mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
Bringing Sphinx RST files up to date; changing generated doc so all modules are documented, not just galaxy.*
This commit is contained in:
Dave Clements
+7
-10
@@ -3,22 +3,19 @@ Galaxy Documentation
|
||||
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||||
Galaxy is an open, web-based platform for accessible, reproducible, and
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||||
transparent computational biomedical research.
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- Accessible: Users without programming experience can easily specify
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parameters and run tools and workflows.
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||||
- Reproducible: Galaxy captures information so that any user can repeat and
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understand a complete computational analysis.
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- Transparent: Users share and publish analyses via the web and create
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||||
Pages, interactive, web-based documents that describe a complete
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||||
analysis.
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||||
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||||
- Accessible: Users without programming experience can easily specify parameters and run tools and workflows.
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||||
- Reproducible: Galaxy captures information so that any user can repeat and understand a complete computational analysis.
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||||
- Transparent: Users share and publish analyses via the web and create Pages, interactive, web-based documents that describe a complete analysis.
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Contents
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========
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.. toctree::
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:maxdepth: 4
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:maxdepth: 5
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API Documentation <lib/galaxy.web.api>
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API Documentation <lib/galaxy.webapps.galaxy.api>
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Application Documentation <lib/galaxy>
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Application Documentation <lib/modules>
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Indices and tables
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==================
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@@ -113,6 +113,14 @@ converters Package
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:undoc-members:
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:show-inheritance:
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||||
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||||
:mod:`interval_to_fli` Module
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-----------------------------
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.. automodule:: galaxy.datatypes.converters.interval_to_fli
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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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:mod:`interval_to_interval_index_converter` Module
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--------------------------------------------------
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@@ -17,6 +17,14 @@ deferred Package
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:undoc-members:
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||||
:show-inheritance:
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||||
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||||
:mod:`genome_index` Module
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--------------------------
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.. automodule:: galaxy.jobs.deferred.genome_index
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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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||||
:mod:`genome_transfer` Module
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-----------------------------
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@@ -25,6 +25,14 @@ jobs Package
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:undoc-members:
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||||
:show-inheritance:
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||||
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||||
:mod:`mapper` Module
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--------------------
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.. automodule:: galaxy.jobs.mapper
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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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:mod:`transfer_manager` Module
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------------------------------
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@@ -40,6 +48,7 @@ Subpackages
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galaxy.jobs.actions
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galaxy.jobs.deferred
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galaxy.jobs.rules
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galaxy.jobs.runners
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galaxy.jobs.splitters
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@@ -0,0 +1,19 @@
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cli_job Package
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===============
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:mod:`cli_job` Package
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----------------------
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.. automodule:: galaxy.jobs.runners.cli_job
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:members:
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:undoc-members:
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:show-inheritance:
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:mod:`torque` Module
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--------------------
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.. automodule:: galaxy.jobs.runners.cli_job.torque
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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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||||
@@ -0,0 +1,19 @@
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cli_shell Package
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=================
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:mod:`cli_shell` Package
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------------------------
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.. automodule:: galaxy.jobs.runners.cli_shell
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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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:mod:`rsh` Module
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-----------------
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.. automodule:: galaxy.jobs.runners.cli_shell.rsh
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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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||||
@@ -9,6 +9,22 @@ runners Package
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:undoc-members:
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:show-inheritance:
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||||
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||||
:mod:`cli` Module
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-----------------
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.. automodule:: galaxy.jobs.runners.cli
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:members:
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:undoc-members:
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:show-inheritance:
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:mod:`condor` Module
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--------------------
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.. automodule:: galaxy.jobs.runners.condor
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:members:
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:undoc-members:
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:show-inheritance:
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:mod:`drmaa` Module
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-------------------
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@@ -57,3 +73,11 @@ runners Package
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:undoc-members:
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||||
:show-inheritance:
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||||
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Subpackages
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-----------
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.. toctree::
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galaxy.jobs.runners.cli_job
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galaxy.jobs.runners.cli_shell
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@@ -0,0 +1,11 @@
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importlib Package
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=================
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:mod:`importlib` Package
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------------------------
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.. automodule:: galaxy.util.backports.importlib
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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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||||
@@ -0,0 +1,18 @@
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backports Package
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=================
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:mod:`backports` Package
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------------------------
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.. automodule:: galaxy.util.backports
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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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Subpackages
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-----------
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.. toctree::
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galaxy.util.backports.importlib
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@@ -137,3 +137,10 @@ util Package
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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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galaxy.util.backports
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@@ -0,0 +1,43 @@
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phyloviz Package
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================
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:mod:`phyloviz` Package
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-----------------------
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.. automodule:: galaxy.visualization.data_providers.phyloviz
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:members:
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:undoc-members:
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:show-inheritance:
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:mod:`baseparser` Module
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------------------------
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.. automodule:: galaxy.visualization.data_providers.phyloviz.baseparser
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:members:
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:undoc-members:
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:show-inheritance:
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:mod:`newickparser` Module
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--------------------------
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.. automodule:: galaxy.visualization.data_providers.phyloviz.newickparser
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:members:
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:undoc-members:
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:show-inheritance:
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:mod:`nexusparser` Module
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-------------------------
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.. automodule:: galaxy.visualization.data_providers.phyloviz.nexusparser
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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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||||
:mod:`phyloxmlparser` Module
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----------------------------
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.. automodule:: galaxy.visualization.data_providers.phyloviz.phyloxmlparser
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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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||||
@@ -0,0 +1,42 @@
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data_providers Package
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======================
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:mod:`data_providers` Package
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-----------------------------
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.. automodule:: galaxy.visualization.data_providers
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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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||||
:mod:`basic` Module
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-------------------
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.. automodule:: galaxy.visualization.data_providers.basic
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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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||||
:mod:`genome` Module
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--------------------
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.. automodule:: galaxy.visualization.data_providers.genome
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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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||||
:mod:`registry` Module
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----------------------
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.. automodule:: galaxy.visualization.data_providers.registry
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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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||||
Subpackages
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-----------
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.. toctree::
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galaxy.visualization.data_providers.phyloviz
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@@ -0,0 +1,19 @@
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genome Package
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==============
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:mod:`genome` Package
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---------------------
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.. automodule:: galaxy.visualization.genome
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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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:mod:`visual_analytics` Module
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------------------------------
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.. automodule:: galaxy.visualization.genome.visual_analytics
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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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@@ -22,5 +22,7 @@ Subpackages
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.. toctree::
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galaxy.visualization.data_providers
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galaxy.visualization.genome
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galaxy.visualization.tracks
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@@ -9,14 +9,6 @@ tracks Package
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:undoc-members:
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:show-inheritance:
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||||
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||||
:mod:`data_providers` Module
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----------------------------
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||||
.. automodule:: galaxy.visualization.tracks.data_providers
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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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||||
:mod:`summary` Module
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||||
---------------------
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||||
@@ -25,11 +17,3 @@ tracks Package
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:undoc-members:
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||||
:show-inheritance:
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||||
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||||
:mod:`visual_analytics` Module
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------------------------------
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||||
.. automodule:: galaxy.visualization.tracks.visual_analytics
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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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||||
@@ -0,0 +1,11 @@
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controllers Package
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===================
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:mod:`admin` Module
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-------------------
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.. automodule:: galaxy.web.base.controllers.admin
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:members:
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||||
:undoc-members:
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||||
:show-inheritance:
|
||||
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||||
@@ -9,3 +9,10 @@ base Package
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||||
:undoc-members:
|
||||
:show-inheritance:
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||||
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||||
Subpackages
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||||
-----------
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||||
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||||
.. toctree::
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||||
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||||
galaxy.web.base.controllers
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@@ -38,9 +38,7 @@ Subpackages
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.. toctree::
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galaxy.web.api
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galaxy.web.base
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galaxy.web.controllers
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galaxy.web.framework
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galaxy.web.security
|
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|
||||
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@@ -41,6 +41,14 @@ controllers Package
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:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`repository_review` Module
|
||||
-------------------------------
|
||||
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||||
.. automodule:: galaxy.webapps.community.controllers.repository_review
|
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:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`upload` Module
|
||||
--------------------
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@@ -49,6 +57,14 @@ controllers Package
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:undoc-members:
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||||
:show-inheritance:
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||||
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:mod:`user` Module
|
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------------------
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.. automodule:: galaxy.webapps.community.controllers.user
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:members:
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||||
:undoc-members:
|
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:show-inheritance:
|
||||
|
||||
:mod:`workflow` Module
|
||||
----------------------
|
||||
|
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@@ -17,3 +17,11 @@ middleware Package
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:undoc-members:
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||||
:show-inheritance:
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||||
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||||
:mod:`remoteuser` Module
|
||||
------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.community.framework.middleware.remoteuser
|
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:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
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@@ -216,7 +216,23 @@ API Controllers
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:mod:`datasets` Module
|
||||
----------------------
|
||||
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.. automodule:: galaxy.web.api.datasets
|
||||
.. automodule:: galaxy.webapps.galaxy.api.datasets
|
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:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`folder_contents` Module
|
||||
-----------------------------
|
||||
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||||
.. automodule:: galaxy.webapps.galaxy.api.folder_contents
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`folders` Module
|
||||
---------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.galaxy.api.folders
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
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||||
@@ -224,7 +240,7 @@ API Controllers
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:mod:`forms` Module
|
||||
-------------------
|
||||
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||||
.. automodule:: galaxy.web.api.forms
|
||||
.. automodule:: galaxy.webapps.galaxy.api.forms
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
@@ -232,7 +248,31 @@ API Controllers
|
||||
:mod:`genomes` Module
|
||||
---------------------
|
||||
|
||||
.. automodule:: galaxy.web.api.genomes
|
||||
.. automodule:: galaxy.webapps.galaxy.api.genomes
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`group_roles` Module
|
||||
-------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.galaxy.api.group_roles
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`group_users` Module
|
||||
-------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.galaxy.api.group_users
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`groups` Module
|
||||
--------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.galaxy.api.groups
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
@@ -240,7 +280,7 @@ API Controllers
|
||||
:mod:`histories` Module
|
||||
-----------------------
|
||||
|
||||
.. automodule:: galaxy.web.api.histories
|
||||
.. automodule:: galaxy.webapps.galaxy.api.histories
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
@@ -248,7 +288,7 @@ API Controllers
|
||||
:mod:`history_contents` Module
|
||||
------------------------------
|
||||
|
||||
.. automodule:: galaxy.web.api.history_contents
|
||||
.. automodule:: galaxy.webapps.galaxy.api.history_contents
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
@@ -256,7 +296,7 @@ API Controllers
|
||||
:mod:`libraries` Module
|
||||
-----------------------
|
||||
|
||||
.. automodule:: galaxy.web.api.libraries
|
||||
.. automodule:: galaxy.webapps.galaxy.api.libraries
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
@@ -264,7 +304,7 @@ API Controllers
|
||||
:mod:`library_contents` Module
|
||||
------------------------------
|
||||
|
||||
.. automodule:: galaxy.web.api.library_contents
|
||||
.. automodule:: galaxy.webapps.galaxy.api.library_contents
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
@@ -272,7 +312,7 @@ API Controllers
|
||||
:mod:`permissions` Module
|
||||
-------------------------
|
||||
|
||||
.. automodule:: galaxy.web.api.permissions
|
||||
.. automodule:: galaxy.webapps.galaxy.api.permissions
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
@@ -280,7 +320,7 @@ API Controllers
|
||||
:mod:`quotas` Module
|
||||
--------------------
|
||||
|
||||
.. automodule:: galaxy.web.api.quotas
|
||||
.. automodule:: galaxy.webapps.galaxy.api.quotas
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
@@ -288,7 +328,7 @@ API Controllers
|
||||
:mod:`request_types` Module
|
||||
---------------------------
|
||||
|
||||
.. automodule:: galaxy.web.api.request_types
|
||||
.. automodule:: galaxy.webapps.galaxy.api.request_types
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
@@ -296,7 +336,7 @@ API Controllers
|
||||
:mod:`requests` Module
|
||||
----------------------
|
||||
|
||||
.. automodule:: galaxy.web.api.requests
|
||||
.. automodule:: galaxy.webapps.galaxy.api.requests
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
@@ -304,7 +344,7 @@ API Controllers
|
||||
:mod:`roles` Module
|
||||
-------------------
|
||||
|
||||
.. automodule:: galaxy.web.api.roles
|
||||
.. automodule:: galaxy.webapps.galaxy.api.roles
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
@@ -312,7 +352,7 @@ API Controllers
|
||||
:mod:`samples` Module
|
||||
---------------------
|
||||
|
||||
.. automodule:: galaxy.web.api.samples
|
||||
.. automodule:: galaxy.webapps.galaxy.api.samples
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
@@ -320,7 +360,7 @@ API Controllers
|
||||
:mod:`tools` Module
|
||||
-------------------
|
||||
|
||||
.. automodule:: galaxy.web.api.tools
|
||||
.. automodule:: galaxy.webapps.galaxy.api.tools
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
@@ -328,7 +368,7 @@ API Controllers
|
||||
:mod:`users` Module
|
||||
-------------------
|
||||
|
||||
.. automodule:: galaxy.web.api.users
|
||||
.. automodule:: galaxy.webapps.galaxy.api.users
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
@@ -336,7 +376,7 @@ API Controllers
|
||||
:mod:`visualizations` Module
|
||||
----------------------------
|
||||
|
||||
.. automodule:: galaxy.web.api.visualizations
|
||||
.. automodule:: galaxy.webapps.galaxy.api.visualizations
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
@@ -344,9 +384,8 @@ API Controllers
|
||||
:mod:`workflows` Module
|
||||
-----------------------
|
||||
|
||||
.. automodule:: galaxy.web.api.workflows
|
||||
.. automodule:: galaxy.webapps.galaxy.api.workflows
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
@@ -0,0 +1,179 @@
|
||||
api Package
|
||||
===========
|
||||
|
||||
:mod:`datasets` Module
|
||||
----------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.galaxy.api.datasets
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`folder_contents` Module
|
||||
-----------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.galaxy.api.folder_contents
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`folders` Module
|
||||
---------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.galaxy.api.folders
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`forms` Module
|
||||
-------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.galaxy.api.forms
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`genomes` Module
|
||||
---------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.galaxy.api.genomes
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`group_roles` Module
|
||||
-------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.galaxy.api.group_roles
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`group_users` Module
|
||||
-------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.galaxy.api.group_users
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`groups` Module
|
||||
--------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.galaxy.api.groups
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`histories` Module
|
||||
-----------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.galaxy.api.histories
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`history_contents` Module
|
||||
------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.galaxy.api.history_contents
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`libraries` Module
|
||||
-----------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.galaxy.api.libraries
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`library_contents` Module
|
||||
------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.galaxy.api.library_contents
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`permissions` Module
|
||||
-------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.galaxy.api.permissions
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`quotas` Module
|
||||
--------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.galaxy.api.quotas
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`request_types` Module
|
||||
---------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.galaxy.api.request_types
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`requests` Module
|
||||
----------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.galaxy.api.requests
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`roles` Module
|
||||
-------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.galaxy.api.roles
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`samples` Module
|
||||
---------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.galaxy.api.samples
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`tools` Module
|
||||
-------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.galaxy.api.tools
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`users` Module
|
||||
-------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.galaxy.api.users
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`visualizations` Module
|
||||
----------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.galaxy.api.visualizations
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`workflows` Module
|
||||
-----------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.galaxy.api.workflows
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
+30
-38
@@ -4,7 +4,7 @@ controllers Package
|
||||
:mod:`controllers` Package
|
||||
--------------------------
|
||||
|
||||
.. automodule:: galaxy.web.controllers
|
||||
.. automodule:: galaxy.webapps.galaxy.controllers
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
@@ -12,7 +12,7 @@ controllers Package
|
||||
:mod:`admin` Module
|
||||
-------------------
|
||||
|
||||
.. automodule:: galaxy.web.controllers.admin
|
||||
.. automodule:: galaxy.webapps.galaxy.controllers.admin
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
@@ -20,7 +20,7 @@ controllers Package
|
||||
:mod:`admin_toolshed` Module
|
||||
----------------------------
|
||||
|
||||
.. automodule:: galaxy.web.controllers.admin_toolshed
|
||||
.. automodule:: galaxy.webapps.galaxy.controllers.admin_toolshed
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
@@ -28,15 +28,15 @@ controllers Package
|
||||
:mod:`async` Module
|
||||
-------------------
|
||||
|
||||
.. automodule:: galaxy.web.controllers.async
|
||||
.. automodule:: galaxy.webapps.galaxy.controllers.async
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`cloud` Module
|
||||
-------------------
|
||||
:mod:`cloudlaunch` Module
|
||||
-------------------------
|
||||
|
||||
.. automodule:: galaxy.web.controllers.cloud
|
||||
.. automodule:: galaxy.webapps.galaxy.controllers.cloudlaunch
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
@@ -44,7 +44,7 @@ controllers Package
|
||||
:mod:`data_admin` Module
|
||||
------------------------
|
||||
|
||||
.. automodule:: galaxy.web.controllers.data_admin
|
||||
.. automodule:: galaxy.webapps.galaxy.controllers.data_admin
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
@@ -52,7 +52,7 @@ controllers Package
|
||||
:mod:`dataset` Module
|
||||
---------------------
|
||||
|
||||
.. automodule:: galaxy.web.controllers.dataset
|
||||
.. automodule:: galaxy.webapps.galaxy.controllers.dataset
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
@@ -60,7 +60,7 @@ controllers Package
|
||||
:mod:`error` Module
|
||||
-------------------
|
||||
|
||||
.. automodule:: galaxy.web.controllers.error
|
||||
.. automodule:: galaxy.webapps.galaxy.controllers.error
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
@@ -68,7 +68,7 @@ controllers Package
|
||||
:mod:`external_service` Module
|
||||
------------------------------
|
||||
|
||||
.. automodule:: galaxy.web.controllers.external_service
|
||||
.. automodule:: galaxy.webapps.galaxy.controllers.external_service
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
@@ -76,7 +76,7 @@ controllers Package
|
||||
:mod:`external_services` Module
|
||||
-------------------------------
|
||||
|
||||
.. automodule:: galaxy.web.controllers.external_services
|
||||
.. automodule:: galaxy.webapps.galaxy.controllers.external_services
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
@@ -84,7 +84,7 @@ controllers Package
|
||||
:mod:`forms` Module
|
||||
-------------------
|
||||
|
||||
.. automodule:: galaxy.web.controllers.forms
|
||||
.. automodule:: galaxy.webapps.galaxy.controllers.forms
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
@@ -92,7 +92,7 @@ controllers Package
|
||||
:mod:`history` Module
|
||||
---------------------
|
||||
|
||||
.. automodule:: galaxy.web.controllers.history
|
||||
.. automodule:: galaxy.webapps.galaxy.controllers.history
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
@@ -100,7 +100,7 @@ controllers Package
|
||||
:mod:`library` Module
|
||||
---------------------
|
||||
|
||||
.. automodule:: galaxy.web.controllers.library
|
||||
.. automodule:: galaxy.webapps.galaxy.controllers.library
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
@@ -108,7 +108,7 @@ controllers Package
|
||||
:mod:`library_admin` Module
|
||||
---------------------------
|
||||
|
||||
.. automodule:: galaxy.web.controllers.library_admin
|
||||
.. automodule:: galaxy.webapps.galaxy.controllers.library_admin
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
@@ -116,7 +116,7 @@ controllers Package
|
||||
:mod:`library_common` Module
|
||||
----------------------------
|
||||
|
||||
.. automodule:: galaxy.web.controllers.library_common
|
||||
.. automodule:: galaxy.webapps.galaxy.controllers.library_common
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
@@ -124,7 +124,7 @@ controllers Package
|
||||
:mod:`mobile` Module
|
||||
--------------------
|
||||
|
||||
.. automodule:: galaxy.web.controllers.mobile
|
||||
.. automodule:: galaxy.webapps.galaxy.controllers.mobile
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
@@ -132,7 +132,7 @@ controllers Package
|
||||
:mod:`page` Module
|
||||
------------------
|
||||
|
||||
.. automodule:: galaxy.web.controllers.page
|
||||
.. automodule:: galaxy.webapps.galaxy.controllers.page
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
@@ -140,7 +140,7 @@ controllers Package
|
||||
:mod:`request_type` Module
|
||||
--------------------------
|
||||
|
||||
.. automodule:: galaxy.web.controllers.request_type
|
||||
.. automodule:: galaxy.webapps.galaxy.controllers.request_type
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
@@ -148,7 +148,7 @@ controllers Package
|
||||
:mod:`requests` Module
|
||||
----------------------
|
||||
|
||||
.. automodule:: galaxy.web.controllers.requests
|
||||
.. automodule:: galaxy.webapps.galaxy.controllers.requests
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
@@ -156,7 +156,7 @@ controllers Package
|
||||
:mod:`requests_admin` Module
|
||||
----------------------------
|
||||
|
||||
.. automodule:: galaxy.web.controllers.requests_admin
|
||||
.. automodule:: galaxy.webapps.galaxy.controllers.requests_admin
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
@@ -164,7 +164,7 @@ controllers Package
|
||||
:mod:`requests_common` Module
|
||||
-----------------------------
|
||||
|
||||
.. automodule:: galaxy.web.controllers.requests_common
|
||||
.. automodule:: galaxy.webapps.galaxy.controllers.requests_common
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
@@ -172,7 +172,7 @@ controllers Package
|
||||
:mod:`root` Module
|
||||
------------------
|
||||
|
||||
.. automodule:: galaxy.web.controllers.root
|
||||
.. automodule:: galaxy.webapps.galaxy.controllers.root
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
@@ -180,7 +180,7 @@ controllers Package
|
||||
:mod:`tag` Module
|
||||
-----------------
|
||||
|
||||
.. automodule:: galaxy.web.controllers.tag
|
||||
.. automodule:: galaxy.webapps.galaxy.controllers.tag
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
@@ -188,15 +188,7 @@ controllers Package
|
||||
:mod:`tool_runner` Module
|
||||
-------------------------
|
||||
|
||||
.. automodule:: galaxy.web.controllers.tool_runner
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`tracks` Module
|
||||
--------------------
|
||||
|
||||
.. automodule:: galaxy.web.controllers.tracks
|
||||
.. automodule:: galaxy.webapps.galaxy.controllers.tool_runner
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
@@ -204,7 +196,7 @@ controllers Package
|
||||
:mod:`ucsc_proxy` Module
|
||||
------------------------
|
||||
|
||||
.. automodule:: galaxy.web.controllers.ucsc_proxy
|
||||
.. automodule:: galaxy.webapps.galaxy.controllers.ucsc_proxy
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
@@ -212,7 +204,7 @@ controllers Package
|
||||
:mod:`user` Module
|
||||
------------------
|
||||
|
||||
.. automodule:: galaxy.web.controllers.user
|
||||
.. automodule:: galaxy.webapps.galaxy.controllers.user
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
@@ -220,7 +212,7 @@ controllers Package
|
||||
:mod:`visualization` Module
|
||||
---------------------------
|
||||
|
||||
.. automodule:: galaxy.web.controllers.visualization
|
||||
.. automodule:: galaxy.webapps.galaxy.controllers.visualization
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
@@ -228,7 +220,7 @@ controllers Package
|
||||
:mod:`workflow` Module
|
||||
----------------------
|
||||
|
||||
.. automodule:: galaxy.web.controllers.workflow
|
||||
.. automodule:: galaxy.webapps.galaxy.controllers.workflow
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
@@ -0,0 +1,19 @@
|
||||
galaxy Package
|
||||
==============
|
||||
|
||||
:mod:`buildapp` Module
|
||||
----------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.galaxy.buildapp
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Subpackages
|
||||
-----------
|
||||
|
||||
.. toctree::
|
||||
|
||||
galaxy.webapps.galaxy.api
|
||||
galaxy.webapps.galaxy.controllers
|
||||
|
||||
@@ -16,5 +16,6 @@ Subpackages
|
||||
|
||||
galaxy.webapps.community
|
||||
galaxy.webapps.demo_sequencer
|
||||
galaxy.webapps.galaxy
|
||||
galaxy.webapps.reports
|
||||
|
||||
|
||||
Reference in New Issue
Block a user