mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
Merge pull request #10963 from nsoranzo/fix_docs_CI
Various documentation fixes
This commit is contained in:
John Chilton
@@ -27,7 +27,7 @@ jobs:
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path: ~/.cache/pip
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key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('requirements.txt') }}
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- name: Install Python dependencies
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run: pip install -r requirements.txt -r lib/galaxy/dependencies/dev-requirements.txt sphinxcontrib-simpleversioning awscli
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run: pip install -r requirements.txt -r lib/galaxy/dependencies/dev-requirements.txt sphinxcontrib-simpleversioning
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- name: Add Google Analytics to doc/source/conf.py
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run: |
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sed -i -e "/html_theme_options = {/a\
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@@ -50,6 +50,7 @@ jobs:
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AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
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AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
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run: |
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pip install awscli
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case "$TARGET_BRANCH" in
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release_[[:digit:]][[:digit:]].[[:digit:]][[:digit:]]|master)
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UPLOAD_DIR=$TARGET_BRANCH
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@@ -200,7 +200,7 @@ Conda Dependency Resolver
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The ``conda`` directive can be used to configure a conda dependency resolver.
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This resolver can be configured with the following options. For a very detailed
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discussion of Conda dependency resolution, check out the :ref:`Conda FAQ <conda_faq>`.
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discussion of Conda dependency resolution, check out the :doc:`Conda FAQ <conda_faq>`.
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prefix
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The conda_prefix used to locate dependencies in (default: ``<tool_dependency_dir>/_conda``).
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@@ -1,6 +1,6 @@
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# Supported Python versions
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Galaxy's core functionality is currently supported on Python **>=3.5** .
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Galaxy's core functionality is currently supported on Python **>=3.6** .
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If Galaxy complains about the version of Python you are using:
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@@ -3,7 +3,7 @@ Containers for Tool Dependencies
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================================
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Galaxy tools (also called wrappers) are able to use Conda packages
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(see more information in our `Galaxy Conda documentation`_) and Docker containers as dependency resolvers.
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(see more information in our :doc:`Galaxy Conda documentation <../conda_faq>`) and Docker containers as dependency resolvers.
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The IUC_ recommends to use Conda packages as the primary dependency resolver, mainly because Docker is not
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available on every (HPC-) system. Conda on the other hand can be installed by Galaxy and maintained
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entirely in user-space. Nevertheless, Docker and containers in general have some unique features and
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@@ -159,7 +159,6 @@ Containers, once generated, should be tested. This can be achieved by affixing `
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$ mulled-singularity-testing --container-list list.txt --filepath /tmp/sing/ --installation /usr/local/bin/singularity --logfile test-output.txt
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.. _Galaxy Conda documentation: ./conda_faq.rst
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.. _IUC: https://galaxyproject.org/iuc/
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.. _container annotation: https://github.com/galaxyproject/galaxy/blob/dev/test/functional/tools/catDocker.xml#L4
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.. _BioContainers: https://github.com/biocontainers
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@@ -2,9 +2,9 @@ galaxy.actions package
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======================
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.. automodule:: galaxy.actions
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||||
:members:
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||||
:undoc-members:
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||||
:show-inheritance:
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||||
:members:
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||||
:undoc-members:
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||||
:show-inheritance:
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||||
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||||
Submodules
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----------
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@@ -13,16 +13,14 @@ galaxy.actions.admin module
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---------------------------
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.. automodule:: galaxy.actions.admin
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:members:
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||||
:undoc-members:
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||||
:show-inheritance:
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||||
:members:
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||||
:undoc-members:
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||||
:show-inheritance:
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||||
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galaxy.actions.library module
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-----------------------------
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.. automodule:: galaxy.actions.library
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:members:
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||||
:undoc-members:
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||||
:show-inheritance:
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||||
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||||
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||||
:members:
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||||
:undoc-members:
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||||
:show-inheritance:
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||||
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@@ -2,9 +2,9 @@ galaxy.auth.providers package
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=============================
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.. automodule:: galaxy.auth.providers
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:members:
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:undoc-members:
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||||
:show-inheritance:
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||||
:members:
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||||
:undoc-members:
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||||
:show-inheritance:
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||||
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||||
Submodules
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----------
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@@ -13,32 +13,30 @@ galaxy.auth.providers.alwaysreject module
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-----------------------------------------
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.. automodule:: galaxy.auth.providers.alwaysreject
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:members:
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:undoc-members:
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:show-inheritance:
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||||
:members:
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:undoc-members:
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||||
:show-inheritance:
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||||
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galaxy.auth.providers.ldap\_ad module
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-------------------------------------
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.. automodule:: galaxy.auth.providers.ldap_ad
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:members:
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:undoc-members:
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:show-inheritance:
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:members:
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:undoc-members:
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:show-inheritance:
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galaxy.auth.providers.localdb module
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------------------------------------
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.. automodule:: galaxy.auth.providers.localdb
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:members:
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:undoc-members:
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:show-inheritance:
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:members:
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:undoc-members:
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:show-inheritance:
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galaxy.auth.providers.pam\_auth module
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--------------------------------------
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.. automodule:: galaxy.auth.providers.pam_auth
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:members:
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:undoc-members:
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:show-inheritance:
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:members:
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:undoc-members:
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:show-inheritance:
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@@ -2,16 +2,17 @@ galaxy.auth package
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===================
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.. automodule:: galaxy.auth
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:members:
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:undoc-members:
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:show-inheritance:
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:members:
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:undoc-members:
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:show-inheritance:
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Subpackages
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-----------
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.. toctree::
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:maxdepth: 4
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galaxy.auth.providers
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galaxy.auth.providers
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Submodules
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----------
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@@ -20,8 +21,6 @@ galaxy.auth.util module
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-----------------------
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.. automodule:: galaxy.auth.util
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:members:
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:undoc-members:
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:show-inheritance:
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:members:
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:undoc-members:
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:show-inheritance:
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@@ -2,9 +2,9 @@ galaxy.authnz package
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=====================
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.. automodule:: galaxy.authnz
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:members:
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:undoc-members:
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:show-inheritance:
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:members:
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:undoc-members:
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:show-inheritance:
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Submodules
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----------
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@@ -13,24 +13,22 @@ galaxy.authnz.custos\_authnz module
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-----------------------------------
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.. automodule:: galaxy.authnz.custos_authnz
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:members:
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:undoc-members:
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:show-inheritance:
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:members:
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:undoc-members:
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:show-inheritance:
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galaxy.authnz.managers module
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-----------------------------
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.. automodule:: galaxy.authnz.managers
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:members:
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:undoc-members:
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:show-inheritance:
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:members:
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:undoc-members:
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||||
:show-inheritance:
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galaxy.authnz.psa\_authnz module
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--------------------------------
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.. automodule:: galaxy.authnz.psa_authnz
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:members:
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:undoc-members:
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||||
:show-inheritance:
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||||
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||||
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:members:
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||||
:undoc-members:
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||||
:show-inheritance:
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||||
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@@ -2,9 +2,9 @@ galaxy.config package
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=====================
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.. automodule:: galaxy.config
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:members:
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||||
:undoc-members:
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||||
:show-inheritance:
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||||
:members:
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||||
:undoc-members:
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||||
:show-inheritance:
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||||
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Submodules
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----------
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@@ -13,24 +13,22 @@ galaxy.config.config\_manage module
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-----------------------------------
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.. automodule:: galaxy.config.config_manage
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:members:
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||||
:undoc-members:
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||||
:show-inheritance:
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||||
:members:
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||||
:undoc-members:
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||||
:show-inheritance:
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galaxy.config.schema module
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---------------------------
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.. automodule:: galaxy.config.schema
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:members:
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||||
:undoc-members:
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||||
:show-inheritance:
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||||
:members:
|
||||
:undoc-members:
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||||
:show-inheritance:
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||||
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galaxy.config.script module
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---------------------------
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.. automodule:: galaxy.config.script
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:members:
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||||
:undoc-members:
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||||
:show-inheritance:
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||||
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||||
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||||
:members:
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||||
:undoc-members:
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||||
:show-inheritance:
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||||
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@@ -2,9 +2,9 @@ galaxy.containers package
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=========================
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.. automodule:: galaxy.containers
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:members:
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||||
:undoc-members:
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||||
:show-inheritance:
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||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
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||||
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||||
Submodules
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||||
----------
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@@ -13,32 +13,30 @@ galaxy.containers.docker module
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-------------------------------
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.. automodule:: galaxy.containers.docker
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:members:
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||||
:undoc-members:
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||||
:show-inheritance:
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||||
:members:
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||||
:undoc-members:
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||||
:show-inheritance:
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||||
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||||
galaxy.containers.docker\_decorators module
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-------------------------------------------
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.. automodule:: galaxy.containers.docker_decorators
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:members:
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||||
:undoc-members:
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||||
:show-inheritance:
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||||
:members:
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||||
:undoc-members:
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||||
:show-inheritance:
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||||
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||||
galaxy.containers.docker\_model module
|
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--------------------------------------
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||||
.. automodule:: galaxy.containers.docker_model
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||||
:members:
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||||
:undoc-members:
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||||
:show-inheritance:
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||||
:members:
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||||
:undoc-members:
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||||
:show-inheritance:
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||||
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||||
galaxy.containers.docker\_swarm module
|
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--------------------------------------
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.. automodule:: galaxy.containers.docker_swarm
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:members:
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||||
:undoc-members:
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||||
:show-inheritance:
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||||
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||||
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||||
:members:
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||||
:undoc-members:
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||||
:show-inheritance:
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||||
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||||
@@ -2,9 +2,9 @@ galaxy.datatypes.converters package
|
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===================================
|
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.. automodule:: galaxy.datatypes.converters
|
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:members:
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||||
:undoc-members:
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||||
:show-inheritance:
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||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
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||||
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||||
Submodules
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----------
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@@ -13,232 +13,230 @@ galaxy.datatypes.converters.bed\_to\_gff\_converter module
|
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----------------------------------------------------------
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.. automodule:: galaxy.datatypes.converters.bed_to_gff_converter
|
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:members:
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||||
:undoc-members:
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||||
:show-inheritance:
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||||
:members:
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||||
:undoc-members:
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||||
:show-inheritance:
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||||
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||||
galaxy.datatypes.converters.bgzip module
|
||||
----------------------------------------
|
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|
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.. automodule:: galaxy.datatypes.converters.bgzip
|
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:members:
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||||
:undoc-members:
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||||
:show-inheritance:
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||||
:members:
|
||||
:undoc-members:
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||||
:show-inheritance:
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||||
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||||
galaxy.datatypes.converters.cram\_to\_bam module
|
||||
------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.converters.cram_to_bam
|
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:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
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||||
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||||
galaxy.datatypes.converters.fasta\_to\_len module
|
||||
-------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.converters.fasta_to_len
|
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:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
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||||
galaxy.datatypes.converters.fasta\_to\_tabular\_converter module
|
||||
----------------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.converters.fasta_to_tabular_converter
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.datatypes.converters.fastq\_to\_fqtoc module
|
||||
---------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.converters.fastq_to_fqtoc
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.datatypes.converters.fastqsolexa\_to\_fasta\_converter module
|
||||
--------------------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.converters.fastqsolexa_to_fasta_converter
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.datatypes.converters.fastqsolexa\_to\_qual\_converter module
|
||||
-------------------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.converters.fastqsolexa_to_qual_converter
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.datatypes.converters.gff\_to\_bed\_converter module
|
||||
----------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.converters.gff_to_bed_converter
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.datatypes.converters.gff\_to\_interval\_index\_converter module
|
||||
----------------------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.converters.gff_to_interval_index_converter
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.datatypes.converters.interval\_to\_bed\_converter module
|
||||
---------------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.converters.interval_to_bed_converter
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.datatypes.converters.interval\_to\_bedstrict\_converter module
|
||||
---------------------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.converters.interval_to_bedstrict_converter
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.datatypes.converters.interval\_to\_fli module
|
||||
----------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.converters.interval_to_fli
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.datatypes.converters.interval\_to\_interval\_index\_converter module
|
||||
---------------------------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.converters.interval_to_interval_index_converter
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.datatypes.converters.interval\_to\_tabix\_converter module
|
||||
-----------------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.converters.interval_to_tabix_converter
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.datatypes.converters.lped\_to\_fped\_converter module
|
||||
------------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.converters.lped_to_fped_converter
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.datatypes.converters.lped\_to\_pbed\_converter module
|
||||
------------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.converters.lped_to_pbed_converter
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.datatypes.converters.maf\_to\_fasta\_converter module
|
||||
------------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.converters.maf_to_fasta_converter
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.datatypes.converters.maf\_to\_interval\_converter module
|
||||
---------------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.converters.maf_to_interval_converter
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.datatypes.converters.pbed\_ldreduced\_converter module
|
||||
-------------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.converters.pbed_ldreduced_converter
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.datatypes.converters.pbed\_to\_lped\_converter module
|
||||
------------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.converters.pbed_to_lped_converter
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.datatypes.converters.picard\_interval\_list\_to\_bed6\_converter module
|
||||
------------------------------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.converters.picard_interval_list_to_bed6_converter
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.datatypes.converters.pileup\_to\_interval\_index\_converter module
|
||||
-------------------------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.converters.pileup_to_interval_index_converter
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.datatypes.converters.ref\_to\_seq\_taxonomy\_converter module
|
||||
--------------------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.converters.ref_to_seq_taxonomy_converter
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.datatypes.converters.tabular\_csv module
|
||||
-----------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.converters.tabular_csv
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.datatypes.converters.tabular\_to\_dbnsfp module
|
||||
------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.converters.tabular_to_dbnsfp
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.datatypes.converters.vcf\_to\_interval\_index\_converter module
|
||||
----------------------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.converters.vcf_to_interval_index_converter
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.datatypes.converters.vcf\_to\_vcf\_bgzip module
|
||||
------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.converters.vcf_to_vcf_bgzip
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.datatypes.converters.wiggle\_to\_simple\_converter module
|
||||
----------------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.converters.wiggle_to_simple_converter
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
@@ -2,9 +2,9 @@ galaxy.datatypes.dataproviders package
|
||||
======================================
|
||||
|
||||
.. automodule:: galaxy.datatypes.dataproviders
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Submodules
|
||||
----------
|
||||
@@ -13,72 +13,70 @@ galaxy.datatypes.dataproviders.base module
|
||||
------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.dataproviders.base
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.datatypes.dataproviders.chunk module
|
||||
-------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.dataproviders.chunk
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.datatypes.dataproviders.column module
|
||||
--------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.dataproviders.column
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.datatypes.dataproviders.dataset module
|
||||
---------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.dataproviders.dataset
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.datatypes.dataproviders.decorators module
|
||||
------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.dataproviders.decorators
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.datatypes.dataproviders.exceptions module
|
||||
------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.dataproviders.exceptions
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.datatypes.dataproviders.external module
|
||||
----------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.dataproviders.external
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.datatypes.dataproviders.hierarchy module
|
||||
-----------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.dataproviders.hierarchy
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.datatypes.dataproviders.line module
|
||||
------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.dataproviders.line
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
@@ -2,9 +2,9 @@ galaxy.datatypes.display\_applications package
|
||||
==============================================
|
||||
|
||||
.. automodule:: galaxy.datatypes.display_applications
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Submodules
|
||||
----------
|
||||
@@ -13,24 +13,22 @@ galaxy.datatypes.display\_applications.application module
|
||||
---------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.display_applications.application
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.datatypes.display\_applications.parameters module
|
||||
--------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.display_applications.parameters
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.datatypes.display\_applications.util module
|
||||
--------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.display_applications.util
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
+135
-120
@@ -2,19 +2,20 @@ galaxy.datatypes package
|
||||
========================
|
||||
|
||||
.. automodule:: galaxy.datatypes
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Subpackages
|
||||
-----------
|
||||
|
||||
.. toctree::
|
||||
:maxdepth: 4
|
||||
|
||||
galaxy.datatypes.converters
|
||||
galaxy.datatypes.dataproviders
|
||||
galaxy.datatypes.display_applications
|
||||
galaxy.datatypes.util
|
||||
galaxy.datatypes.converters
|
||||
galaxy.datatypes.dataproviders
|
||||
galaxy.datatypes.display_applications
|
||||
galaxy.datatypes.util
|
||||
|
||||
Submodules
|
||||
----------
|
||||
@@ -23,296 +24,310 @@ galaxy.datatypes.annotation module
|
||||
----------------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.annotation
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.datatypes.anvio module
|
||||
-----------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.anvio
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.datatypes.assembly module
|
||||
--------------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.assembly
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.datatypes.binary module
|
||||
------------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.binary
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.datatypes.blast module
|
||||
-----------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.blast
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.datatypes.checkers module
|
||||
--------------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.checkers
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.datatypes.chrominfo module
|
||||
---------------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.chrominfo
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.datatypes.constructive\_solid\_geometry module
|
||||
-----------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.constructive_solid_geometry
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.datatypes.coverage module
|
||||
--------------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.coverage
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.datatypes.data module
|
||||
----------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.data
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.datatypes.genetics module
|
||||
--------------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.genetics
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.datatypes.gis module
|
||||
---------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.gis
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.datatypes.graph module
|
||||
-----------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.graph
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.datatypes.images module
|
||||
------------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.images
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.datatypes.interval module
|
||||
--------------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.interval
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.datatypes.isa module
|
||||
---------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.isa
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.datatypes.media module
|
||||
-----------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.media
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.datatypes.metadata module
|
||||
--------------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.metadata
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.datatypes.microarrays module
|
||||
-----------------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.microarrays
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.datatypes.molecules module
|
||||
---------------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.molecules
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.datatypes.mothur module
|
||||
------------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.mothur
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.datatypes.msa module
|
||||
---------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.msa
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.datatypes.neo4j module
|
||||
-----------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.neo4j
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.datatypes.ngsindex module
|
||||
--------------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.ngsindex
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.datatypes.phylip module
|
||||
------------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.phylip
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.datatypes.plant\_tribes module
|
||||
-------------------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.plant_tribes
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.datatypes.proteomics module
|
||||
----------------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.proteomics
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.datatypes.qualityscore module
|
||||
------------------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.qualityscore
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.datatypes.registry module
|
||||
--------------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.registry
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.datatypes.sequence module
|
||||
--------------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.sequence
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.datatypes.sniff module
|
||||
-----------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.sniff
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.datatypes.spaln module
|
||||
-----------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.spaln
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.datatypes.speech module
|
||||
------------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.speech
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.datatypes.tabular module
|
||||
-------------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.tabular
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.datatypes.text module
|
||||
----------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.text
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.datatypes.tracks module
|
||||
------------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.tracks
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.datatypes.triples module
|
||||
-------------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.triples
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.datatypes.upload\_util module
|
||||
------------------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.upload_util
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.datatypes.xml module
|
||||
---------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.xml
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
@@ -2,9 +2,9 @@ galaxy.datatypes.util package
|
||||
=============================
|
||||
|
||||
.. automodule:: galaxy.datatypes.util
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Submodules
|
||||
----------
|
||||
@@ -13,24 +13,22 @@ galaxy.datatypes.util.generic\_util module
|
||||
------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.util.generic_util
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.datatypes.util.gff\_util module
|
||||
--------------------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.util.gff_util
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.datatypes.util.maf\_utilities module
|
||||
-------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.util.maf_utilities
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
@@ -2,7 +2,6 @@ galaxy.dependencies package
|
||||
===========================
|
||||
|
||||
.. automodule:: galaxy.dependencies
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
@@ -2,7 +2,6 @@ galaxy.eggs package
|
||||
===================
|
||||
|
||||
.. automodule:: galaxy.eggs
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
@@ -2,9 +2,9 @@ galaxy.exceptions package
|
||||
=========================
|
||||
|
||||
.. automodule:: galaxy.exceptions
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Submodules
|
||||
----------
|
||||
@@ -13,8 +13,6 @@ galaxy.exceptions.error\_codes module
|
||||
-------------------------------------
|
||||
|
||||
.. automodule:: galaxy.exceptions.error_codes
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
@@ -0,0 +1,15 @@
|
||||
galaxy.files package
|
||||
====================
|
||||
|
||||
.. automodule:: galaxy.files
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Subpackages
|
||||
-----------
|
||||
|
||||
.. toctree::
|
||||
:maxdepth: 4
|
||||
|
||||
galaxy.files.sources
|
||||
@@ -0,0 +1,50 @@
|
||||
galaxy.files.sources package
|
||||
============================
|
||||
|
||||
.. automodule:: galaxy.files.sources
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Submodules
|
||||
----------
|
||||
|
||||
galaxy.files.sources.dropbox module
|
||||
-----------------------------------
|
||||
|
||||
.. automodule:: galaxy.files.sources.dropbox
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.files.sources.galaxy module
|
||||
----------------------------------
|
||||
|
||||
.. automodule:: galaxy.files.sources.galaxy
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.files.sources.posix module
|
||||
---------------------------------
|
||||
|
||||
.. automodule:: galaxy.files.sources.posix
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.files.sources.s3 module
|
||||
------------------------------
|
||||
|
||||
.. automodule:: galaxy.files.sources.s3
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.files.sources.webdav module
|
||||
----------------------------------
|
||||
|
||||
.. automodule:: galaxy.files.sources.webdav
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
@@ -2,9 +2,9 @@ galaxy.forms package
|
||||
====================
|
||||
|
||||
.. automodule:: galaxy.forms
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Submodules
|
||||
----------
|
||||
@@ -13,8 +13,6 @@ galaxy.forms.forms module
|
||||
-------------------------
|
||||
|
||||
.. automodule:: galaxy.forms.forms
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
@@ -2,9 +2,9 @@ galaxy.job\_execution.ports package
|
||||
===================================
|
||||
|
||||
.. automodule:: galaxy.job_execution.ports
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Submodules
|
||||
----------
|
||||
@@ -13,8 +13,6 @@ galaxy.job\_execution.ports.view module
|
||||
---------------------------------------
|
||||
|
||||
.. automodule:: galaxy.job_execution.ports.view
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
@@ -2,16 +2,17 @@ galaxy.job\_execution package
|
||||
=============================
|
||||
|
||||
.. automodule:: galaxy.job_execution
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Subpackages
|
||||
-----------
|
||||
|
||||
.. toctree::
|
||||
:maxdepth: 4
|
||||
|
||||
galaxy.job_execution.ports
|
||||
galaxy.job_execution.ports
|
||||
|
||||
Submodules
|
||||
----------
|
||||
@@ -20,24 +21,22 @@ galaxy.job\_execution.datasets module
|
||||
-------------------------------------
|
||||
|
||||
.. automodule:: galaxy.job_execution.datasets
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.job\_execution.output\_collect module
|
||||
--------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.job_execution.output_collect
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.job\_execution.setup module
|
||||
----------------------------------
|
||||
|
||||
.. automodule:: galaxy.job_execution.setup
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
@@ -2,9 +2,9 @@ galaxy.job\_metrics.collectl package
|
||||
====================================
|
||||
|
||||
.. automodule:: galaxy.job_metrics.collectl
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Submodules
|
||||
----------
|
||||
@@ -13,32 +13,30 @@ galaxy.job\_metrics.collectl.cli module
|
||||
---------------------------------------
|
||||
|
||||
.. automodule:: galaxy.job_metrics.collectl.cli
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.job\_metrics.collectl.processes module
|
||||
---------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.job_metrics.collectl.processes
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.job\_metrics.collectl.stats module
|
||||
-----------------------------------------
|
||||
|
||||
.. automodule:: galaxy.job_metrics.collectl.stats
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.job\_metrics.collectl.subsystems module
|
||||
----------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.job_metrics.collectl.subsystems
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
@@ -2,9 +2,9 @@ galaxy.job\_metrics.instrumenters package
|
||||
=========================================
|
||||
|
||||
.. automodule:: galaxy.job_metrics.instrumenters
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Submodules
|
||||
----------
|
||||
@@ -13,64 +13,62 @@ galaxy.job\_metrics.instrumenters.cgroup module
|
||||
-----------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.job_metrics.instrumenters.cgroup
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.job\_metrics.instrumenters.collectl module
|
||||
-------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.job_metrics.instrumenters.collectl
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.job\_metrics.instrumenters.core module
|
||||
---------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.job_metrics.instrumenters.core
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.job\_metrics.instrumenters.cpuinfo module
|
||||
------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.job_metrics.instrumenters.cpuinfo
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.job\_metrics.instrumenters.env module
|
||||
--------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.job_metrics.instrumenters.env
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.job\_metrics.instrumenters.hostname module
|
||||
-------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.job_metrics.instrumenters.hostname
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.job\_metrics.instrumenters.meminfo module
|
||||
------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.job_metrics.instrumenters.meminfo
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.job\_metrics.instrumenters.uname module
|
||||
----------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.job_metrics.instrumenters.uname
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
@@ -2,17 +2,18 @@ galaxy.job\_metrics package
|
||||
===========================
|
||||
|
||||
.. automodule:: galaxy.job_metrics
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Subpackages
|
||||
-----------
|
||||
|
||||
.. toctree::
|
||||
:maxdepth: 4
|
||||
|
||||
galaxy.job_metrics.collectl
|
||||
galaxy.job_metrics.instrumenters
|
||||
galaxy.job_metrics.collectl
|
||||
galaxy.job_metrics.instrumenters
|
||||
|
||||
Submodules
|
||||
----------
|
||||
@@ -21,8 +22,6 @@ galaxy.job\_metrics.formatting module
|
||||
-------------------------------------
|
||||
|
||||
.. automodule:: galaxy.job_metrics.formatting
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
@@ -2,9 +2,9 @@ galaxy.jobs.actions package
|
||||
===========================
|
||||
|
||||
.. automodule:: galaxy.jobs.actions
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Submodules
|
||||
----------
|
||||
@@ -13,8 +13,6 @@ galaxy.jobs.actions.post module
|
||||
-------------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.actions.post
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
@@ -2,19 +2,20 @@ galaxy.jobs package
|
||||
===================
|
||||
|
||||
.. automodule:: galaxy.jobs
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Subpackages
|
||||
-----------
|
||||
|
||||
.. toctree::
|
||||
:maxdepth: 4
|
||||
|
||||
galaxy.jobs.actions
|
||||
galaxy.jobs.rules
|
||||
galaxy.jobs.runners
|
||||
galaxy.jobs.splitters
|
||||
galaxy.jobs.actions
|
||||
galaxy.jobs.rules
|
||||
galaxy.jobs.runners
|
||||
galaxy.jobs.splitters
|
||||
|
||||
Submodules
|
||||
----------
|
||||
@@ -23,64 +24,62 @@ galaxy.jobs.command\_factory module
|
||||
-----------------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.command_factory
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.jobs.dynamic\_tool\_destination module
|
||||
---------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.dynamic_tool_destination
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.jobs.handler module
|
||||
--------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.handler
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.jobs.manager module
|
||||
--------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.manager
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.jobs.mapper module
|
||||
-------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.mapper
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.jobs.rule\_helper module
|
||||
-------------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.rule_helper
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.jobs.stock\_rules module
|
||||
-------------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.stock_rules
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.jobs.transfer\_manager module
|
||||
------------------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.transfer_manager
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
@@ -2,7 +2,6 @@ galaxy.jobs.rules package
|
||||
=========================
|
||||
|
||||
.. automodule:: galaxy.jobs.rules
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
@@ -2,17 +2,18 @@ galaxy.jobs.runners package
|
||||
===========================
|
||||
|
||||
.. automodule:: galaxy.jobs.runners
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Subpackages
|
||||
-----------
|
||||
|
||||
.. toctree::
|
||||
:maxdepth: 4
|
||||
|
||||
galaxy.jobs.runners.state_handlers
|
||||
galaxy.jobs.runners.util
|
||||
galaxy.jobs.runners.state_handlers
|
||||
galaxy.jobs.runners.util
|
||||
|
||||
Submodules
|
||||
----------
|
||||
@@ -21,104 +22,102 @@ galaxy.jobs.runners.chronos module
|
||||
----------------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.runners.chronos
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.jobs.runners.cli module
|
||||
------------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.runners.cli
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.jobs.runners.condor module
|
||||
---------------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.runners.condor
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.jobs.runners.drmaa module
|
||||
--------------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.runners.drmaa
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.jobs.runners.godocker module
|
||||
-----------------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.runners.godocker
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.jobs.runners.kubernetes module
|
||||
-------------------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.runners.kubernetes
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.jobs.runners.local module
|
||||
--------------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.runners.local
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.jobs.runners.pbs module
|
||||
------------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.runners.pbs
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.jobs.runners.pulsar module
|
||||
---------------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.runners.pulsar
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.jobs.runners.slurm module
|
||||
--------------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.runners.slurm
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.jobs.runners.state\_handler\_factory module
|
||||
--------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.runners.state_handler_factory
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.jobs.runners.tasks module
|
||||
--------------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.runners.tasks
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.jobs.runners.univa module
|
||||
--------------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.runners.univa
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
@@ -2,9 +2,9 @@ galaxy.jobs.runners.state\_handlers package
|
||||
===========================================
|
||||
|
||||
.. automodule:: galaxy.jobs.runners.state_handlers
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Submodules
|
||||
----------
|
||||
@@ -13,8 +13,6 @@ galaxy.jobs.runners.state\_handlers.resubmit module
|
||||
---------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.runners.state_handlers.resubmit
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
@@ -2,9 +2,9 @@ galaxy.jobs.runners.util.cli.job package
|
||||
========================================
|
||||
|
||||
.. automodule:: galaxy.jobs.runners.util.cli.job
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Submodules
|
||||
----------
|
||||
@@ -13,32 +13,30 @@ galaxy.jobs.runners.util.cli.job.lsf module
|
||||
-------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.runners.util.cli.job.lsf
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.jobs.runners.util.cli.job.slurm module
|
||||
---------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.runners.util.cli.job.slurm
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.jobs.runners.util.cli.job.slurm\_torque module
|
||||
-----------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.runners.util.cli.job.slurm_torque
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.jobs.runners.util.cli.job.torque module
|
||||
----------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.runners.util.cli.job.torque
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
@@ -2,17 +2,18 @@ galaxy.jobs.runners.util.cli package
|
||||
====================================
|
||||
|
||||
.. automodule:: galaxy.jobs.runners.util.cli
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Subpackages
|
||||
-----------
|
||||
|
||||
.. toctree::
|
||||
:maxdepth: 4
|
||||
|
||||
galaxy.jobs.runners.util.cli.job
|
||||
galaxy.jobs.runners.util.cli.shell
|
||||
galaxy.jobs.runners.util.cli.job
|
||||
galaxy.jobs.runners.util.cli.shell
|
||||
|
||||
Submodules
|
||||
----------
|
||||
@@ -21,8 +22,6 @@ galaxy.jobs.runners.util.cli.factory module
|
||||
-------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.runners.util.cli.factory
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
@@ -2,9 +2,9 @@ galaxy.jobs.runners.util.cli.shell package
|
||||
==========================================
|
||||
|
||||
.. automodule:: galaxy.jobs.runners.util.cli.shell
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Submodules
|
||||
----------
|
||||
@@ -13,16 +13,14 @@ galaxy.jobs.runners.util.cli.shell.local module
|
||||
-----------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.runners.util.cli.shell.local
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.jobs.runners.util.cli.shell.rsh module
|
||||
---------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.runners.util.cli.shell.rsh
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
@@ -2,7 +2,6 @@ galaxy.jobs.runners.util.condor package
|
||||
=======================================
|
||||
|
||||
.. automodule:: galaxy.jobs.runners.util.condor
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
@@ -2,7 +2,6 @@ galaxy.jobs.runners.util.job\_script package
|
||||
============================================
|
||||
|
||||
.. automodule:: galaxy.jobs.runners.util.job_script
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
@@ -2,18 +2,19 @@ galaxy.jobs.runners.util package
|
||||
================================
|
||||
|
||||
.. automodule:: galaxy.jobs.runners.util
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Subpackages
|
||||
-----------
|
||||
|
||||
.. toctree::
|
||||
:maxdepth: 4
|
||||
|
||||
galaxy.jobs.runners.util.cli
|
||||
galaxy.jobs.runners.util.condor
|
||||
galaxy.jobs.runners.util.job_script
|
||||
galaxy.jobs.runners.util.cli
|
||||
galaxy.jobs.runners.util.condor
|
||||
galaxy.jobs.runners.util.job_script
|
||||
|
||||
Submodules
|
||||
----------
|
||||
@@ -22,48 +23,46 @@ galaxy.jobs.runners.util.env module
|
||||
-----------------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.runners.util.env
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.jobs.runners.util.external module
|
||||
----------------------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.runners.util.external
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.jobs.runners.util.kill module
|
||||
------------------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.runners.util.kill
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.jobs.runners.util.process\_groups module
|
||||
-----------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.runners.util.process_groups
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.jobs.runners.util.pykube\_util module
|
||||
--------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.runners.util.pykube_util
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.jobs.runners.util.sudo module
|
||||
------------------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.runners.util.sudo
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
@@ -2,9 +2,9 @@ galaxy.jobs.splitters package
|
||||
=============================
|
||||
|
||||
.. automodule:: galaxy.jobs.splitters
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Submodules
|
||||
----------
|
||||
@@ -13,16 +13,14 @@ galaxy.jobs.splitters.basic module
|
||||
----------------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.splitters.basic
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.jobs.splitters.multi module
|
||||
----------------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.splitters.multi
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
+122
-116
@@ -2,9 +2,9 @@ galaxy.managers package
|
||||
=======================
|
||||
|
||||
.. automodule:: galaxy.managers
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Submodules
|
||||
----------
|
||||
@@ -13,296 +13,302 @@ galaxy.managers.annotatable module
|
||||
----------------------------------
|
||||
|
||||
.. automodule:: galaxy.managers.annotatable
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.managers.api\_keys module
|
||||
--------------------------------
|
||||
|
||||
.. automodule:: galaxy.managers.api_keys
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.managers.base module
|
||||
---------------------------
|
||||
|
||||
.. automodule:: galaxy.managers.base
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.managers.citations module
|
||||
--------------------------------
|
||||
|
||||
.. automodule:: galaxy.managers.citations
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.managers.cloud module
|
||||
----------------------------
|
||||
|
||||
.. automodule:: galaxy.managers.cloud
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.managers.cloudauthzs module
|
||||
----------------------------------
|
||||
|
||||
.. automodule:: galaxy.managers.cloudauthzs
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.managers.collections module
|
||||
----------------------------------
|
||||
|
||||
.. automodule:: galaxy.managers.collections
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.managers.collections\_util module
|
||||
----------------------------------------
|
||||
|
||||
.. automodule:: galaxy.managers.collections_util
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.managers.configuration module
|
||||
------------------------------------
|
||||
|
||||
.. automodule:: galaxy.managers.configuration
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.managers.containers module
|
||||
---------------------------------
|
||||
|
||||
.. automodule:: galaxy.managers.containers
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.managers.context module
|
||||
------------------------------
|
||||
|
||||
.. automodule:: galaxy.managers.context
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.managers.datasets module
|
||||
-------------------------------
|
||||
|
||||
.. automodule:: galaxy.managers.datasets
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.managers.deletable module
|
||||
--------------------------------
|
||||
|
||||
.. automodule:: galaxy.managers.deletable
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.managers.executables module
|
||||
----------------------------------
|
||||
|
||||
.. automodule:: galaxy.managers.executables
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.managers.folders module
|
||||
------------------------------
|
||||
|
||||
.. automodule:: galaxy.managers.folders
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.managers.hdas module
|
||||
---------------------------
|
||||
|
||||
.. automodule:: galaxy.managers.hdas
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.managers.hdcas module
|
||||
----------------------------
|
||||
|
||||
.. automodule:: galaxy.managers.hdcas
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.managers.histories module
|
||||
--------------------------------
|
||||
|
||||
.. automodule:: galaxy.managers.histories
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.managers.history\_contents module
|
||||
----------------------------------------
|
||||
|
||||
.. automodule:: galaxy.managers.history_contents
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.managers.interactivetool module
|
||||
--------------------------------------
|
||||
|
||||
.. automodule:: galaxy.managers.interactivetool
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.managers.jobs module
|
||||
---------------------------
|
||||
|
||||
.. automodule:: galaxy.managers.jobs
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.managers.lddas module
|
||||
----------------------------
|
||||
|
||||
.. automodule:: galaxy.managers.lddas
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.managers.libraries module
|
||||
--------------------------------
|
||||
|
||||
.. automodule:: galaxy.managers.libraries
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.managers.library\_datasets module
|
||||
----------------------------------------
|
||||
|
||||
.. automodule:: galaxy.managers.library_datasets
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.managers.licenses module
|
||||
-------------------------------
|
||||
|
||||
.. automodule:: galaxy.managers.licenses
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.managers.markdown\_parse module
|
||||
--------------------------------------
|
||||
|
||||
.. automodule:: galaxy.managers.markdown_parse
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.managers.markdown\_util module
|
||||
-------------------------------------
|
||||
|
||||
.. automodule:: galaxy.managers.markdown_util
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.managers.pages module
|
||||
----------------------------
|
||||
|
||||
.. automodule:: galaxy.managers.pages
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.managers.ratable module
|
||||
------------------------------
|
||||
|
||||
.. automodule:: galaxy.managers.ratable
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.managers.rbac\_secured module
|
||||
------------------------------------
|
||||
|
||||
.. automodule:: galaxy.managers.rbac_secured
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.managers.roles module
|
||||
----------------------------
|
||||
|
||||
.. automodule:: galaxy.managers.roles
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.managers.secured module
|
||||
------------------------------
|
||||
|
||||
.. automodule:: galaxy.managers.secured
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.managers.sharable module
|
||||
-------------------------------
|
||||
|
||||
.. automodule:: galaxy.managers.sharable
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.managers.taggable module
|
||||
-------------------------------
|
||||
|
||||
.. automodule:: galaxy.managers.taggable
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.managers.tools module
|
||||
----------------------------
|
||||
|
||||
.. automodule:: galaxy.managers.tools
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.managers.users module
|
||||
----------------------------
|
||||
|
||||
.. automodule:: galaxy.managers.users
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.managers.visualizations module
|
||||
-------------------------------------
|
||||
|
||||
.. automodule:: galaxy.managers.visualizations
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.managers.workflows module
|
||||
--------------------------------
|
||||
|
||||
.. automodule:: galaxy.managers.workflows
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
@@ -2,9 +2,9 @@ galaxy.metadata package
|
||||
=======================
|
||||
|
||||
.. automodule:: galaxy.metadata
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Submodules
|
||||
----------
|
||||
@@ -13,8 +13,6 @@ galaxy.metadata.set\_metadata module
|
||||
------------------------------------
|
||||
|
||||
.. automodule:: galaxy.metadata.set_metadata
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
@@ -2,16 +2,17 @@ galaxy.model.dataset\_collections package
|
||||
=========================================
|
||||
|
||||
.. automodule:: galaxy.model.dataset_collections
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Subpackages
|
||||
-----------
|
||||
|
||||
.. toctree::
|
||||
:maxdepth: 4
|
||||
|
||||
galaxy.model.dataset_collections.types
|
||||
galaxy.model.dataset_collections.types
|
||||
|
||||
Submodules
|
||||
----------
|
||||
@@ -20,48 +21,46 @@ galaxy.model.dataset\_collections.builder module
|
||||
------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.model.dataset_collections.builder
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.model.dataset\_collections.matching module
|
||||
-------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.model.dataset_collections.matching
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.model.dataset\_collections.registry module
|
||||
-------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.model.dataset_collections.registry
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.model.dataset\_collections.structure module
|
||||
--------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.model.dataset_collections.structure
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.model.dataset\_collections.subcollections module
|
||||
-------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.model.dataset_collections.subcollections
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.model.dataset\_collections.type\_description module
|
||||
----------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.model.dataset_collections.type_description
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
@@ -2,9 +2,9 @@ galaxy.model.dataset\_collections.types package
|
||||
===============================================
|
||||
|
||||
.. automodule:: galaxy.model.dataset_collections.types
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Submodules
|
||||
----------
|
||||
@@ -13,16 +13,14 @@ galaxy.model.dataset\_collections.types.list module
|
||||
---------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.model.dataset_collections.types.list
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.model.dataset\_collections.types.paired module
|
||||
-----------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.model.dataset_collections.types.paired
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
@@ -2,16 +2,17 @@ galaxy.model.migrate package
|
||||
============================
|
||||
|
||||
.. automodule:: galaxy.model.migrate
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Subpackages
|
||||
-----------
|
||||
|
||||
.. toctree::
|
||||
:maxdepth: 4
|
||||
|
||||
galaxy.model.migrate.versions
|
||||
galaxy.model.migrate.versions
|
||||
|
||||
Submodules
|
||||
----------
|
||||
@@ -20,8 +21,6 @@ galaxy.model.migrate.check module
|
||||
---------------------------------
|
||||
|
||||
.. automodule:: galaxy.model.migrate.check
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
File diff suppressed because it is too large
Load Diff
@@ -2,9 +2,9 @@ galaxy.model.orm package
|
||||
========================
|
||||
|
||||
.. automodule:: galaxy.model.orm
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Submodules
|
||||
----------
|
||||
@@ -13,32 +13,22 @@ galaxy.model.orm.engine\_factory module
|
||||
---------------------------------------
|
||||
|
||||
.. automodule:: galaxy.model.orm.engine_factory
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.model.orm.logging\_connection\_proxy module
|
||||
--------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.model.orm.logging_connection_proxy
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.model.orm.now module
|
||||
---------------------------
|
||||
|
||||
.. automodule:: galaxy.model.orm.now
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.model.orm.scripts module
|
||||
-------------------------------
|
||||
|
||||
.. automodule:: galaxy.model.orm.scripts
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
@@ -2,20 +2,22 @@ galaxy.model package
|
||||
====================
|
||||
|
||||
.. automodule:: galaxy.model
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Subpackages
|
||||
-----------
|
||||
|
||||
.. toctree::
|
||||
:maxdepth: 4
|
||||
|
||||
galaxy.model.dataset_collections
|
||||
galaxy.model.migrate
|
||||
galaxy.model.orm
|
||||
galaxy.model.store
|
||||
galaxy.model.tool_shed_install
|
||||
galaxy.model.dataset_collections
|
||||
galaxy.model.migrate
|
||||
galaxy.model.orm
|
||||
galaxy.model.store
|
||||
galaxy.model.tool_shed_install
|
||||
galaxy.model.view
|
||||
|
||||
Submodules
|
||||
----------
|
||||
@@ -24,88 +26,86 @@ galaxy.model.base module
|
||||
------------------------
|
||||
|
||||
.. automodule:: galaxy.model.base
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.model.custom\_types module
|
||||
---------------------------------
|
||||
|
||||
.. automodule:: galaxy.model.custom_types
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.model.database\_heartbeat module
|
||||
---------------------------------------
|
||||
|
||||
.. automodule:: galaxy.model.database_heartbeat
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.model.item\_attrs module
|
||||
-------------------------------
|
||||
|
||||
.. automodule:: galaxy.model.item_attrs
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.model.mapping module
|
||||
---------------------------
|
||||
|
||||
.. automodule:: galaxy.model.mapping
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.model.metadata module
|
||||
----------------------------
|
||||
|
||||
.. automodule:: galaxy.model.metadata
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.model.none\_like module
|
||||
------------------------------
|
||||
|
||||
.. automodule:: galaxy.model.none_like
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.model.search module
|
||||
--------------------------
|
||||
|
||||
.. automodule:: galaxy.model.search
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.model.security module
|
||||
----------------------------
|
||||
|
||||
.. automodule:: galaxy.model.security
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.model.tags module
|
||||
------------------------
|
||||
|
||||
.. automodule:: galaxy.model.tags
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.model.triggers module
|
||||
----------------------------
|
||||
|
||||
.. automodule:: galaxy.model.triggers
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
@@ -2,9 +2,9 @@ galaxy.model.store package
|
||||
==========================
|
||||
|
||||
.. automodule:: galaxy.model.store
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Submodules
|
||||
----------
|
||||
@@ -13,16 +13,14 @@ galaxy.model.store.build\_objects module
|
||||
----------------------------------------
|
||||
|
||||
.. automodule:: galaxy.model.store.build_objects
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.model.store.discover module
|
||||
----------------------------------
|
||||
|
||||
.. automodule:: galaxy.model.store.discover
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
@@ -2,9 +2,9 @@ galaxy.model.tool\_shed\_install.migrate package
|
||||
================================================
|
||||
|
||||
.. automodule:: galaxy.model.tool_shed_install.migrate
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Submodules
|
||||
----------
|
||||
@@ -13,8 +13,6 @@ galaxy.model.tool\_shed\_install.migrate.check module
|
||||
-----------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.model.tool_shed_install.migrate.check
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
@@ -2,16 +2,17 @@ galaxy.model.tool\_shed\_install package
|
||||
========================================
|
||||
|
||||
.. automodule:: galaxy.model.tool_shed_install
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Subpackages
|
||||
-----------
|
||||
|
||||
.. toctree::
|
||||
:maxdepth: 4
|
||||
|
||||
galaxy.model.tool_shed_install.migrate
|
||||
galaxy.model.tool_shed_install.migrate
|
||||
|
||||
Submodules
|
||||
----------
|
||||
@@ -20,8 +21,6 @@ galaxy.model.tool\_shed\_install.mapping module
|
||||
-----------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.model.tool_shed_install.mapping
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
@@ -0,0 +1,18 @@
|
||||
galaxy.model.view package
|
||||
=========================
|
||||
|
||||
.. automodule:: galaxy.model.view
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Submodules
|
||||
----------
|
||||
|
||||
galaxy.model.view.utils module
|
||||
------------------------------
|
||||
|
||||
.. automodule:: galaxy.model.view.utils
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
@@ -2,9 +2,9 @@ galaxy.objectstore package
|
||||
==========================
|
||||
|
||||
.. automodule:: galaxy.objectstore
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Submodules
|
||||
----------
|
||||
@@ -13,56 +13,54 @@ galaxy.objectstore.azure\_blob module
|
||||
-------------------------------------
|
||||
|
||||
.. automodule:: galaxy.objectstore.azure_blob
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.objectstore.cloud module
|
||||
-------------------------------
|
||||
|
||||
.. automodule:: galaxy.objectstore.cloud
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.objectstore.irods module
|
||||
-------------------------------
|
||||
|
||||
.. automodule:: galaxy.objectstore.irods
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.objectstore.pithos module
|
||||
--------------------------------
|
||||
|
||||
.. automodule:: galaxy.objectstore.pithos
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.objectstore.pulsar module
|
||||
--------------------------------
|
||||
|
||||
.. automodule:: galaxy.objectstore.pulsar
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.objectstore.s3 module
|
||||
----------------------------
|
||||
|
||||
.. automodule:: galaxy.objectstore.s3
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.objectstore.s3\_multipart\_upload module
|
||||
-----------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.objectstore.s3_multipart_upload
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
@@ -2,9 +2,9 @@ galaxy.openid package
|
||||
=====================
|
||||
|
||||
.. automodule:: galaxy.openid
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Submodules
|
||||
----------
|
||||
@@ -13,16 +13,14 @@ galaxy.openid.openid\_manager module
|
||||
------------------------------------
|
||||
|
||||
.. automodule:: galaxy.openid.openid_manager
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.openid.providers module
|
||||
------------------------------
|
||||
|
||||
.. automodule:: galaxy.openid.providers
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
@@ -2,7 +2,6 @@ galaxy.quota package
|
||||
====================
|
||||
|
||||
.. automodule:: galaxy.quota
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
+56
-56
@@ -2,48 +2,50 @@ galaxy package
|
||||
==============
|
||||
|
||||
.. automodule:: galaxy
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Subpackages
|
||||
-----------
|
||||
|
||||
.. toctree::
|
||||
:maxdepth: 4
|
||||
|
||||
galaxy.actions
|
||||
galaxy.auth
|
||||
galaxy.authnz
|
||||
galaxy.config
|
||||
galaxy.containers
|
||||
galaxy.datatypes
|
||||
galaxy.dependencies
|
||||
galaxy.eggs
|
||||
galaxy.exceptions
|
||||
galaxy.forms
|
||||
galaxy.job_execution
|
||||
galaxy.job_metrics
|
||||
galaxy.jobs
|
||||
galaxy.managers
|
||||
galaxy.metadata
|
||||
galaxy.model
|
||||
galaxy.objectstore
|
||||
galaxy.openid
|
||||
galaxy.quota
|
||||
galaxy.security
|
||||
galaxy.selenium
|
||||
galaxy.tool_shed
|
||||
galaxy.tool_util
|
||||
galaxy.tools
|
||||
galaxy.tours
|
||||
galaxy.util
|
||||
galaxy.visualization
|
||||
galaxy.web
|
||||
galaxy.web_stack
|
||||
galaxy.webapps
|
||||
galaxy.webhooks
|
||||
galaxy.work
|
||||
galaxy.workflow
|
||||
galaxy.actions
|
||||
galaxy.auth
|
||||
galaxy.authnz
|
||||
galaxy.config
|
||||
galaxy.containers
|
||||
galaxy.datatypes
|
||||
galaxy.dependencies
|
||||
galaxy.eggs
|
||||
galaxy.exceptions
|
||||
galaxy.files
|
||||
galaxy.forms
|
||||
galaxy.job_execution
|
||||
galaxy.job_metrics
|
||||
galaxy.jobs
|
||||
galaxy.managers
|
||||
galaxy.metadata
|
||||
galaxy.model
|
||||
galaxy.objectstore
|
||||
galaxy.openid
|
||||
galaxy.quota
|
||||
galaxy.security
|
||||
galaxy.selenium
|
||||
galaxy.tool_shed
|
||||
galaxy.tool_util
|
||||
galaxy.tools
|
||||
galaxy.tours
|
||||
galaxy.util
|
||||
galaxy.visualization
|
||||
galaxy.web
|
||||
galaxy.web_stack
|
||||
galaxy.webapps
|
||||
galaxy.webhooks
|
||||
galaxy.work
|
||||
galaxy.workflow
|
||||
|
||||
Submodules
|
||||
----------
|
||||
@@ -52,48 +54,46 @@ galaxy.app module
|
||||
-----------------
|
||||
|
||||
.. automodule:: galaxy.app
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.config\_watchers module
|
||||
------------------------------
|
||||
|
||||
.. automodule:: galaxy.config_watchers
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.main module
|
||||
------------------
|
||||
|
||||
.. automodule:: galaxy.main
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.queue\_worker module
|
||||
---------------------------
|
||||
|
||||
.. automodule:: galaxy.queue_worker
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.queues module
|
||||
--------------------
|
||||
|
||||
.. automodule:: galaxy.queues
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.version module
|
||||
---------------------
|
||||
|
||||
.. automodule:: galaxy.version
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
@@ -2,9 +2,9 @@ galaxy.security package
|
||||
=======================
|
||||
|
||||
.. automodule:: galaxy.security
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Submodules
|
||||
----------
|
||||
@@ -13,24 +13,22 @@ galaxy.security.idencoding module
|
||||
---------------------------------
|
||||
|
||||
.. automodule:: galaxy.security.idencoding
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.security.passwords module
|
||||
--------------------------------
|
||||
|
||||
.. automodule:: galaxy.security.passwords
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.security.validate\_user\_input module
|
||||
--------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.security.validate_user_input
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
@@ -2,16 +2,18 @@ galaxy.selenium package
|
||||
=======================
|
||||
|
||||
.. automodule:: galaxy.selenium
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Subpackages
|
||||
-----------
|
||||
|
||||
.. toctree::
|
||||
:maxdepth: 4
|
||||
|
||||
galaxy.selenium.scripts
|
||||
galaxy.selenium.scripts
|
||||
galaxy.selenium.toolbox
|
||||
|
||||
Submodules
|
||||
----------
|
||||
@@ -20,64 +22,62 @@ galaxy.selenium.cli module
|
||||
--------------------------
|
||||
|
||||
.. automodule:: galaxy.selenium.cli
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.selenium.components module
|
||||
---------------------------------
|
||||
|
||||
.. automodule:: galaxy.selenium.components
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.selenium.data module
|
||||
---------------------------
|
||||
|
||||
.. automodule:: galaxy.selenium.data
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.selenium.driver\_factory module
|
||||
--------------------------------------
|
||||
|
||||
.. automodule:: galaxy.selenium.driver_factory
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.selenium.has\_driver module
|
||||
----------------------------------
|
||||
|
||||
.. automodule:: galaxy.selenium.has_driver
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.selenium.navigates\_galaxy module
|
||||
----------------------------------------
|
||||
|
||||
.. automodule:: galaxy.selenium.navigates_galaxy
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.selenium.sizzle module
|
||||
-----------------------------
|
||||
|
||||
.. automodule:: galaxy.selenium.sizzle
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.selenium.smart\_components module
|
||||
----------------------------------------
|
||||
|
||||
.. automodule:: galaxy.selenium.smart_components
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
@@ -2,9 +2,9 @@ galaxy.selenium.scripts package
|
||||
===============================
|
||||
|
||||
.. automodule:: galaxy.selenium.scripts
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Submodules
|
||||
----------
|
||||
@@ -13,8 +13,6 @@ galaxy.selenium.scripts.dump\_tour module
|
||||
-----------------------------------------
|
||||
|
||||
.. automodule:: galaxy.selenium.scripts.dump_tour
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
@@ -0,0 +1,18 @@
|
||||
galaxy.selenium.toolbox package
|
||||
===============================
|
||||
|
||||
.. automodule:: galaxy.selenium.toolbox
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Submodules
|
||||
----------
|
||||
|
||||
galaxy.selenium.toolbox.filters module
|
||||
--------------------------------------
|
||||
|
||||
.. automodule:: galaxy.selenium.toolbox.filters
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
@@ -2,9 +2,9 @@ galaxy.tool\_shed.galaxy\_install.datatypes package
|
||||
===================================================
|
||||
|
||||
.. automodule:: galaxy.tool_shed.galaxy_install.datatypes
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Submodules
|
||||
----------
|
||||
@@ -13,8 +13,6 @@ galaxy.tool\_shed.galaxy\_install.datatypes.custom\_datatype\_manager module
|
||||
----------------------------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_shed.galaxy_install.datatypes.custom_datatype_manager
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
@@ -2,9 +2,9 @@ galaxy.tool\_shed.galaxy\_install.metadata package
|
||||
==================================================
|
||||
|
||||
.. automodule:: galaxy.tool_shed.galaxy_install.metadata
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Submodules
|
||||
----------
|
||||
@@ -13,8 +13,6 @@ galaxy.tool\_shed.galaxy\_install.metadata.installed\_repository\_metadata\_mana
|
||||
------------------------------------------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_shed.galaxy_install.metadata.installed_repository_metadata_manager
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
@@ -2,16 +2,17 @@ galaxy.tool\_shed.galaxy\_install.migrate package
|
||||
=================================================
|
||||
|
||||
.. automodule:: galaxy.tool_shed.galaxy_install.migrate
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Subpackages
|
||||
-----------
|
||||
|
||||
.. toctree::
|
||||
:maxdepth: 4
|
||||
|
||||
galaxy.tool_shed.galaxy_install.migrate.versions
|
||||
galaxy.tool_shed.galaxy_install.migrate.versions
|
||||
|
||||
Submodules
|
||||
----------
|
||||
@@ -20,16 +21,14 @@ galaxy.tool\_shed.galaxy\_install.migrate.check module
|
||||
------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_shed.galaxy_install.migrate.check
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_shed.galaxy\_install.migrate.common module
|
||||
-------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_shed.galaxy_install.migrate.common
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
@@ -2,9 +2,9 @@ galaxy.tool\_shed.galaxy\_install.migrate.versions package
|
||||
==========================================================
|
||||
|
||||
.. automodule:: galaxy.tool_shed.galaxy_install.migrate.versions
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Submodules
|
||||
----------
|
||||
@@ -13,96 +13,94 @@ galaxy.tool\_shed.galaxy\_install.migrate.versions.0001\_tools module
|
||||
---------------------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_shed.galaxy_install.migrate.versions.0001_tools
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_shed.galaxy\_install.migrate.versions.0002\_tools module
|
||||
---------------------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_shed.galaxy_install.migrate.versions.0002_tools
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_shed.galaxy\_install.migrate.versions.0003\_tools module
|
||||
---------------------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_shed.galaxy_install.migrate.versions.0003_tools
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_shed.galaxy\_install.migrate.versions.0004\_tools module
|
||||
---------------------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_shed.galaxy_install.migrate.versions.0004_tools
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_shed.galaxy\_install.migrate.versions.0005\_tools module
|
||||
---------------------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_shed.galaxy_install.migrate.versions.0005_tools
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_shed.galaxy\_install.migrate.versions.0006\_tools module
|
||||
---------------------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_shed.galaxy_install.migrate.versions.0006_tools
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_shed.galaxy\_install.migrate.versions.0007\_tools module
|
||||
---------------------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_shed.galaxy_install.migrate.versions.0007_tools
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_shed.galaxy\_install.migrate.versions.0008\_tools module
|
||||
---------------------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_shed.galaxy_install.migrate.versions.0008_tools
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_shed.galaxy\_install.migrate.versions.0009\_tools module
|
||||
---------------------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_shed.galaxy_install.migrate.versions.0009_tools
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_shed.galaxy\_install.migrate.versions.0010\_tools module
|
||||
---------------------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_shed.galaxy_install.migrate.versions.0010_tools
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_shed.galaxy\_install.migrate.versions.0011\_tools module
|
||||
---------------------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_shed.galaxy_install.migrate.versions.0011_tools
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_shed.galaxy\_install.migrate.versions.0012\_tools module
|
||||
---------------------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_shed.galaxy_install.migrate.versions.0012_tools
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
@@ -2,9 +2,9 @@ galaxy.tool\_shed.galaxy\_install.repository\_dependencies package
|
||||
==================================================================
|
||||
|
||||
.. automodule:: galaxy.tool_shed.galaxy_install.repository_dependencies
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Submodules
|
||||
----------
|
||||
@@ -13,8 +13,6 @@ galaxy.tool\_shed.galaxy\_install.repository\_dependencies.repository\_dependenc
|
||||
-------------------------------------------------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
@@ -2,21 +2,22 @@ galaxy.tool\_shed.galaxy\_install package
|
||||
=========================================
|
||||
|
||||
.. automodule:: galaxy.tool_shed.galaxy_install
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Subpackages
|
||||
-----------
|
||||
|
||||
.. toctree::
|
||||
:maxdepth: 4
|
||||
|
||||
galaxy.tool_shed.galaxy_install.datatypes
|
||||
galaxy.tool_shed.galaxy_install.metadata
|
||||
galaxy.tool_shed.galaxy_install.migrate
|
||||
galaxy.tool_shed.galaxy_install.repository_dependencies
|
||||
galaxy.tool_shed.galaxy_install.tool_dependencies
|
||||
galaxy.tool_shed.galaxy_install.tools
|
||||
galaxy.tool_shed.galaxy_install.datatypes
|
||||
galaxy.tool_shed.galaxy_install.metadata
|
||||
galaxy.tool_shed.galaxy_install.migrate
|
||||
galaxy.tool_shed.galaxy_install.repository_dependencies
|
||||
galaxy.tool_shed.galaxy_install.tool_dependencies
|
||||
galaxy.tool_shed.galaxy_install.tools
|
||||
|
||||
Submodules
|
||||
----------
|
||||
@@ -25,32 +26,30 @@ galaxy.tool\_shed.galaxy\_install.install\_manager module
|
||||
---------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_shed.galaxy_install.install_manager
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_shed.galaxy\_install.installed\_repository\_manager module
|
||||
-----------------------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_shed.galaxy_install.installed_repository_manager
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_shed.galaxy\_install.tool\_migration\_manager module
|
||||
-----------------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_shed.galaxy_install.tool_migration_manager
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_shed.galaxy\_install.update\_repository\_manager module
|
||||
--------------------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_shed.galaxy_install.update_repository_manager
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
@@ -2,9 +2,9 @@ galaxy.tool\_shed.galaxy\_install.tool\_dependencies.recipe package
|
||||
===================================================================
|
||||
|
||||
.. automodule:: galaxy.tool_shed.galaxy_install.tool_dependencies.recipe
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Submodules
|
||||
----------
|
||||
@@ -13,48 +13,46 @@ galaxy.tool\_shed.galaxy\_install.tool\_dependencies.recipe.asynchronous\_reader
|
||||
---------------------------------------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.asynchronous_reader
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_shed.galaxy\_install.tool\_dependencies.recipe.env\_file\_builder module
|
||||
-------------------------------------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.env_file_builder
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_shed.galaxy\_install.tool\_dependencies.recipe.install\_environment module
|
||||
---------------------------------------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.install_environment
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_shed.galaxy\_install.tool\_dependencies.recipe.recipe\_manager module
|
||||
----------------------------------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.recipe_manager
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_shed.galaxy\_install.tool\_dependencies.recipe.step\_handler module
|
||||
--------------------------------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_shed.galaxy\_install.tool\_dependencies.recipe.tag\_handler module
|
||||
-------------------------------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.tag_handler
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
@@ -2,16 +2,17 @@ galaxy.tool\_shed.galaxy\_install.tool\_dependencies package
|
||||
============================================================
|
||||
|
||||
.. automodule:: galaxy.tool_shed.galaxy_install.tool_dependencies
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Subpackages
|
||||
-----------
|
||||
|
||||
.. toctree::
|
||||
:maxdepth: 4
|
||||
|
||||
galaxy.tool_shed.galaxy_install.tool_dependencies.recipe
|
||||
galaxy.tool_shed.galaxy_install.tool_dependencies.recipe
|
||||
|
||||
Submodules
|
||||
----------
|
||||
@@ -20,8 +21,6 @@ galaxy.tool\_shed.galaxy\_install.tool\_dependencies.env\_manager module
|
||||
------------------------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_shed.galaxy_install.tool_dependencies.env_manager
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
@@ -2,9 +2,9 @@ galaxy.tool\_shed.galaxy\_install.tools package
|
||||
===============================================
|
||||
|
||||
.. automodule:: galaxy.tool_shed.galaxy_install.tools
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Submodules
|
||||
----------
|
||||
@@ -13,16 +13,14 @@ galaxy.tool\_shed.galaxy\_install.tools.data\_manager module
|
||||
------------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_shed.galaxy_install.tools.data_manager
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_shed.galaxy\_install.tools.tool\_panel\_manager module
|
||||
-------------------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_shed.galaxy_install.tools.tool_panel_manager
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
@@ -2,9 +2,9 @@ galaxy.tool\_shed.metadata package
|
||||
==================================
|
||||
|
||||
.. automodule:: galaxy.tool_shed.metadata
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Submodules
|
||||
----------
|
||||
@@ -13,8 +13,6 @@ galaxy.tool\_shed.metadata.metadata\_generator module
|
||||
-----------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_shed.metadata.metadata_generator
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
@@ -2,19 +2,20 @@ galaxy.tool\_shed package
|
||||
=========================
|
||||
|
||||
.. automodule:: galaxy.tool_shed
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Subpackages
|
||||
-----------
|
||||
|
||||
.. toctree::
|
||||
:maxdepth: 4
|
||||
|
||||
galaxy.tool_shed.galaxy_install
|
||||
galaxy.tool_shed.metadata
|
||||
galaxy.tool_shed.tools
|
||||
galaxy.tool_shed.util
|
||||
galaxy.tool_shed.galaxy_install
|
||||
galaxy.tool_shed.metadata
|
||||
galaxy.tool_shed.tools
|
||||
galaxy.tool_shed.util
|
||||
|
||||
Submodules
|
||||
----------
|
||||
@@ -23,16 +24,14 @@ galaxy.tool\_shed.repository\_type module
|
||||
-----------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_shed.repository_type
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_shed.tool\_shed\_registry module
|
||||
---------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_shed.tool_shed_registry
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
@@ -2,9 +2,9 @@ galaxy.tool\_shed.tools package
|
||||
===============================
|
||||
|
||||
.. automodule:: galaxy.tool_shed.tools
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Submodules
|
||||
----------
|
||||
@@ -13,16 +13,14 @@ galaxy.tool\_shed.tools.data\_table\_manager module
|
||||
---------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_shed.tools.data_table_manager
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_shed.tools.tool\_validator module
|
||||
----------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_shed.tools.tool_validator
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
@@ -2,9 +2,9 @@ galaxy.tool\_shed.util package
|
||||
==============================
|
||||
|
||||
.. automodule:: galaxy.tool_shed.util
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Submodules
|
||||
----------
|
||||
@@ -13,64 +13,62 @@ galaxy.tool\_shed.util.basic\_util module
|
||||
-----------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_shed.util.basic_util
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_shed.util.container\_util module
|
||||
---------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_shed.util.container_util
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_shed.util.hg\_util module
|
||||
--------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_shed.util.hg_util
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_shed.util.metadata\_util module
|
||||
--------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_shed.util.metadata_util
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_shed.util.repository\_util module
|
||||
----------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_shed.util.repository_util
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_shed.util.shed\_util\_common module
|
||||
------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_shed.util.shed_util_common
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_shed.util.tool\_dependency\_util module
|
||||
----------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_shed.util.tool_dependency_util
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_shed.util.tool\_util module
|
||||
----------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_shed.util.tool_util
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
@@ -2,9 +2,9 @@ galaxy.tool\_util.cwl package
|
||||
=============================
|
||||
|
||||
.. automodule:: galaxy.tool_util.cwl
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Submodules
|
||||
----------
|
||||
@@ -13,48 +13,54 @@ galaxy.tool\_util.cwl.cwltool\_deps module
|
||||
------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_util.cwl.cwltool_deps
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_util.cwl.parser module
|
||||
-----------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_util.cwl.parser
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_util.cwl.representation module
|
||||
-------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_util.cwl.representation
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_util.cwl.runnable module
|
||||
-------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_util.cwl.runnable
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_util.cwl.runtime\_actions module
|
||||
---------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_util.cwl.runtime_actions
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_util.cwl.schema module
|
||||
-----------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_util.cwl.schema
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_util.cwl.util module
|
||||
---------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_util.cwl.util
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
@@ -2,9 +2,9 @@ galaxy.tool\_util.deps.container\_resolvers package
|
||||
===================================================
|
||||
|
||||
.. automodule:: galaxy.tool_util.deps.container_resolvers
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Submodules
|
||||
----------
|
||||
@@ -13,16 +13,14 @@ galaxy.tool\_util.deps.container\_resolvers.explicit module
|
||||
-----------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_util.deps.container_resolvers.explicit
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_util.deps.container\_resolvers.mulled module
|
||||
---------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_util.deps.container_resolvers.mulled
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
@@ -2,9 +2,9 @@ galaxy.tool\_util.deps.mulled package
|
||||
=====================================
|
||||
|
||||
.. automodule:: galaxy.tool_util.deps.mulled
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Submodules
|
||||
----------
|
||||
@@ -13,72 +13,70 @@ galaxy.tool\_util.deps.mulled.get\_tests module
|
||||
-----------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_util.deps.mulled.get_tests
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_util.deps.mulled.mulled\_build module
|
||||
--------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_util.deps.mulled.mulled_build
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_util.deps.mulled.mulled\_build\_channel module
|
||||
-----------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_util.deps.mulled.mulled_build_channel
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_util.deps.mulled.mulled\_build\_files module
|
||||
---------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_util.deps.mulled.mulled_build_files
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_util.deps.mulled.mulled\_build\_tool module
|
||||
--------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_util.deps.mulled.mulled_build_tool
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_util.deps.mulled.mulled\_list module
|
||||
-------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_util.deps.mulled.mulled_list
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_util.deps.mulled.mulled\_search module
|
||||
---------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_util.deps.mulled.mulled_search
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_util.deps.mulled.mulled\_update\_singularity\_containers module
|
||||
----------------------------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_util.deps.mulled.mulled_update_singularity_containers
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_util.deps.mulled.util module
|
||||
-----------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_util.deps.mulled.util
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
@@ -2,9 +2,9 @@ galaxy.tool\_util.deps.resolvers package
|
||||
========================================
|
||||
|
||||
.. automodule:: galaxy.tool_util.deps.resolvers
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Submodules
|
||||
----------
|
||||
@@ -13,72 +13,70 @@ galaxy.tool\_util.deps.resolvers.brewed\_tool\_shed\_packages module
|
||||
--------------------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_util.deps.resolvers.brewed_tool_shed_packages
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_util.deps.resolvers.conda module
|
||||
---------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_util.deps.resolvers.conda
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_util.deps.resolvers.galaxy\_packages module
|
||||
--------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_util.deps.resolvers.galaxy_packages
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_util.deps.resolvers.homebrew module
|
||||
------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_util.deps.resolvers.homebrew
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_util.deps.resolvers.lmod module
|
||||
--------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_util.deps.resolvers.lmod
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_util.deps.resolvers.modules module
|
||||
-----------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_util.deps.resolvers.modules
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_util.deps.resolvers.resolver\_mixins module
|
||||
--------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_util.deps.resolvers.resolver_mixins
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_util.deps.resolvers.tool\_shed\_packages module
|
||||
------------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_util.deps.resolvers.tool_shed_packages
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_util.deps.resolvers.unlinked\_tool\_shed\_packages module
|
||||
----------------------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_util.deps.resolvers.unlinked_tool_shed_packages
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
@@ -2,18 +2,19 @@ galaxy.tool\_util.deps package
|
||||
==============================
|
||||
|
||||
.. automodule:: galaxy.tool_util.deps
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Subpackages
|
||||
-----------
|
||||
|
||||
.. toctree::
|
||||
:maxdepth: 4
|
||||
|
||||
galaxy.tool_util.deps.container_resolvers
|
||||
galaxy.tool_util.deps.mulled
|
||||
galaxy.tool_util.deps.resolvers
|
||||
galaxy.tool_util.deps.container_resolvers
|
||||
galaxy.tool_util.deps.mulled
|
||||
galaxy.tool_util.deps.resolvers
|
||||
|
||||
Submodules
|
||||
----------
|
||||
@@ -22,104 +23,110 @@ galaxy.tool\_util.deps.brew\_exts module
|
||||
----------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_util.deps.brew_exts
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_util.deps.brew\_util module
|
||||
----------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_util.deps.brew_util
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_util.deps.commands module
|
||||
--------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_util.deps.commands
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_util.deps.conda\_compat module
|
||||
-------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_util.deps.conda_compat
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_util.deps.conda\_util module
|
||||
-----------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_util.deps.conda_util
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_util.deps.container\_classes module
|
||||
------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_util.deps.container_classes
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_util.deps.containers module
|
||||
----------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_util.deps.containers
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_util.deps.dependencies module
|
||||
------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_util.deps.dependencies
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_util.deps.docker\_util module
|
||||
------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_util.deps.docker_util
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_util.deps.dockerfiles module
|
||||
-----------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_util.deps.dockerfiles
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_util.deps.installable module
|
||||
-----------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_util.deps.installable
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_util.deps.requirements module
|
||||
------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_util.deps.requirements
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_util.deps.singularity\_util module
|
||||
-----------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_util.deps.singularity_util
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_util.deps.views module
|
||||
-----------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_util.deps.views
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
@@ -2,9 +2,9 @@ galaxy.tool\_util.linters package
|
||||
=================================
|
||||
|
||||
.. automodule:: galaxy.tool_util.linters
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Submodules
|
||||
----------
|
||||
@@ -13,80 +13,78 @@ galaxy.tool\_util.linters.citations module
|
||||
------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_util.linters.citations
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_util.linters.command module
|
||||
----------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_util.linters.command
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_util.linters.cwl module
|
||||
------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_util.linters.cwl
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_util.linters.general module
|
||||
----------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_util.linters.general
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_util.linters.help module
|
||||
-------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_util.linters.help
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_util.linters.inputs module
|
||||
---------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_util.linters.inputs
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_util.linters.outputs module
|
||||
----------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_util.linters.outputs
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_util.linters.stdio module
|
||||
--------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_util.linters.stdio
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_util.linters.tests module
|
||||
--------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_util.linters.tests
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_util.linters.xml\_order module
|
||||
-------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_util.linters.xml_order
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
@@ -2,9 +2,9 @@ galaxy.tool\_util.locations package
|
||||
===================================
|
||||
|
||||
.. automodule:: galaxy.tool_util.locations
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Submodules
|
||||
----------
|
||||
@@ -13,24 +13,22 @@ galaxy.tool\_util.locations.dockstore module
|
||||
--------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_util.locations.dockstore
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_util.locations.file module
|
||||
---------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_util.locations.file
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_util.locations.http module
|
||||
---------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_util.locations.http
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
@@ -2,9 +2,9 @@ galaxy.tool\_util.parser package
|
||||
================================
|
||||
|
||||
.. automodule:: galaxy.tool_util.parser
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Submodules
|
||||
----------
|
||||
@@ -13,80 +13,78 @@ galaxy.tool\_util.parser.cwl module
|
||||
-----------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_util.parser.cwl
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_util.parser.factory module
|
||||
---------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_util.parser.factory
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_util.parser.interface module
|
||||
-----------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_util.parser.interface
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_util.parser.output\_actions module
|
||||
-----------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_util.parser.output_actions
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_util.parser.output\_collection\_def module
|
||||
-------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_util.parser.output_collection_def
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_util.parser.output\_objects module
|
||||
-----------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_util.parser.output_objects
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_util.parser.stdio module
|
||||
-------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_util.parser.stdio
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_util.parser.util module
|
||||
------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_util.parser.util
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_util.parser.xml module
|
||||
-----------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_util.parser.xml
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_util.parser.yaml module
|
||||
------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_util.parser.yaml
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
@@ -2,21 +2,22 @@ galaxy.tool\_util package
|
||||
=========================
|
||||
|
||||
.. automodule:: galaxy.tool_util
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Subpackages
|
||||
-----------
|
||||
|
||||
.. toctree::
|
||||
:maxdepth: 4
|
||||
|
||||
galaxy.tool_util.cwl
|
||||
galaxy.tool_util.deps
|
||||
galaxy.tool_util.linters
|
||||
galaxy.tool_util.locations
|
||||
galaxy.tool_util.parser
|
||||
galaxy.tool_util.verify
|
||||
galaxy.tool_util.cwl
|
||||
galaxy.tool_util.deps
|
||||
galaxy.tool_util.linters
|
||||
galaxy.tool_util.locations
|
||||
galaxy.tool_util.parser
|
||||
galaxy.tool_util.verify
|
||||
|
||||
Submodules
|
||||
----------
|
||||
@@ -25,48 +26,46 @@ galaxy.tool\_util.fetcher module
|
||||
--------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_util.fetcher
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_util.lint module
|
||||
-----------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_util.lint
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_util.loader module
|
||||
-------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_util.loader
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_util.loader\_directory module
|
||||
------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_util.loader_directory
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_util.output\_checker module
|
||||
----------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_util.output_checker
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_util.provided\_metadata module
|
||||
-------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_util.provided_metadata
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
@@ -2,9 +2,9 @@ galaxy.tool\_util.verify.asserts package
|
||||
========================================
|
||||
|
||||
.. automodule:: galaxy.tool_util.verify.asserts
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Submodules
|
||||
----------
|
||||
@@ -13,48 +13,46 @@ galaxy.tool\_util.verify.asserts.archive module
|
||||
-----------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_util.verify.asserts.archive
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_util.verify.asserts.hdf5 module
|
||||
--------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_util.verify.asserts.hdf5
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_util.verify.asserts.size module
|
||||
--------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_util.verify.asserts.size
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_util.verify.asserts.tabular module
|
||||
-----------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_util.verify.asserts.tabular
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_util.verify.asserts.text module
|
||||
--------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_util.verify.asserts.text
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_util.verify.asserts.xml module
|
||||
-------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_util.verify.asserts.xml
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
@@ -2,16 +2,17 @@ galaxy.tool\_util.verify package
|
||||
================================
|
||||
|
||||
.. automodule:: galaxy.tool_util.verify
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Subpackages
|
||||
-----------
|
||||
|
||||
.. toctree::
|
||||
:maxdepth: 4
|
||||
|
||||
galaxy.tool_util.verify.asserts
|
||||
galaxy.tool_util.verify.asserts
|
||||
|
||||
Submodules
|
||||
----------
|
||||
@@ -20,24 +21,30 @@ galaxy.tool\_util.verify.interactor module
|
||||
------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_util.verify.interactor
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_util.verify.script module
|
||||
--------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_util.verify.script
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_util.verify.test\_data module
|
||||
------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_util.verify.test_data
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_util.verify.wait module
|
||||
------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_util.verify.wait
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
@@ -2,9 +2,9 @@ galaxy.tools.actions package
|
||||
============================
|
||||
|
||||
.. automodule:: galaxy.tools.actions
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Submodules
|
||||
----------
|
||||
@@ -13,56 +13,54 @@ galaxy.tools.actions.data\_manager module
|
||||
-----------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.actions.data_manager
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tools.actions.data\_source module
|
||||
----------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.actions.data_source
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tools.actions.history\_imp\_exp module
|
||||
---------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.actions.history_imp_exp
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tools.actions.metadata module
|
||||
------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.actions.metadata
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tools.actions.model\_operations module
|
||||
---------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.actions.model_operations
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tools.actions.upload module
|
||||
----------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.actions.upload
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tools.actions.upload\_common module
|
||||
------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.actions.upload_common
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
@@ -2,7 +2,6 @@ galaxy.tools.data package
|
||||
=========================
|
||||
|
||||
.. automodule:: galaxy.tools.data
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
@@ -2,9 +2,9 @@ galaxy.tools.data\_manager package
|
||||
==================================
|
||||
|
||||
.. automodule:: galaxy.tools.data_manager
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Submodules
|
||||
----------
|
||||
@@ -13,8 +13,6 @@ galaxy.tools.data\_manager.manager module
|
||||
-----------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.data_manager.manager
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
@@ -2,9 +2,9 @@ galaxy.tools.error\_reports.plugins package
|
||||
===========================================
|
||||
|
||||
.. automodule:: galaxy.tools.error_reports.plugins
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Submodules
|
||||
----------
|
||||
@@ -13,56 +13,54 @@ galaxy.tools.error\_reports.plugins.base\_git module
|
||||
----------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.error_reports.plugins.base_git
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tools.error\_reports.plugins.email module
|
||||
------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.error_reports.plugins.email
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tools.error\_reports.plugins.github module
|
||||
-------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.error_reports.plugins.github
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tools.error\_reports.plugins.gitlab module
|
||||
-------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.error_reports.plugins.gitlab
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tools.error\_reports.plugins.influxdb module
|
||||
---------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.error_reports.plugins.influxdb
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tools.error\_reports.plugins.json module
|
||||
-----------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.error_reports.plugins.json
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tools.error\_reports.plugins.sentry module
|
||||
-------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.error_reports.plugins.sentry
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
@@ -2,14 +2,14 @@ galaxy.tools.error\_reports package
|
||||
===================================
|
||||
|
||||
.. automodule:: galaxy.tools.error_reports
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Subpackages
|
||||
-----------
|
||||
|
||||
.. toctree::
|
||||
:maxdepth: 4
|
||||
|
||||
galaxy.tools.error_reports.plugins
|
||||
|
||||
galaxy.tools.error_reports.plugins
|
||||
|
||||
@@ -2,9 +2,9 @@ galaxy.tools.expressions package
|
||||
================================
|
||||
|
||||
.. automodule:: galaxy.tools.expressions
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Submodules
|
||||
----------
|
||||
@@ -13,24 +13,22 @@ galaxy.tools.expressions.evaluation module
|
||||
------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.expressions.evaluation
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tools.expressions.script module
|
||||
--------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.expressions.script
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tools.expressions.util module
|
||||
------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.expressions.util
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
@@ -2,7 +2,6 @@ galaxy.tools.filters package
|
||||
============================
|
||||
|
||||
.. automodule:: galaxy.tools.filters
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
@@ -2,9 +2,9 @@ galaxy.tools.imp\_exp package
|
||||
=============================
|
||||
|
||||
.. automodule:: galaxy.tools.imp_exp
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Submodules
|
||||
----------
|
||||
@@ -13,16 +13,14 @@ galaxy.tools.imp\_exp.export\_history module
|
||||
--------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.imp_exp.export_history
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tools.imp\_exp.unpack\_tar\_gz\_archive module
|
||||
-----------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.imp_exp.unpack_tar_gz_archive
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
@@ -2,9 +2,9 @@ galaxy.tools.parameters package
|
||||
===============================
|
||||
|
||||
.. automodule:: galaxy.tools.parameters
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Submodules
|
||||
----------
|
||||
@@ -13,88 +13,86 @@ galaxy.tools.parameters.basic module
|
||||
------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.parameters.basic
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tools.parameters.dataset\_matcher module
|
||||
-----------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.parameters.dataset_matcher
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tools.parameters.dynamic\_options module
|
||||
-----------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.parameters.dynamic_options
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tools.parameters.grouping module
|
||||
---------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.parameters.grouping
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tools.parameters.history\_query module
|
||||
---------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.parameters.history_query
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tools.parameters.input\_translation module
|
||||
-------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.parameters.input_translation
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tools.parameters.meta module
|
||||
-----------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.parameters.meta
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tools.parameters.sanitize module
|
||||
---------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.parameters.sanitize
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tools.parameters.validation module
|
||||
-----------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.parameters.validation
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tools.parameters.wrapped module
|
||||
--------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.parameters.wrapped
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tools.parameters.wrapped\_json module
|
||||
--------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.parameters.wrapped_json
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
@@ -2,26 +2,27 @@ galaxy.tools package
|
||||
====================
|
||||
|
||||
.. automodule:: galaxy.tools
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Subpackages
|
||||
-----------
|
||||
|
||||
.. toctree::
|
||||
:maxdepth: 4
|
||||
|
||||
galaxy.tools.actions
|
||||
galaxy.tools.data
|
||||
galaxy.tools.data_manager
|
||||
galaxy.tools.error_reports
|
||||
galaxy.tools.expressions
|
||||
galaxy.tools.filters
|
||||
galaxy.tools.imp_exp
|
||||
galaxy.tools.parameters
|
||||
galaxy.tools.search
|
||||
galaxy.tools.toolbox
|
||||
galaxy.tools.util
|
||||
galaxy.tools.actions
|
||||
galaxy.tools.data
|
||||
galaxy.tools.data_manager
|
||||
galaxy.tools.error_reports
|
||||
galaxy.tools.expressions
|
||||
galaxy.tools.filters
|
||||
galaxy.tools.imp_exp
|
||||
galaxy.tools.parameters
|
||||
galaxy.tools.search
|
||||
galaxy.tools.toolbox
|
||||
galaxy.tools.util
|
||||
|
||||
Submodules
|
||||
----------
|
||||
@@ -30,88 +31,86 @@ galaxy.tools.cache module
|
||||
-------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.cache
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tools.data\_fetch module
|
||||
-------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.data_fetch
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tools.errors module
|
||||
--------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.errors
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tools.evaluation module
|
||||
------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.evaluation
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tools.exception\_handling module
|
||||
---------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.exception_handling
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tools.execute module
|
||||
---------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.execute
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tools.recommendations module
|
||||
-----------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.recommendations
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tools.repositories module
|
||||
--------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.repositories
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tools.special\_tools module
|
||||
----------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.special_tools
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tools.test module
|
||||
------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.test
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tools.wrappers module
|
||||
----------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.wrappers
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
@@ -2,7 +2,6 @@ galaxy.tools.search package
|
||||
===========================
|
||||
|
||||
.. automodule:: galaxy.tools.search
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
@@ -2,7 +2,6 @@ galaxy.tools.toolbox.filters package
|
||||
====================================
|
||||
|
||||
.. automodule:: galaxy.tools.toolbox.filters
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
@@ -2,9 +2,9 @@ galaxy.tools.toolbox.lineages package
|
||||
=====================================
|
||||
|
||||
.. automodule:: galaxy.tools.toolbox.lineages
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Submodules
|
||||
----------
|
||||
@@ -13,16 +13,14 @@ galaxy.tools.toolbox.lineages.factory module
|
||||
--------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.toolbox.lineages.factory
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tools.toolbox.lineages.interface module
|
||||
----------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.toolbox.lineages.interface
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
@@ -2,17 +2,18 @@ galaxy.tools.toolbox package
|
||||
============================
|
||||
|
||||
.. automodule:: galaxy.tools.toolbox
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Subpackages
|
||||
-----------
|
||||
|
||||
.. toctree::
|
||||
:maxdepth: 4
|
||||
|
||||
galaxy.tools.toolbox.filters
|
||||
galaxy.tools.toolbox.lineages
|
||||
galaxy.tools.toolbox.filters
|
||||
galaxy.tools.toolbox.lineages
|
||||
|
||||
Submodules
|
||||
----------
|
||||
@@ -21,48 +22,46 @@ galaxy.tools.toolbox.base module
|
||||
--------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.toolbox.base
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tools.toolbox.integrated\_panel module
|
||||
---------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.toolbox.integrated_panel
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tools.toolbox.panel module
|
||||
---------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.toolbox.panel
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tools.toolbox.parser module
|
||||
----------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.toolbox.parser
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tools.toolbox.tags module
|
||||
--------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.toolbox.tags
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tools.toolbox.watcher module
|
||||
-----------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.toolbox.watcher
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
@@ -2,7 +2,6 @@ galaxy.tools.util.galaxyops package
|
||||
===================================
|
||||
|
||||
.. automodule:: galaxy.tools.util.galaxyops
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
@@ -2,16 +2,17 @@ galaxy.tools.util package
|
||||
=========================
|
||||
|
||||
.. automodule:: galaxy.tools.util
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Subpackages
|
||||
-----------
|
||||
|
||||
.. toctree::
|
||||
:maxdepth: 4
|
||||
|
||||
galaxy.tools.util.galaxyops
|
||||
galaxy.tools.util.galaxyops
|
||||
|
||||
Submodules
|
||||
----------
|
||||
@@ -20,8 +21,6 @@ galaxy.tools.util.maf\_utilities module
|
||||
---------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.util.maf_utilities
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
@@ -2,7 +2,6 @@ galaxy.tours package
|
||||
====================
|
||||
|
||||
.. automodule:: galaxy.tours
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
@@ -0,0 +1,18 @@
|
||||
galaxy.util.custom\_logging package
|
||||
===================================
|
||||
|
||||
.. automodule:: galaxy.util.custom_logging
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Submodules
|
||||
----------
|
||||
|
||||
galaxy.util.custom\_logging.fluent\_log module
|
||||
----------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.util.custom_logging.fluent_log
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
Some files were not shown because too many files have changed in this diff Show More
Reference in New Issue
Block a user