository category for .shed.yml (may
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specify multiple).
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--owner TEXT Tool Shed repository owner (username).

‎docs/commands/shed_serve.rst

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packages.
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--conda_auto_init / --no_conda_auto_init
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Conda dependency resolution for Galaxy will
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auto install conda itself using miniconda if
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auto install conda itself using miniforge if
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not availabe on conda_prefix.
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--simultaneous_uploads / --no_simultaneous_uploads
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When uploading files to Galaxy for tool or

‎docs/commands/shed_test.rst

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packages.
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--conda_auto_init / --no_conda_auto_init
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Conda dependency resolution for Galaxy will
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auto install conda itself using miniconda if
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auto install conda itself using miniforge if
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not availabe on conda_prefix.
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--simultaneous_uploads / --no_simultaneous_uploads
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When uploading files to Galaxy for tool or

‎docs/commands/test.rst

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packages.
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--conda_auto_init / --no_conda_auto_init
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Conda dependency resolution for Galaxy will
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auto install conda itself using miniconda if
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auto install conda itself using miniforge if
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not availabe on conda_prefix.
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--simultaneous_uploads / --no_simultaneous_uploads
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When uploading files to Galaxy for tool or

‎docs/commands/training_generate_from_wf.rst

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packages.
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--conda_auto_init / --no_conda_auto_init
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Conda dependency resolution for Galaxy will
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auto install conda itself using miniforge if
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--simultaneous_uploads / --no_simultaneous_uploads
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When uploading files to Galaxy for tool or

‎docs/commands/training_init.rst

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packages.
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--conda_auto_init / --no_conda_auto_init
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Conda dependency resolution for Galaxy will
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auto install conda itself using miniforge if
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--simultaneous_uploads / --no_simultaneous_uploads
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When uploading files to Galaxy for tool or

‎docs/commands/upload_data.rst

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packages.
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--conda_auto_init / --no_conda_auto_init
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Conda dependency resolution for Galaxy will
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auto install conda itself using miniforge if
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--simultaneous_uploads / --no_simultaneous_uploads
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When uploading files to Galaxy for tool or

‎docs/commands/workflow_convert.rst

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packages.
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--conda_auto_init / --no_conda_auto_init
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Conda dependency resolution for Galaxy will
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auto install conda itself using miniforge if
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--simultaneous_uploads / --no_simultaneous_uploads
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When uploading files to Galaxy for tool or

‎docs/commands/workflow_edit.rst

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packages.
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--conda_auto_init / --no_conda_auto_init
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Conda dependency resolution for Galaxy will
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auto install conda itself using miniforge if
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not availabe on conda_prefix.
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--simultaneous_uploads / --no_simultaneous_uploads
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‎docs/planemo.autopygen.commands.rst

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planemo.autopygen.commands package
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==================================
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Submodules
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----------
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planemo.autopygen.commands.command\_utils module
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------------------------------------------------
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.. automodule:: planemo.autopygen.commands.command_utils
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:members:
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:show-inheritance:
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:undoc-members:
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Module contents
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---------------
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.. automodule:: planemo.autopygen.commands
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:members:
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:show-inheritance:
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:undoc-members:

‎docs/planemo.autopygen.rst

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planemo.autopygen package
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=========================
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Subpackages
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-----------
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.. toctree::
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:maxdepth: 4
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planemo.autopygen.commands
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planemo.autopygen.source_file_parsing
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planemo.autopygen.xml
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Submodules
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----------
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planemo.autopygen.argument\_parser\_conversion module
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-----------------------------------------------------
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.. automodule:: planemo.autopygen.argument_parser_conversion
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:members:
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:show-inheritance:
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:undoc-members:
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planemo.autopygen.param\_info module
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------------------------------------
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.. automodule:: planemo.autopygen.param_info
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:members:
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:show-inheritance:
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:undoc-members:
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Module contents
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---------------
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.. automodule:: planemo.autopygen
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:members:
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:show-inheritance:
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:undoc-members:

‎docs/planemo.autopygen.source_file_parsing.rst

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planemo.autopygen.source\_file\_parsing package
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===============================================
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Submodules
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----------
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planemo.autopygen.source\_file\_parsing.constants module
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--------------------------------------------------------
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.. automodule:: planemo.autopygen.source_file_parsing.constants
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:members:
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:show-inheritance:
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:undoc-members:
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planemo.autopygen.source\_file\_parsing.decoy\_parser module
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------------------------------------------------------------
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.. automodule:: planemo.autopygen.source_file_parsing.decoy_parser
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:members:
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:show-inheritance:
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:undoc-members:
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planemo.autopygen.source\_file\_parsing.local\_module\_parsing module
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---------------------------------------------------------------------
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.. automodule:: planemo.autopygen.source_file_parsing.local_module_parsing
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:members:
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:show-inheritance:
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:undoc-members:
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planemo.autopygen.source\_file\_parsing.parser\_discovery\_and\_init module
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---------------------------------------------------------------------------
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.. automodule:: planemo.autopygen.source_file_parsing.parser_discovery_and_init
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:members:
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:show-inheritance:
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:undoc-members:
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planemo.autopygen.source\_file\_parsing.parsing\_commons module
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---------------------------------------------------------------
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.. automodule:: planemo.autopygen.source_file_parsing.parsing_commons
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:members:
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:show-inheritance:
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:undoc-members:
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planemo.autopygen.source\_file\_parsing.parsing\_exceptions module
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------------------------------------------------------------------
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.. automodule:: planemo.autopygen.source_file_parsing.parsing_exceptions
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:members:
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:show-inheritance:
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:undoc-members:
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planemo.autopygen.source\_file\_parsing.unknown\_names\_discovery module
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------------------------------------------------------------------------
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.. automodule:: planemo.autopygen.source_file_parsing.unknown_names_discovery
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:members:
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:show-inheritance:
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:undoc-members:
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Module contents
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---------------
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.. automodule:: planemo.autopygen.source_file_parsing
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:members:
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:show-inheritance:
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:undoc-members:

‎docs/planemo.autopygen.xml.rst

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planemo.autopygen.xml package
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=============================
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Submodules
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----------
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planemo.autopygen.xml.xml\_utils module
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---------------------------------------
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.. automodule:: planemo.autopygen.xml.xml_utils
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:members:
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:show-inheritance:
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:undoc-members:
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Module contents
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---------------
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.. automodule:: planemo.autopygen.xml
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:members:
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:show-inheritance:
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:undoc-members:

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