mirror of
https://github.com/galaxyproject/galaxy.git
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Update to sphinx-apidoc v1.3.1 .
sphinx-apidoc -M -o doc/source/lib/ lib/
This commit is contained in:
Nicola Soranzo
+1
-3
@@ -17,8 +17,6 @@ import sys, os, datetime
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####### REQUIRED GALAXY INCLUDES
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sys.path.append(os.path.join(os.getcwd(), '../../lib'))
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import galaxy
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from galaxy import eggs
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#######
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@@ -103,7 +101,7 @@ pygments_style = 'sphinx'
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# The theme to use for HTML and HTML Help pages. See the documentation for
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# a list of builtin themes.
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html_theme = 'default'
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html_theme = 'classic'
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# Theme options are theme-specific and customize the look and feel of a theme
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# further. For a list of options available for each theme, see the
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@@ -1,11 +1,20 @@
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actions Package
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===============
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galaxy.actions package
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======================
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:mod:`admin` Module
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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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Submodules
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----------
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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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@@ -1,35 +1,36 @@
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providers Package
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=================
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:mod:`providers` Package
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------------------------
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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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:mod:`alwaysreject` Module
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--------------------------
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Submodules
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----------
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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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:mod:`ldap_ad` Module
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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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:mod:`localdb` Module
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---------------------
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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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@@ -1,8 +1,5 @@
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auth Package
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============
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:mod:`auth` Package
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-------------------
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galaxy.auth package
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===================
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.. automodule:: galaxy.auth
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:members:
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@@ -1,50 +1,7 @@
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dataset_collections Package
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===========================
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galaxy.dataset_collections package
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==================================
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:mod:`builder` Module
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---------------------
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.. automodule:: galaxy.dataset_collections.builder
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:members:
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:undoc-members:
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:show-inheritance:
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:mod:`matching` Module
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----------------------
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.. automodule:: galaxy.dataset_collections.matching
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:members:
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:undoc-members:
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:show-inheritance:
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:mod:`registry` Module
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----------------------
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.. automodule:: galaxy.dataset_collections.registry
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:members:
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:undoc-members:
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:show-inheritance:
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:mod:`structure` Module
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-----------------------
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.. automodule:: galaxy.dataset_collections.structure
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:members:
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:undoc-members:
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:show-inheritance:
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:mod:`subcollections` Module
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----------------------------
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.. automodule:: galaxy.dataset_collections.subcollections
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:members:
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:undoc-members:
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:show-inheritance:
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:mod:`type_description` Module
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------------------------------
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.. automodule:: galaxy.dataset_collections.type_description
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.. automodule:: galaxy.dataset_collections
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:members:
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:undoc-members:
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:show-inheritance:
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@@ -56,3 +13,55 @@ Subpackages
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galaxy.dataset_collections.types
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Submodules
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----------
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galaxy.dataset_collections.builder module
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-----------------------------------------
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.. automodule:: galaxy.dataset_collections.builder
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:members:
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:undoc-members:
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:show-inheritance:
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galaxy.dataset_collections.matching module
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------------------------------------------
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.. automodule:: galaxy.dataset_collections.matching
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:members:
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:undoc-members:
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:show-inheritance:
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galaxy.dataset_collections.registry module
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------------------------------------------
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.. automodule:: galaxy.dataset_collections.registry
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:members:
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:undoc-members:
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:show-inheritance:
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galaxy.dataset_collections.structure module
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-------------------------------------------
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.. automodule:: galaxy.dataset_collections.structure
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:members:
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:undoc-members:
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:show-inheritance:
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galaxy.dataset_collections.subcollections module
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------------------------------------------------
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.. automodule:: galaxy.dataset_collections.subcollections
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:members:
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:undoc-members:
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:show-inheritance:
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galaxy.dataset_collections.type_description module
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--------------------------------------------------
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.. automodule:: galaxy.dataset_collections.type_description
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:members:
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:undoc-members:
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:show-inheritance:
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@@ -1,27 +1,28 @@
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types Package
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=============
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:mod:`types` Package
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--------------------
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galaxy.dataset_collections.types package
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========================================
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.. automodule:: galaxy.dataset_collections.types
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:members:
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:undoc-members:
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:show-inheritance:
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:mod:`list` Module
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------------------
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Submodules
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----------
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galaxy.dataset_collections.types.list module
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--------------------------------------------
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.. automodule:: galaxy.dataset_collections.types.list
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:members:
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:undoc-members:
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:show-inheritance:
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:mod:`paired` Module
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--------------------
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galaxy.dataset_collections.types.paired module
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----------------------------------------------
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.. automodule:: galaxy.dataset_collections.types.paired
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:members:
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:undoc-members:
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:show-inheritance:
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@@ -1,235 +1,244 @@
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converters Package
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==================
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galaxy.datatypes.converters package
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===================================
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:mod:`bed_to_gff_converter` Module
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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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Submodules
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----------
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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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:mod:`bedgraph_to_array_tree_converter` Module
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----------------------------------------------
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galaxy.datatypes.converters.bedgraph_to_array_tree_converter module
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-------------------------------------------------------------------
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.. automodule:: galaxy.datatypes.converters.bedgraph_to_array_tree_converter
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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:`bgzip` Module
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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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||||
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:mod:`fasta_to_len` Module
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--------------------------
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galaxy.datatypes.converters.fasta_to_len module
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-----------------------------------------------
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.. automodule:: galaxy.datatypes.converters.fasta_to_len
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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:`fasta_to_tabular_converter` Module
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----------------------------------------
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galaxy.datatypes.converters.fasta_to_tabular_converter module
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-------------------------------------------------------------
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.. automodule:: galaxy.datatypes.converters.fasta_to_tabular_converter
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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:`fastq_to_fqtoc` Module
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----------------------------
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galaxy.datatypes.converters.fastq_to_fqtoc module
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-------------------------------------------------
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.. automodule:: galaxy.datatypes.converters.fastq_to_fqtoc
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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:`fastqsolexa_to_fasta_converter` Module
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--------------------------------------------
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galaxy.datatypes.converters.fastqsolexa_to_fasta_converter module
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-----------------------------------------------------------------
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.. automodule:: galaxy.datatypes.converters.fastqsolexa_to_fasta_converter
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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:`fastqsolexa_to_qual_converter` Module
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-------------------------------------------
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galaxy.datatypes.converters.fastqsolexa_to_qual_converter module
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----------------------------------------------------------------
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.. automodule:: galaxy.datatypes.converters.fastqsolexa_to_qual_converter
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:members:
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||||
:undoc-members:
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||||
:show-inheritance:
|
||||
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||||
:mod:`gff_to_bed_converter` Module
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----------------------------------
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galaxy.datatypes.converters.gff_to_bed_converter module
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-------------------------------------------------------
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||||
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.. automodule:: galaxy.datatypes.converters.gff_to_bed_converter
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:members:
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||||
:undoc-members:
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||||
:show-inheritance:
|
||||
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:mod:`gff_to_interval_index_converter` Module
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---------------------------------------------
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galaxy.datatypes.converters.gff_to_interval_index_converter module
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------------------------------------------------------------------
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.. automodule:: galaxy.datatypes.converters.gff_to_interval_index_converter
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:members:
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||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
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:mod:`interval_to_bed_converter` Module
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---------------------------------------
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galaxy.datatypes.converters.interval_to_bed_converter module
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------------------------------------------------------------
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.. automodule:: galaxy.datatypes.converters.interval_to_bed_converter
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:members:
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||||
:undoc-members:
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||||
:show-inheritance:
|
||||
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:mod:`interval_to_bedstrict_converter` Module
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---------------------------------------------
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galaxy.datatypes.converters.interval_to_bedstrict_converter module
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------------------------------------------------------------------
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.. automodule:: galaxy.datatypes.converters.interval_to_bedstrict_converter
|
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:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
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:mod:`interval_to_coverage` Module
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----------------------------------
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galaxy.datatypes.converters.interval_to_coverage module
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-------------------------------------------------------
|
||||
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.. automodule:: galaxy.datatypes.converters.interval_to_coverage
|
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:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`interval_to_fli` Module
|
||||
-----------------------------
|
||||
galaxy.datatypes.converters.interval_to_fli module
|
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--------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.converters.interval_to_fli
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`interval_to_interval_index_converter` Module
|
||||
--------------------------------------------------
|
||||
galaxy.datatypes.converters.interval_to_interval_index_converter module
|
||||
-----------------------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.converters.interval_to_interval_index_converter
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`interval_to_tabix_converter` Module
|
||||
-----------------------------------------
|
||||
galaxy.datatypes.converters.interval_to_tabix_converter module
|
||||
--------------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.converters.interval_to_tabix_converter
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`lped_to_fped_converter` Module
|
||||
------------------------------------
|
||||
galaxy.datatypes.converters.lped_to_fped_converter module
|
||||
---------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.converters.lped_to_fped_converter
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`lped_to_pbed_converter` Module
|
||||
------------------------------------
|
||||
galaxy.datatypes.converters.lped_to_pbed_converter module
|
||||
---------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.converters.lped_to_pbed_converter
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`maf_to_fasta_converter` Module
|
||||
------------------------------------
|
||||
galaxy.datatypes.converters.maf_to_fasta_converter module
|
||||
---------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.converters.maf_to_fasta_converter
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`maf_to_interval_converter` Module
|
||||
---------------------------------------
|
||||
galaxy.datatypes.converters.maf_to_interval_converter module
|
||||
------------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.converters.maf_to_interval_converter
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`pbed_ldreduced_converter` Module
|
||||
--------------------------------------
|
||||
galaxy.datatypes.converters.pbed_ldreduced_converter module
|
||||
-----------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.converters.pbed_ldreduced_converter
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`pbed_to_lped_converter` Module
|
||||
------------------------------------
|
||||
galaxy.datatypes.converters.pbed_to_lped_converter module
|
||||
---------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.converters.pbed_to_lped_converter
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`picard_interval_list_to_bed6_converter` Module
|
||||
----------------------------------------------------
|
||||
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:
|
||||
|
||||
:mod:`pileup_to_interval_index_converter` Module
|
||||
------------------------------------------------
|
||||
galaxy.datatypes.converters.pileup_to_interval_index_converter module
|
||||
---------------------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.converters.pileup_to_interval_index_converter
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`sam_to_bam` Module
|
||||
------------------------
|
||||
galaxy.datatypes.converters.sam_to_bam module
|
||||
---------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.converters.sam_to_bam
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`vcf_to_interval_index_converter` Module
|
||||
---------------------------------------------
|
||||
galaxy.datatypes.converters.vcf_to_interval_index_converter module
|
||||
------------------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.converters.vcf_to_interval_index_converter
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`vcf_to_vcf_bgzip` Module
|
||||
------------------------------
|
||||
galaxy.datatypes.converters.vcf_to_vcf_bgzip module
|
||||
---------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.converters.vcf_to_vcf_bgzip
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`wiggle_to_array_tree_converter` Module
|
||||
--------------------------------------------
|
||||
galaxy.datatypes.converters.wiggle_to_array_tree_converter module
|
||||
-----------------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.converters.wiggle_to_array_tree_converter
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`wiggle_to_simple_converter` Module
|
||||
----------------------------------------
|
||||
galaxy.datatypes.converters.wiggle_to_simple_converter module
|
||||
-------------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.converters.wiggle_to_simple_converter
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
|
||||
@@ -1,83 +1,84 @@
|
||||
dataproviders Package
|
||||
=====================
|
||||
|
||||
:mod:`dataproviders` Package
|
||||
----------------------------
|
||||
galaxy.datatypes.dataproviders package
|
||||
======================================
|
||||
|
||||
.. automodule:: galaxy.datatypes.dataproviders
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`base` Module
|
||||
------------------
|
||||
Submodules
|
||||
----------
|
||||
|
||||
galaxy.datatypes.dataproviders.base module
|
||||
------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.dataproviders.base
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`chunk` Module
|
||||
-------------------
|
||||
galaxy.datatypes.dataproviders.chunk module
|
||||
-------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.dataproviders.chunk
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`column` Module
|
||||
--------------------
|
||||
galaxy.datatypes.dataproviders.column module
|
||||
--------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.dataproviders.column
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`dataset` Module
|
||||
---------------------
|
||||
galaxy.datatypes.dataproviders.dataset module
|
||||
---------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.dataproviders.dataset
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`decorators` Module
|
||||
------------------------
|
||||
galaxy.datatypes.dataproviders.decorators module
|
||||
------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.dataproviders.decorators
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`exceptions` Module
|
||||
------------------------
|
||||
galaxy.datatypes.dataproviders.exceptions module
|
||||
------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.dataproviders.exceptions
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`external` Module
|
||||
----------------------
|
||||
galaxy.datatypes.dataproviders.external module
|
||||
----------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.dataproviders.external
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`hierarchy` Module
|
||||
-----------------------
|
||||
galaxy.datatypes.dataproviders.hierarchy module
|
||||
-----------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.dataproviders.hierarchy
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`line` Module
|
||||
------------------
|
||||
galaxy.datatypes.dataproviders.line module
|
||||
------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.dataproviders.line
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
|
||||
@@ -1,35 +1,36 @@
|
||||
display_applications Package
|
||||
============================
|
||||
|
||||
:mod:`display_applications` Package
|
||||
-----------------------------------
|
||||
galaxy.datatypes.display_applications package
|
||||
=============================================
|
||||
|
||||
.. automodule:: galaxy.datatypes.display_applications
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`application` Module
|
||||
-------------------------
|
||||
Submodules
|
||||
----------
|
||||
|
||||
galaxy.datatypes.display_applications.application module
|
||||
--------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.display_applications.application
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`parameters` Module
|
||||
------------------------
|
||||
galaxy.datatypes.display_applications.parameters module
|
||||
-------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.display_applications.parameters
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`util` Module
|
||||
------------------
|
||||
galaxy.datatypes.display_applications.util module
|
||||
-------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.display_applications.util
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
|
||||
+183
-166
@@ -1,170 +1,7 @@
|
||||
datatypes Package
|
||||
=================
|
||||
galaxy.datatypes package
|
||||
========================
|
||||
|
||||
:mod:`assembly` Module
|
||||
----------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.assembly
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`binary` Module
|
||||
--------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.binary
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`checkers` Module
|
||||
----------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.checkers
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`chrominfo` Module
|
||||
-----------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.chrominfo
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`coverage` Module
|
||||
----------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.coverage
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`data` Module
|
||||
------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.data
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`genetics` Module
|
||||
----------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.genetics
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`graph` Module
|
||||
-------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.graph
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`images` Module
|
||||
--------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.images
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`interval` Module
|
||||
----------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.interval
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`metadata` Module
|
||||
----------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.metadata
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`msa` Module
|
||||
-----------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.msa
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`ngsindex` Module
|
||||
----------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.ngsindex
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`qualityscore` Module
|
||||
--------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.qualityscore
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`registry` Module
|
||||
----------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.registry
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`sequence` Module
|
||||
----------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.sequence
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`sniff` Module
|
||||
-------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.sniff
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`tabular` Module
|
||||
---------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.tabular
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`text` Module
|
||||
------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.text
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`tracks` Module
|
||||
--------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.tracks
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`xml` Module
|
||||
-----------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.xml
|
||||
.. automodule:: galaxy.datatypes
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
@@ -179,3 +16,183 @@ Subpackages
|
||||
galaxy.datatypes.display_applications
|
||||
galaxy.datatypes.util
|
||||
|
||||
Submodules
|
||||
----------
|
||||
|
||||
galaxy.datatypes.assembly module
|
||||
--------------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.assembly
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.datatypes.binary module
|
||||
------------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.binary
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.datatypes.checkers module
|
||||
--------------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.checkers
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.datatypes.chrominfo module
|
||||
---------------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.chrominfo
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.datatypes.coverage module
|
||||
--------------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.coverage
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.datatypes.data module
|
||||
----------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.data
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.datatypes.genetics module
|
||||
--------------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.genetics
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.datatypes.graph module
|
||||
-----------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.graph
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.datatypes.images module
|
||||
------------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.images
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.datatypes.interval module
|
||||
--------------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.interval
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.datatypes.metadata module
|
||||
--------------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.metadata
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.datatypes.msa module
|
||||
---------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.msa
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.datatypes.ngsindex module
|
||||
--------------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.ngsindex
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.datatypes.proteomics module
|
||||
----------------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.proteomics
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.datatypes.qualityscore module
|
||||
------------------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.qualityscore
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.datatypes.registry module
|
||||
--------------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.registry
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.datatypes.sequence module
|
||||
--------------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.sequence
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.datatypes.sniff module
|
||||
-----------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.sniff
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.datatypes.tabular module
|
||||
-------------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.tabular
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.datatypes.text module
|
||||
----------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.text
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.datatypes.tracks module
|
||||
------------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.tracks
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.datatypes.xml module
|
||||
---------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.xml
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
|
||||
@@ -1,35 +1,36 @@
|
||||
util Package
|
||||
============
|
||||
|
||||
:mod:`util` Package
|
||||
-------------------
|
||||
galaxy.datatypes.util package
|
||||
=============================
|
||||
|
||||
.. automodule:: galaxy.datatypes.util
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`generic_util` Module
|
||||
--------------------------
|
||||
Submodules
|
||||
----------
|
||||
|
||||
galaxy.datatypes.util.generic_util module
|
||||
-----------------------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.util.generic_util
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`gff_util` Module
|
||||
----------------------
|
||||
galaxy.datatypes.util.gff_util module
|
||||
-------------------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.util.gff_util
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`image_util` Module
|
||||
------------------------
|
||||
galaxy.datatypes.util.image_util module
|
||||
---------------------------------------
|
||||
|
||||
.. automodule:: galaxy.datatypes.util.image_util
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
|
||||
@@ -1,27 +1,28 @@
|
||||
eggs Package
|
||||
============
|
||||
|
||||
:mod:`eggs` Package
|
||||
-------------------
|
||||
galaxy.eggs package
|
||||
===================
|
||||
|
||||
.. automodule:: galaxy.eggs
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`dist` Module
|
||||
------------------
|
||||
Submodules
|
||||
----------
|
||||
|
||||
galaxy.eggs.dist module
|
||||
-----------------------
|
||||
|
||||
.. automodule:: galaxy.eggs.dist
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`scramble` Module
|
||||
----------------------
|
||||
galaxy.eggs.scramble module
|
||||
---------------------------
|
||||
|
||||
.. automodule:: galaxy.eggs.scramble
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
|
||||
@@ -1,19 +1,20 @@
|
||||
exceptions Package
|
||||
==================
|
||||
|
||||
:mod:`exceptions` Package
|
||||
-------------------------
|
||||
galaxy.exceptions package
|
||||
=========================
|
||||
|
||||
.. automodule:: galaxy.exceptions
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`error_codes` Module
|
||||
-------------------------
|
||||
Submodules
|
||||
----------
|
||||
|
||||
galaxy.exceptions.error_codes module
|
||||
------------------------------------
|
||||
|
||||
.. automodule:: galaxy.exceptions.error_codes
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
|
||||
@@ -1,11 +1,20 @@
|
||||
result_handlers Package
|
||||
=======================
|
||||
galaxy.external_services.result_handlers package
|
||||
================================================
|
||||
|
||||
:mod:`basic` Module
|
||||
-------------------
|
||||
.. automodule:: galaxy.external_services.result_handlers
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Submodules
|
||||
----------
|
||||
|
||||
galaxy.external_services.result_handlers.basic module
|
||||
-----------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.external_services.result_handlers.basic
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
|
||||
@@ -1,26 +1,7 @@
|
||||
external_services Package
|
||||
=========================
|
||||
galaxy.external_services package
|
||||
================================
|
||||
|
||||
:mod:`actions` Module
|
||||
---------------------
|
||||
|
||||
.. automodule:: galaxy.external_services.actions
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`parameters` Module
|
||||
------------------------
|
||||
|
||||
.. automodule:: galaxy.external_services.parameters
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`service` Module
|
||||
---------------------
|
||||
|
||||
.. automodule:: galaxy.external_services.service
|
||||
.. automodule:: galaxy.external_services
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
@@ -32,3 +13,31 @@ Subpackages
|
||||
|
||||
galaxy.external_services.result_handlers
|
||||
|
||||
Submodules
|
||||
----------
|
||||
|
||||
galaxy.external_services.actions module
|
||||
---------------------------------------
|
||||
|
||||
.. automodule:: galaxy.external_services.actions
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.external_services.parameters module
|
||||
------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.external_services.parameters
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.external_services.service module
|
||||
---------------------------------------
|
||||
|
||||
.. automodule:: galaxy.external_services.service
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
|
||||
@@ -1,11 +1,20 @@
|
||||
forms Package
|
||||
=============
|
||||
galaxy.forms package
|
||||
====================
|
||||
|
||||
:mod:`forms` Module
|
||||
-------------------
|
||||
.. automodule:: galaxy.forms
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Submodules
|
||||
----------
|
||||
|
||||
galaxy.forms.forms module
|
||||
-------------------------
|
||||
|
||||
.. automodule:: galaxy.forms.forms
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
|
||||
@@ -1,19 +1,20 @@
|
||||
actions Package
|
||||
===============
|
||||
|
||||
:mod:`actions` Package
|
||||
----------------------
|
||||
galaxy.jobs.actions package
|
||||
===========================
|
||||
|
||||
.. automodule:: galaxy.jobs.actions
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`post` Module
|
||||
------------------
|
||||
Submodules
|
||||
----------
|
||||
|
||||
galaxy.jobs.actions.post module
|
||||
-------------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.actions.post
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
|
||||
@@ -1,35 +1,36 @@
|
||||
deferred Package
|
||||
================
|
||||
|
||||
:mod:`deferred` Package
|
||||
-----------------------
|
||||
galaxy.jobs.deferred package
|
||||
============================
|
||||
|
||||
.. automodule:: galaxy.jobs.deferred
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`data_transfer` Module
|
||||
---------------------------
|
||||
Submodules
|
||||
----------
|
||||
|
||||
galaxy.jobs.deferred.data_transfer module
|
||||
-----------------------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.deferred.data_transfer
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`manual_data_transfer` Module
|
||||
----------------------------------
|
||||
galaxy.jobs.deferred.manual_data_transfer module
|
||||
------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.deferred.manual_data_transfer
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`pacific_biosciences_smrt_portal` Module
|
||||
---------------------------------------------
|
||||
galaxy.jobs.deferred.pacific_biosciences_smrt_portal module
|
||||
-----------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.deferred.pacific_biosciences_smrt_portal
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
|
||||
@@ -1,43 +1,44 @@
|
||||
collectl Package
|
||||
================
|
||||
|
||||
:mod:`collectl` Package
|
||||
-----------------------
|
||||
galaxy.jobs.metrics.collectl package
|
||||
====================================
|
||||
|
||||
.. automodule:: galaxy.jobs.metrics.collectl
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`cli` Module
|
||||
-----------------
|
||||
Submodules
|
||||
----------
|
||||
|
||||
galaxy.jobs.metrics.collectl.cli module
|
||||
---------------------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.metrics.collectl.cli
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`processes` Module
|
||||
-----------------------
|
||||
galaxy.jobs.metrics.collectl.processes module
|
||||
---------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.metrics.collectl.processes
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`stats` Module
|
||||
-------------------
|
||||
galaxy.jobs.metrics.collectl.stats module
|
||||
-----------------------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.metrics.collectl.stats
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`subsystems` Module
|
||||
------------------------
|
||||
galaxy.jobs.metrics.collectl.subsystems module
|
||||
----------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.metrics.collectl.subsystems
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
|
||||
@@ -1,59 +1,60 @@
|
||||
instrumenters Package
|
||||
=====================
|
||||
|
||||
:mod:`instrumenters` Package
|
||||
----------------------------
|
||||
galaxy.jobs.metrics.instrumenters package
|
||||
=========================================
|
||||
|
||||
.. automodule:: galaxy.jobs.metrics.instrumenters
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`collectl` Module
|
||||
----------------------
|
||||
Submodules
|
||||
----------
|
||||
|
||||
galaxy.jobs.metrics.instrumenters.collectl module
|
||||
-------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.metrics.instrumenters.collectl
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`core` Module
|
||||
------------------
|
||||
galaxy.jobs.metrics.instrumenters.core module
|
||||
---------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.metrics.instrumenters.core
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`cpuinfo` Module
|
||||
---------------------
|
||||
galaxy.jobs.metrics.instrumenters.cpuinfo module
|
||||
------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.metrics.instrumenters.cpuinfo
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`env` Module
|
||||
-----------------
|
||||
galaxy.jobs.metrics.instrumenters.env module
|
||||
--------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.metrics.instrumenters.env
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`meminfo` Module
|
||||
---------------------
|
||||
galaxy.jobs.metrics.instrumenters.meminfo module
|
||||
------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.metrics.instrumenters.meminfo
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`uname` Module
|
||||
-------------------
|
||||
galaxy.jobs.metrics.instrumenters.uname module
|
||||
----------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.metrics.instrumenters.uname
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
|
||||
@@ -1,22 +1,11 @@
|
||||
metrics Package
|
||||
===============
|
||||
|
||||
:mod:`metrics` Package
|
||||
----------------------
|
||||
galaxy.jobs.metrics package
|
||||
===========================
|
||||
|
||||
.. automodule:: galaxy.jobs.metrics
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`formatting` Module
|
||||
------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.metrics.formatting
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Subpackages
|
||||
-----------
|
||||
|
||||
@@ -25,3 +14,15 @@ Subpackages
|
||||
galaxy.jobs.metrics.collectl
|
||||
galaxy.jobs.metrics.instrumenters
|
||||
|
||||
Submodules
|
||||
----------
|
||||
|
||||
galaxy.jobs.metrics.formatting module
|
||||
-------------------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.metrics.formatting
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
|
||||
@@ -1,94 +1,11 @@
|
||||
jobs Package
|
||||
============
|
||||
|
||||
:mod:`jobs` Package
|
||||
-------------------
|
||||
galaxy.jobs package
|
||||
===================
|
||||
|
||||
.. automodule:: galaxy.jobs
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`command_factory` Module
|
||||
-----------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.command_factory
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`datasets` Module
|
||||
----------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.datasets
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`error_level` Module
|
||||
-------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.error_level
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`handler` Module
|
||||
---------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.handler
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`manager` Module
|
||||
---------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.manager
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`mapper` Module
|
||||
--------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.mapper
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`output_checker` Module
|
||||
----------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.output_checker
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`rule_helper` Module
|
||||
-------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.rule_helper
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`stock_rules` Module
|
||||
-------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.stock_rules
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`transfer_manager` Module
|
||||
------------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.transfer_manager
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Subpackages
|
||||
-----------
|
||||
|
||||
@@ -101,3 +18,87 @@ Subpackages
|
||||
galaxy.jobs.runners
|
||||
galaxy.jobs.splitters
|
||||
|
||||
Submodules
|
||||
----------
|
||||
|
||||
galaxy.jobs.command_factory module
|
||||
----------------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.command_factory
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.jobs.datasets module
|
||||
---------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.datasets
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.jobs.error_level module
|
||||
------------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.error_level
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.jobs.handler module
|
||||
--------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.handler
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.jobs.manager module
|
||||
--------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.manager
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.jobs.mapper module
|
||||
-------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.mapper
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.jobs.output_checker module
|
||||
---------------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.output_checker
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.jobs.rule_helper module
|
||||
------------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.rule_helper
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.jobs.stock_rules module
|
||||
------------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.stock_rules
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.jobs.transfer_manager module
|
||||
-----------------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.transfer_manager
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
|
||||
@@ -1,126 +1,11 @@
|
||||
lwr_client Package
|
||||
==================
|
||||
|
||||
:mod:`lwr_client` Package
|
||||
-------------------------
|
||||
galaxy.jobs.runners.lwr_client package
|
||||
======================================
|
||||
|
||||
.. automodule:: galaxy.jobs.runners.lwr_client
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`action_mapper` Module
|
||||
---------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.runners.lwr_client.action_mapper
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`amqp_exchange` Module
|
||||
---------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.runners.lwr_client.amqp_exchange
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`amqp_exchange_factory` Module
|
||||
-----------------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.runners.lwr_client.amqp_exchange_factory
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`client` Module
|
||||
--------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.runners.lwr_client.client
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`config_util` Module
|
||||
-------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.runners.lwr_client.config_util
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`decorators` Module
|
||||
------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.runners.lwr_client.decorators
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`destination` Module
|
||||
-------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.runners.lwr_client.destination
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`interface` Module
|
||||
-----------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.runners.lwr_client.interface
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`job_directory` Module
|
||||
---------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.runners.lwr_client.job_directory
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`manager` Module
|
||||
---------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.runners.lwr_client.manager
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`object_client` Module
|
||||
---------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.runners.lwr_client.object_client
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`path_mapper` Module
|
||||
-------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.runners.lwr_client.path_mapper
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`setup_handler` Module
|
||||
---------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.runners.lwr_client.setup_handler
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`util` Module
|
||||
------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.runners.lwr_client.util
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Subpackages
|
||||
-----------
|
||||
|
||||
@@ -129,3 +14,119 @@ Subpackages
|
||||
galaxy.jobs.runners.lwr_client.staging
|
||||
galaxy.jobs.runners.lwr_client.transport
|
||||
|
||||
Submodules
|
||||
----------
|
||||
|
||||
galaxy.jobs.runners.lwr_client.action_mapper module
|
||||
---------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.runners.lwr_client.action_mapper
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.jobs.runners.lwr_client.amqp_exchange module
|
||||
---------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.runners.lwr_client.amqp_exchange
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.jobs.runners.lwr_client.amqp_exchange_factory module
|
||||
-----------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.runners.lwr_client.amqp_exchange_factory
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.jobs.runners.lwr_client.client module
|
||||
--------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.runners.lwr_client.client
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.jobs.runners.lwr_client.config_util module
|
||||
-------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.runners.lwr_client.config_util
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.jobs.runners.lwr_client.decorators module
|
||||
------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.runners.lwr_client.decorators
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.jobs.runners.lwr_client.destination module
|
||||
-------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.runners.lwr_client.destination
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.jobs.runners.lwr_client.interface module
|
||||
-----------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.runners.lwr_client.interface
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.jobs.runners.lwr_client.job_directory module
|
||||
---------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.runners.lwr_client.job_directory
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.jobs.runners.lwr_client.manager module
|
||||
---------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.runners.lwr_client.manager
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.jobs.runners.lwr_client.object_client module
|
||||
---------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.runners.lwr_client.object_client
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.jobs.runners.lwr_client.path_mapper module
|
||||
-------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.runners.lwr_client.path_mapper
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.jobs.runners.lwr_client.setup_handler module
|
||||
---------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.runners.lwr_client.setup_handler
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.jobs.runners.lwr_client.util module
|
||||
------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.runners.lwr_client.util
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
|
||||
@@ -1,27 +1,28 @@
|
||||
staging Package
|
||||
===============
|
||||
|
||||
:mod:`staging` Package
|
||||
----------------------
|
||||
galaxy.jobs.runners.lwr_client.staging package
|
||||
==============================================
|
||||
|
||||
.. automodule:: galaxy.jobs.runners.lwr_client.staging
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`down` Module
|
||||
------------------
|
||||
Submodules
|
||||
----------
|
||||
|
||||
galaxy.jobs.runners.lwr_client.staging.down module
|
||||
--------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.runners.lwr_client.staging.down
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`up` Module
|
||||
----------------
|
||||
galaxy.jobs.runners.lwr_client.staging.up module
|
||||
------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.runners.lwr_client.staging.up
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
|
||||
@@ -1,27 +1,28 @@
|
||||
transport Package
|
||||
=================
|
||||
|
||||
:mod:`transport` Package
|
||||
------------------------
|
||||
galaxy.jobs.runners.lwr_client.transport package
|
||||
================================================
|
||||
|
||||
.. automodule:: galaxy.jobs.runners.lwr_client.transport
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`curl` Module
|
||||
------------------
|
||||
Submodules
|
||||
----------
|
||||
|
||||
galaxy.jobs.runners.lwr_client.transport.curl module
|
||||
----------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.runners.lwr_client.transport.curl
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`standard` Module
|
||||
----------------------
|
||||
galaxy.jobs.runners.lwr_client.transport.standard module
|
||||
--------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.runners.lwr_client.transport.standard
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
|
||||
@@ -1,94 +1,11 @@
|
||||
runners Package
|
||||
===============
|
||||
|
||||
:mod:`runners` Package
|
||||
----------------------
|
||||
galaxy.jobs.runners package
|
||||
===========================
|
||||
|
||||
.. automodule:: galaxy.jobs.runners
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`cli` Module
|
||||
-----------------
|
||||
|
||||
.. automodule:: galaxy.jobs.runners.cli
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`condor` Module
|
||||
--------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.runners.condor
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`drmaa` Module
|
||||
-------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.runners.drmaa
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`local` Module
|
||||
-------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.runners.local
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`lwr` Module
|
||||
-----------------
|
||||
|
||||
.. automodule:: galaxy.jobs.runners.lwr
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`pbs` Module
|
||||
-----------------
|
||||
|
||||
.. automodule:: galaxy.jobs.runners.pbs
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`pulsar` Module
|
||||
--------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.runners.pulsar
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`slurm` Module
|
||||
-------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.runners.slurm
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`state_handler_factory` Module
|
||||
-----------------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.runners.state_handler_factory
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`tasks` Module
|
||||
-------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.runners.tasks
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Subpackages
|
||||
-----------
|
||||
|
||||
@@ -98,3 +15,87 @@ Subpackages
|
||||
galaxy.jobs.runners.state_handlers
|
||||
galaxy.jobs.runners.util
|
||||
|
||||
Submodules
|
||||
----------
|
||||
|
||||
galaxy.jobs.runners.cli module
|
||||
------------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.runners.cli
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.jobs.runners.condor module
|
||||
---------------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.runners.condor
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.jobs.runners.drmaa module
|
||||
--------------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.runners.drmaa
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.jobs.runners.local module
|
||||
--------------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.runners.local
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.jobs.runners.lwr module
|
||||
------------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.runners.lwr
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.jobs.runners.pbs module
|
||||
------------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.runners.pbs
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.jobs.runners.pulsar module
|
||||
---------------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.runners.pulsar
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.jobs.runners.slurm module
|
||||
--------------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.runners.slurm
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.jobs.runners.state_handler_factory module
|
||||
------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.runners.state_handler_factory
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.jobs.runners.tasks module
|
||||
--------------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.runners.tasks
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
|
||||
@@ -1,11 +1,20 @@
|
||||
state_handlers Package
|
||||
======================
|
||||
galaxy.jobs.runners.state_handlers package
|
||||
==========================================
|
||||
|
||||
:mod:`resubmit` Module
|
||||
----------------------
|
||||
.. automodule:: galaxy.jobs.runners.state_handlers
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Submodules
|
||||
----------
|
||||
|
||||
galaxy.jobs.runners.state_handlers.resubmit module
|
||||
--------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.runners.state_handlers.resubmit
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
|
||||
@@ -1,35 +1,36 @@
|
||||
job Package
|
||||
===========
|
||||
|
||||
:mod:`job` Package
|
||||
------------------
|
||||
galaxy.jobs.runners.util.cli.job package
|
||||
========================================
|
||||
|
||||
.. automodule:: galaxy.jobs.runners.util.cli.job
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`slurm` Module
|
||||
-------------------
|
||||
Submodules
|
||||
----------
|
||||
|
||||
galaxy.jobs.runners.util.cli.job.slurm module
|
||||
---------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.runners.util.cli.job.slurm
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`slurm_torque` Module
|
||||
--------------------------
|
||||
galaxy.jobs.runners.util.cli.job.slurm_torque module
|
||||
----------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.runners.util.cli.job.slurm_torque
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`torque` Module
|
||||
--------------------
|
||||
galaxy.jobs.runners.util.cli.job.torque module
|
||||
----------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.runners.util.cli.job.torque
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
|
||||
@@ -1,22 +1,11 @@
|
||||
cli Package
|
||||
===========
|
||||
|
||||
:mod:`cli` Package
|
||||
------------------
|
||||
galaxy.jobs.runners.util.cli package
|
||||
====================================
|
||||
|
||||
.. automodule:: galaxy.jobs.runners.util.cli
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`factory` Module
|
||||
---------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.runners.util.cli.factory
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Subpackages
|
||||
-----------
|
||||
|
||||
@@ -25,3 +14,15 @@ Subpackages
|
||||
galaxy.jobs.runners.util.cli.job
|
||||
galaxy.jobs.runners.util.cli.shell
|
||||
|
||||
Submodules
|
||||
----------
|
||||
|
||||
galaxy.jobs.runners.util.cli.factory module
|
||||
-------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.runners.util.cli.factory
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
|
||||
@@ -1,27 +1,28 @@
|
||||
shell Package
|
||||
=============
|
||||
|
||||
:mod:`shell` Package
|
||||
--------------------
|
||||
galaxy.jobs.runners.util.cli.shell package
|
||||
==========================================
|
||||
|
||||
.. automodule:: galaxy.jobs.runners.util.cli.shell
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`local` Module
|
||||
-------------------
|
||||
Submodules
|
||||
----------
|
||||
|
||||
galaxy.jobs.runners.util.cli.shell.local module
|
||||
-----------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.runners.util.cli.shell.local
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`rsh` Module
|
||||
-----------------
|
||||
galaxy.jobs.runners.util.cli.shell.rsh module
|
||||
---------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.runners.util.cli.shell.rsh
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
|
||||
@@ -1,8 +1,5 @@
|
||||
condor Package
|
||||
==============
|
||||
|
||||
:mod:`condor` Package
|
||||
---------------------
|
||||
galaxy.jobs.runners.util.condor package
|
||||
=======================================
|
||||
|
||||
.. automodule:: galaxy.jobs.runners.util.condor
|
||||
:members:
|
||||
|
||||
@@ -1,8 +1,5 @@
|
||||
job_script Package
|
||||
==================
|
||||
|
||||
:mod:`job_script` Package
|
||||
-------------------------
|
||||
galaxy.jobs.runners.util.job_script package
|
||||
===========================================
|
||||
|
||||
.. automodule:: galaxy.jobs.runners.util.job_script
|
||||
:members:
|
||||
|
||||
@@ -1,38 +1,11 @@
|
||||
util Package
|
||||
============
|
||||
|
||||
:mod:`util` Package
|
||||
-------------------
|
||||
galaxy.jobs.runners.util package
|
||||
================================
|
||||
|
||||
.. automodule:: galaxy.jobs.runners.util
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`env` Module
|
||||
-----------------
|
||||
|
||||
.. automodule:: galaxy.jobs.runners.util.env
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`external` Module
|
||||
----------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.runners.util.external
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`kill` Module
|
||||
------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.runners.util.kill
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Subpackages
|
||||
-----------
|
||||
|
||||
@@ -42,3 +15,31 @@ Subpackages
|
||||
galaxy.jobs.runners.util.condor
|
||||
galaxy.jobs.runners.util.job_script
|
||||
|
||||
Submodules
|
||||
----------
|
||||
|
||||
galaxy.jobs.runners.util.env module
|
||||
-----------------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.runners.util.env
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.jobs.runners.util.external module
|
||||
----------------------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.runners.util.external
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.jobs.runners.util.kill module
|
||||
------------------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.runners.util.kill
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
|
||||
@@ -1,19 +1,28 @@
|
||||
splitters Package
|
||||
=================
|
||||
galaxy.jobs.splitters package
|
||||
=============================
|
||||
|
||||
:mod:`basic` Module
|
||||
-------------------
|
||||
.. automodule:: galaxy.jobs.splitters
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Submodules
|
||||
----------
|
||||
|
||||
galaxy.jobs.splitters.basic module
|
||||
----------------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.splitters.basic
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`multi` Module
|
||||
-------------------
|
||||
galaxy.jobs.splitters.multi module
|
||||
----------------------------------
|
||||
|
||||
.. automodule:: galaxy.jobs.splitters.multi
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
|
||||
@@ -1,227 +1,228 @@
|
||||
managers Package
|
||||
================
|
||||
|
||||
:mod:`managers` Package
|
||||
-----------------------
|
||||
galaxy.managers package
|
||||
=======================
|
||||
|
||||
.. automodule:: galaxy.managers
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`annotatable` Module
|
||||
-------------------------
|
||||
Submodules
|
||||
----------
|
||||
|
||||
galaxy.managers.annotatable module
|
||||
----------------------------------
|
||||
|
||||
.. automodule:: galaxy.managers.annotatable
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`api_keys` Module
|
||||
----------------------
|
||||
galaxy.managers.api_keys module
|
||||
-------------------------------
|
||||
|
||||
.. automodule:: galaxy.managers.api_keys
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`base` Module
|
||||
------------------
|
||||
galaxy.managers.base module
|
||||
---------------------------
|
||||
|
||||
.. automodule:: galaxy.managers.base
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`citations` Module
|
||||
-----------------------
|
||||
galaxy.managers.citations module
|
||||
--------------------------------
|
||||
|
||||
.. automodule:: galaxy.managers.citations
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`collections` Module
|
||||
-------------------------
|
||||
galaxy.managers.collections module
|
||||
----------------------------------
|
||||
|
||||
.. automodule:: galaxy.managers.collections
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`collections_util` Module
|
||||
------------------------------
|
||||
galaxy.managers.collections_util module
|
||||
---------------------------------------
|
||||
|
||||
.. automodule:: galaxy.managers.collections_util
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`configuration` Module
|
||||
---------------------------
|
||||
galaxy.managers.configuration module
|
||||
------------------------------------
|
||||
|
||||
.. automodule:: galaxy.managers.configuration
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`containers` Module
|
||||
------------------------
|
||||
galaxy.managers.containers module
|
||||
---------------------------------
|
||||
|
||||
.. automodule:: galaxy.managers.containers
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`context` Module
|
||||
---------------------
|
||||
galaxy.managers.context module
|
||||
------------------------------
|
||||
|
||||
.. automodule:: galaxy.managers.context
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`datasets` Module
|
||||
----------------------
|
||||
galaxy.managers.datasets module
|
||||
-------------------------------
|
||||
|
||||
.. automodule:: galaxy.managers.datasets
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`deletable` Module
|
||||
-----------------------
|
||||
galaxy.managers.deletable module
|
||||
--------------------------------
|
||||
|
||||
.. automodule:: galaxy.managers.deletable
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`folders` Module
|
||||
---------------------
|
||||
galaxy.managers.folders module
|
||||
------------------------------
|
||||
|
||||
.. automodule:: galaxy.managers.folders
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`hdas` Module
|
||||
------------------
|
||||
galaxy.managers.hdas module
|
||||
---------------------------
|
||||
|
||||
.. automodule:: galaxy.managers.hdas
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`histories` Module
|
||||
-----------------------
|
||||
galaxy.managers.histories module
|
||||
--------------------------------
|
||||
|
||||
.. automodule:: galaxy.managers.histories
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`lddas` Module
|
||||
-------------------
|
||||
galaxy.managers.lddas module
|
||||
----------------------------
|
||||
|
||||
.. automodule:: galaxy.managers.lddas
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`libraries` Module
|
||||
-----------------------
|
||||
galaxy.managers.libraries module
|
||||
--------------------------------
|
||||
|
||||
.. automodule:: galaxy.managers.libraries
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`pages` Module
|
||||
-------------------
|
||||
galaxy.managers.pages module
|
||||
----------------------------
|
||||
|
||||
.. automodule:: galaxy.managers.pages
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`ratable` Module
|
||||
---------------------
|
||||
galaxy.managers.ratable module
|
||||
------------------------------
|
||||
|
||||
.. automodule:: galaxy.managers.ratable
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`rbac_secured` Module
|
||||
--------------------------
|
||||
galaxy.managers.rbac_secured module
|
||||
-----------------------------------
|
||||
|
||||
.. automodule:: galaxy.managers.rbac_secured
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`roles` Module
|
||||
-------------------
|
||||
galaxy.managers.roles module
|
||||
----------------------------
|
||||
|
||||
.. automodule:: galaxy.managers.roles
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`secured` Module
|
||||
---------------------
|
||||
galaxy.managers.secured module
|
||||
------------------------------
|
||||
|
||||
.. automodule:: galaxy.managers.secured
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`sharable` Module
|
||||
----------------------
|
||||
galaxy.managers.sharable module
|
||||
-------------------------------
|
||||
|
||||
.. automodule:: galaxy.managers.sharable
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`taggable` Module
|
||||
----------------------
|
||||
galaxy.managers.taggable module
|
||||
-------------------------------
|
||||
|
||||
.. automodule:: galaxy.managers.taggable
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`tags` Module
|
||||
------------------
|
||||
galaxy.managers.tags module
|
||||
---------------------------
|
||||
|
||||
.. automodule:: galaxy.managers.tags
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`users` Module
|
||||
-------------------
|
||||
galaxy.managers.users module
|
||||
----------------------------
|
||||
|
||||
.. automodule:: galaxy.managers.users
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`visualizations` Module
|
||||
----------------------------
|
||||
galaxy.managers.visualizations module
|
||||
-------------------------------------
|
||||
|
||||
.. automodule:: galaxy.managers.visualizations
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`workflows` Module
|
||||
-----------------------
|
||||
galaxy.managers.workflows module
|
||||
--------------------------------
|
||||
|
||||
.. automodule:: galaxy.managers.workflows
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
|
||||
@@ -1,11 +1,20 @@
|
||||
migrate Package
|
||||
===============
|
||||
galaxy.model.migrate package
|
||||
============================
|
||||
|
||||
:mod:`check` Module
|
||||
-------------------
|
||||
.. automodule:: galaxy.model.migrate
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Submodules
|
||||
----------
|
||||
|
||||
galaxy.model.migrate.check module
|
||||
---------------------------------
|
||||
|
||||
.. automodule:: galaxy.model.migrate.check
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
|
||||
@@ -1,43 +1,44 @@
|
||||
orm Package
|
||||
===========
|
||||
|
||||
:mod:`orm` Package
|
||||
------------------
|
||||
galaxy.model.orm package
|
||||
========================
|
||||
|
||||
.. automodule:: galaxy.model.orm
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`engine_factory` Module
|
||||
----------------------------
|
||||
Submodules
|
||||
----------
|
||||
|
||||
galaxy.model.orm.engine_factory module
|
||||
--------------------------------------
|
||||
|
||||
.. automodule:: galaxy.model.orm.engine_factory
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`logging_connection_proxy` Module
|
||||
--------------------------------------
|
||||
galaxy.model.orm.logging_connection_proxy module
|
||||
------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.model.orm.logging_connection_proxy
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`now` Module
|
||||
-----------------
|
||||
galaxy.model.orm.now module
|
||||
---------------------------
|
||||
|
||||
.. automodule:: galaxy.model.orm.now
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`scripts` Module
|
||||
---------------------
|
||||
galaxy.model.orm.scripts module
|
||||
-------------------------------
|
||||
|
||||
.. automodule:: galaxy.model.orm.scripts
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
|
||||
@@ -1,62 +1,11 @@
|
||||
model Package
|
||||
=============
|
||||
|
||||
:mod:`model` Package
|
||||
--------------------
|
||||
galaxy.model package
|
||||
====================
|
||||
|
||||
.. automodule:: galaxy.model
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`base` Module
|
||||
------------------
|
||||
|
||||
.. automodule:: galaxy.model.base
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`custom_types` Module
|
||||
--------------------------
|
||||
|
||||
.. automodule:: galaxy.model.custom_types
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`item_attrs` Module
|
||||
------------------------
|
||||
|
||||
.. automodule:: galaxy.model.item_attrs
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`mapping` Module
|
||||
---------------------
|
||||
|
||||
.. automodule:: galaxy.model.mapping
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`search` Module
|
||||
--------------------
|
||||
|
||||
.. automodule:: galaxy.model.search
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`util` Module
|
||||
------------------
|
||||
|
||||
.. automodule:: galaxy.model.util
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Subpackages
|
||||
-----------
|
||||
|
||||
@@ -66,3 +15,55 @@ Subpackages
|
||||
galaxy.model.orm
|
||||
galaxy.model.tool_shed_install
|
||||
|
||||
Submodules
|
||||
----------
|
||||
|
||||
galaxy.model.base module
|
||||
------------------------
|
||||
|
||||
.. automodule:: galaxy.model.base
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.model.custom_types module
|
||||
--------------------------------
|
||||
|
||||
.. automodule:: galaxy.model.custom_types
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.model.item_attrs module
|
||||
------------------------------
|
||||
|
||||
.. automodule:: galaxy.model.item_attrs
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.model.mapping module
|
||||
---------------------------
|
||||
|
||||
.. automodule:: galaxy.model.mapping
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.model.search module
|
||||
--------------------------
|
||||
|
||||
.. automodule:: galaxy.model.search
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.model.util module
|
||||
------------------------
|
||||
|
||||
.. automodule:: galaxy.model.util
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
|
||||
@@ -1,11 +1,20 @@
|
||||
migrate Package
|
||||
===============
|
||||
galaxy.model.tool_shed_install.migrate package
|
||||
==============================================
|
||||
|
||||
:mod:`check` Module
|
||||
-------------------
|
||||
.. automodule:: galaxy.model.tool_shed_install.migrate
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Submodules
|
||||
----------
|
||||
|
||||
galaxy.model.tool_shed_install.migrate.check module
|
||||
---------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.model.tool_shed_install.migrate.check
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
|
||||
@@ -1,22 +1,11 @@
|
||||
tool_shed_install Package
|
||||
=========================
|
||||
|
||||
:mod:`tool_shed_install` Package
|
||||
--------------------------------
|
||||
galaxy.model.tool_shed_install package
|
||||
======================================
|
||||
|
||||
.. automodule:: galaxy.model.tool_shed_install
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`mapping` Module
|
||||
---------------------
|
||||
|
||||
.. automodule:: galaxy.model.tool_shed_install.mapping
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Subpackages
|
||||
-----------
|
||||
|
||||
@@ -24,3 +13,15 @@ Subpackages
|
||||
|
||||
galaxy.model.tool_shed_install.migrate
|
||||
|
||||
Submodules
|
||||
----------
|
||||
|
||||
galaxy.model.tool_shed_install.mapping module
|
||||
---------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.model.tool_shed_install.mapping
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
|
||||
@@ -1,43 +1,44 @@
|
||||
objectstore Package
|
||||
===================
|
||||
|
||||
:mod:`objectstore` Package
|
||||
--------------------------
|
||||
galaxy.objectstore package
|
||||
==========================
|
||||
|
||||
.. automodule:: galaxy.objectstore
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`pulsar` Module
|
||||
--------------------
|
||||
Submodules
|
||||
----------
|
||||
|
||||
galaxy.objectstore.pulsar module
|
||||
--------------------------------
|
||||
|
||||
.. automodule:: galaxy.objectstore.pulsar
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`rods` Module
|
||||
------------------
|
||||
galaxy.objectstore.rods module
|
||||
------------------------------
|
||||
|
||||
.. automodule:: galaxy.objectstore.rods
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`s3` Module
|
||||
----------------
|
||||
galaxy.objectstore.s3 module
|
||||
----------------------------
|
||||
|
||||
.. automodule:: galaxy.objectstore.s3
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`s3_multipart_upload` Module
|
||||
---------------------------------
|
||||
galaxy.objectstore.s3_multipart_upload module
|
||||
---------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.objectstore.s3_multipart_upload
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
|
||||
@@ -1,19 +1,20 @@
|
||||
openid Package
|
||||
==============
|
||||
|
||||
:mod:`openid` Package
|
||||
---------------------
|
||||
galaxy.openid package
|
||||
=====================
|
||||
|
||||
.. automodule:: galaxy.openid
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`providers` Module
|
||||
-----------------------
|
||||
Submodules
|
||||
----------
|
||||
|
||||
galaxy.openid.providers module
|
||||
------------------------------
|
||||
|
||||
.. automodule:: galaxy.openid.providers
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
|
||||
@@ -1,8 +1,5 @@
|
||||
quota Package
|
||||
=============
|
||||
|
||||
:mod:`quota` Package
|
||||
--------------------
|
||||
galaxy.quota package
|
||||
====================
|
||||
|
||||
.. automodule:: galaxy.quota
|
||||
:members:
|
||||
|
||||
+53
-52
@@ -1,62 +1,11 @@
|
||||
galaxy Package
|
||||
galaxy package
|
||||
==============
|
||||
|
||||
:mod:`galaxy` Package
|
||||
---------------------
|
||||
|
||||
.. automodule:: galaxy
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`app` Module
|
||||
-----------------
|
||||
|
||||
.. automodule:: galaxy.app
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`config` Module
|
||||
--------------------
|
||||
|
||||
.. automodule:: galaxy.config
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`main` Module
|
||||
------------------
|
||||
|
||||
.. automodule:: galaxy.main
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`queue_worker` Module
|
||||
--------------------------
|
||||
|
||||
.. automodule:: galaxy.queue_worker
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`queues` Module
|
||||
--------------------
|
||||
|
||||
.. automodule:: galaxy.queues
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`version` Module
|
||||
---------------------
|
||||
|
||||
.. automodule:: galaxy.version
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Subpackages
|
||||
-----------
|
||||
|
||||
@@ -88,3 +37,55 @@ Subpackages
|
||||
galaxy.work
|
||||
galaxy.workflow
|
||||
|
||||
Submodules
|
||||
----------
|
||||
|
||||
galaxy.app module
|
||||
-----------------
|
||||
|
||||
.. automodule:: galaxy.app
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.config module
|
||||
--------------------
|
||||
|
||||
.. automodule:: galaxy.config
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.main module
|
||||
------------------
|
||||
|
||||
.. automodule:: galaxy.main
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.queue_worker module
|
||||
--------------------------
|
||||
|
||||
.. automodule:: galaxy.queue_worker
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.queues module
|
||||
--------------------
|
||||
|
||||
.. automodule:: galaxy.queues
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.version module
|
||||
---------------------
|
||||
|
||||
.. automodule:: galaxy.version
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
|
||||
@@ -1,35 +1,44 @@
|
||||
sample_tracking Package
|
||||
=======================
|
||||
galaxy.sample_tracking package
|
||||
==============================
|
||||
|
||||
:mod:`data_transfer` Module
|
||||
---------------------------
|
||||
.. automodule:: galaxy.sample_tracking
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Submodules
|
||||
----------
|
||||
|
||||
galaxy.sample_tracking.data_transfer module
|
||||
-------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.sample_tracking.data_transfer
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`external_service_types` Module
|
||||
------------------------------------
|
||||
galaxy.sample_tracking.external_service_types module
|
||||
----------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.sample_tracking.external_service_types
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`request_types` Module
|
||||
---------------------------
|
||||
galaxy.sample_tracking.request_types module
|
||||
-------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.sample_tracking.request_types
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`sample` Module
|
||||
--------------------
|
||||
galaxy.sample_tracking.sample module
|
||||
------------------------------------
|
||||
|
||||
.. automodule:: galaxy.sample_tracking.sample
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
|
||||
@@ -1,27 +1,28 @@
|
||||
security Package
|
||||
================
|
||||
|
||||
:mod:`security` Package
|
||||
-----------------------
|
||||
galaxy.security package
|
||||
=======================
|
||||
|
||||
.. automodule:: galaxy.security
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`passwords` Module
|
||||
-----------------------
|
||||
Submodules
|
||||
----------
|
||||
|
||||
galaxy.security.passwords module
|
||||
--------------------------------
|
||||
|
||||
.. automodule:: galaxy.security.passwords
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`validate_user_input` Module
|
||||
---------------------------------
|
||||
galaxy.security.validate_user_input module
|
||||
------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.security.validate_user_input
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
|
||||
@@ -1,8 +1,5 @@
|
||||
tags Package
|
||||
============
|
||||
|
||||
:mod:`tags` Package
|
||||
-------------------
|
||||
galaxy.tags package
|
||||
===================
|
||||
|
||||
.. automodule:: galaxy.tags
|
||||
:members:
|
||||
|
||||
@@ -1,59 +1,60 @@
|
||||
actions Package
|
||||
===============
|
||||
|
||||
:mod:`actions` Package
|
||||
----------------------
|
||||
galaxy.tools.actions package
|
||||
============================
|
||||
|
||||
.. automodule:: galaxy.tools.actions
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`data_manager` Module
|
||||
--------------------------
|
||||
Submodules
|
||||
----------
|
||||
|
||||
galaxy.tools.actions.data_manager module
|
||||
----------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.actions.data_manager
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`data_source` Module
|
||||
-------------------------
|
||||
galaxy.tools.actions.data_source module
|
||||
---------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.actions.data_source
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`history_imp_exp` Module
|
||||
-----------------------------
|
||||
galaxy.tools.actions.history_imp_exp module
|
||||
-------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.actions.history_imp_exp
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`metadata` Module
|
||||
----------------------
|
||||
galaxy.tools.actions.metadata module
|
||||
------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.actions.metadata
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`upload` Module
|
||||
--------------------
|
||||
galaxy.tools.actions.upload module
|
||||
----------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.actions.upload
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`upload_common` Module
|
||||
---------------------------
|
||||
galaxy.tools.actions.upload_common module
|
||||
-----------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.actions.upload_common
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
|
||||
@@ -1,8 +1,5 @@
|
||||
data Package
|
||||
============
|
||||
|
||||
:mod:`data` Package
|
||||
-------------------
|
||||
galaxy.tools.data package
|
||||
=========================
|
||||
|
||||
.. automodule:: galaxy.tools.data
|
||||
:members:
|
||||
|
||||
@@ -1,19 +1,20 @@
|
||||
data_manager Package
|
||||
====================
|
||||
|
||||
:mod:`data_manager` Package
|
||||
---------------------------
|
||||
galaxy.tools.data_manager package
|
||||
=================================
|
||||
|
||||
.. automodule:: galaxy.tools.data_manager
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`manager` Module
|
||||
---------------------
|
||||
Submodules
|
||||
----------
|
||||
|
||||
galaxy.tools.data_manager.manager module
|
||||
----------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.data_manager.manager
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
|
||||
@@ -1,59 +1,60 @@
|
||||
resolvers Package
|
||||
=================
|
||||
|
||||
:mod:`resolvers` Package
|
||||
------------------------
|
||||
galaxy.tools.deps.resolvers package
|
||||
===================================
|
||||
|
||||
.. automodule:: galaxy.tools.deps.resolvers
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`brewed_tool_shed_packages` Module
|
||||
---------------------------------------
|
||||
Submodules
|
||||
----------
|
||||
|
||||
galaxy.tools.deps.resolvers.brewed_tool_shed_packages module
|
||||
------------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.deps.resolvers.brewed_tool_shed_packages
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`galaxy_packages` Module
|
||||
-----------------------------
|
||||
galaxy.tools.deps.resolvers.galaxy_packages module
|
||||
--------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.deps.resolvers.galaxy_packages
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`homebrew` Module
|
||||
----------------------
|
||||
galaxy.tools.deps.resolvers.homebrew module
|
||||
-------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.deps.resolvers.homebrew
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`modules` Module
|
||||
---------------------
|
||||
galaxy.tools.deps.resolvers.modules module
|
||||
------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.deps.resolvers.modules
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`resolver_mixins` Module
|
||||
-----------------------------
|
||||
galaxy.tools.deps.resolvers.resolver_mixins module
|
||||
--------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.deps.resolvers.resolver_mixins
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`tool_shed_packages` Module
|
||||
--------------------------------
|
||||
galaxy.tools.deps.resolvers.tool_shed_packages module
|
||||
-----------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.deps.resolvers.tool_shed_packages
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
|
||||
@@ -1,78 +1,11 @@
|
||||
deps Package
|
||||
============
|
||||
|
||||
:mod:`deps` Package
|
||||
-------------------
|
||||
galaxy.tools.deps package
|
||||
=========================
|
||||
|
||||
.. automodule:: galaxy.tools.deps
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`brew_exts` Module
|
||||
-----------------------
|
||||
|
||||
.. automodule:: galaxy.tools.deps.brew_exts
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`brew_util` Module
|
||||
-----------------------
|
||||
|
||||
.. automodule:: galaxy.tools.deps.brew_util
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`commands` Module
|
||||
----------------------
|
||||
|
||||
.. automodule:: galaxy.tools.deps.commands
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`containers` Module
|
||||
------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.deps.containers
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`dependencies` Module
|
||||
--------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.deps.dependencies
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`docker_util` Module
|
||||
-------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.deps.docker_util
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`dockerfiles` Module
|
||||
-------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.deps.dockerfiles
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`requirements` Module
|
||||
--------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.deps.requirements
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Subpackages
|
||||
-----------
|
||||
|
||||
@@ -80,3 +13,71 @@ Subpackages
|
||||
|
||||
galaxy.tools.deps.resolvers
|
||||
|
||||
Submodules
|
||||
----------
|
||||
|
||||
galaxy.tools.deps.brew_exts module
|
||||
----------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.deps.brew_exts
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tools.deps.brew_util module
|
||||
----------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.deps.brew_util
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tools.deps.commands module
|
||||
---------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.deps.commands
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tools.deps.containers module
|
||||
-----------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.deps.containers
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tools.deps.dependencies module
|
||||
-------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.deps.dependencies
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tools.deps.docker_util module
|
||||
------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.deps.docker_util
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tools.deps.dockerfiles module
|
||||
------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.deps.dockerfiles
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tools.deps.requirements module
|
||||
-------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.deps.requirements
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
|
||||
@@ -1,8 +1,5 @@
|
||||
filters Package
|
||||
===============
|
||||
|
||||
:mod:`filters` Package
|
||||
----------------------
|
||||
galaxy.tools.filters package
|
||||
============================
|
||||
|
||||
.. automodule:: galaxy.tools.filters
|
||||
:members:
|
||||
|
||||
@@ -1,27 +1,28 @@
|
||||
imp_exp Package
|
||||
===============
|
||||
|
||||
:mod:`imp_exp` Package
|
||||
----------------------
|
||||
galaxy.tools.imp_exp package
|
||||
============================
|
||||
|
||||
.. automodule:: galaxy.tools.imp_exp
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`export_history` Module
|
||||
----------------------------
|
||||
Submodules
|
||||
----------
|
||||
|
||||
galaxy.tools.imp_exp.export_history module
|
||||
------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.imp_exp.export_history
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`unpack_tar_gz_archive` Module
|
||||
-----------------------------------
|
||||
galaxy.tools.imp_exp.unpack_tar_gz_archive module
|
||||
-------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.imp_exp.unpack_tar_gz_archive
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
|
||||
@@ -1,67 +1,68 @@
|
||||
linters Package
|
||||
===============
|
||||
|
||||
:mod:`linters` Package
|
||||
----------------------
|
||||
galaxy.tools.linters package
|
||||
============================
|
||||
|
||||
.. automodule:: galaxy.tools.linters
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`citations` Module
|
||||
-----------------------
|
||||
Submodules
|
||||
----------
|
||||
|
||||
galaxy.tools.linters.citations module
|
||||
-------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.linters.citations
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`command` Module
|
||||
---------------------
|
||||
galaxy.tools.linters.command module
|
||||
-----------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.linters.command
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`help` Module
|
||||
------------------
|
||||
galaxy.tools.linters.help module
|
||||
--------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.linters.help
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`inputs` Module
|
||||
--------------------
|
||||
galaxy.tools.linters.inputs module
|
||||
----------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.linters.inputs
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`outputs` Module
|
||||
---------------------
|
||||
galaxy.tools.linters.outputs module
|
||||
-----------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.linters.outputs
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`tests` Module
|
||||
-------------------
|
||||
galaxy.tools.linters.tests module
|
||||
---------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.linters.tests
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`top_level` Module
|
||||
-----------------------
|
||||
galaxy.tools.linters.top_level module
|
||||
-------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.linters.top_level
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
|
||||
@@ -1,107 +1,108 @@
|
||||
parameters Package
|
||||
==================
|
||||
|
||||
:mod:`parameters` Package
|
||||
-------------------------
|
||||
galaxy.tools.parameters package
|
||||
===============================
|
||||
|
||||
.. automodule:: galaxy.tools.parameters
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`basic` Module
|
||||
-------------------
|
||||
Submodules
|
||||
----------
|
||||
|
||||
galaxy.tools.parameters.basic module
|
||||
------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.parameters.basic
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`dataset_matcher` Module
|
||||
-----------------------------
|
||||
galaxy.tools.parameters.dataset_matcher module
|
||||
----------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.parameters.dataset_matcher
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`dynamic_options` Module
|
||||
-----------------------------
|
||||
galaxy.tools.parameters.dynamic_options module
|
||||
----------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.parameters.dynamic_options
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`grouping` Module
|
||||
----------------------
|
||||
galaxy.tools.parameters.grouping module
|
||||
---------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.parameters.grouping
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`history_query` Module
|
||||
---------------------------
|
||||
galaxy.tools.parameters.history_query module
|
||||
--------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.parameters.history_query
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`input_translation` Module
|
||||
-------------------------------
|
||||
galaxy.tools.parameters.input_translation module
|
||||
------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.parameters.input_translation
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`meta` Module
|
||||
------------------
|
||||
galaxy.tools.parameters.meta module
|
||||
-----------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.parameters.meta
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`output` Module
|
||||
--------------------
|
||||
galaxy.tools.parameters.output module
|
||||
-------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.parameters.output
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`output_collect` Module
|
||||
----------------------------
|
||||
galaxy.tools.parameters.output_collect module
|
||||
---------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.parameters.output_collect
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`sanitize` Module
|
||||
----------------------
|
||||
galaxy.tools.parameters.sanitize module
|
||||
---------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.parameters.sanitize
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`validation` Module
|
||||
------------------------
|
||||
galaxy.tools.parameters.validation module
|
||||
-----------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.parameters.validation
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`wrapped` Module
|
||||
---------------------
|
||||
galaxy.tools.parameters.wrapped module
|
||||
--------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.parameters.wrapped
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
|
||||
@@ -1,51 +1,52 @@
|
||||
parser Package
|
||||
==============
|
||||
|
||||
:mod:`parser` Package
|
||||
---------------------
|
||||
galaxy.tools.parser package
|
||||
===========================
|
||||
|
||||
.. automodule:: galaxy.tools.parser
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`factory` Module
|
||||
---------------------
|
||||
Submodules
|
||||
----------
|
||||
|
||||
galaxy.tools.parser.factory module
|
||||
----------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.parser.factory
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`interface` Module
|
||||
-----------------------
|
||||
galaxy.tools.parser.interface module
|
||||
------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.parser.interface
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`util` Module
|
||||
------------------
|
||||
galaxy.tools.parser.util module
|
||||
-------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.parser.util
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`xml` Module
|
||||
-----------------
|
||||
galaxy.tools.parser.xml module
|
||||
------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.parser.xml
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`yaml` Module
|
||||
------------------
|
||||
galaxy.tools.parser.yaml module
|
||||
-------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.parser.yaml
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
|
||||
@@ -1,86 +1,11 @@
|
||||
tools Package
|
||||
=============
|
||||
|
||||
:mod:`tools` Package
|
||||
--------------------
|
||||
galaxy.tools package
|
||||
====================
|
||||
|
||||
.. automodule:: galaxy.tools
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`errors` Module
|
||||
--------------------
|
||||
|
||||
.. automodule:: galaxy.tools.errors
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`evaluation` Module
|
||||
------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.evaluation
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`exception_handling` Module
|
||||
--------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.exception_handling
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`execute` Module
|
||||
---------------------
|
||||
|
||||
.. automodule:: galaxy.tools.execute
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`lint` Module
|
||||
------------------
|
||||
|
||||
.. automodule:: galaxy.tools.lint
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`loader` Module
|
||||
--------------------
|
||||
|
||||
.. automodule:: galaxy.tools.loader
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`loader_directory` Module
|
||||
------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.loader_directory
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`test` Module
|
||||
------------------
|
||||
|
||||
.. automodule:: galaxy.tools.test
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`wrappers` Module
|
||||
----------------------
|
||||
|
||||
.. automodule:: galaxy.tools.wrappers
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Subpackages
|
||||
-----------
|
||||
|
||||
@@ -99,3 +24,79 @@ Subpackages
|
||||
galaxy.tools.toolbox
|
||||
galaxy.tools.util
|
||||
|
||||
Submodules
|
||||
----------
|
||||
|
||||
galaxy.tools.errors module
|
||||
--------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.errors
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tools.evaluation module
|
||||
------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.evaluation
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tools.exception_handling module
|
||||
--------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.exception_handling
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tools.execute module
|
||||
---------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.execute
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tools.lint module
|
||||
------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.lint
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tools.loader module
|
||||
--------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.loader
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tools.loader_directory module
|
||||
------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.loader_directory
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tools.test module
|
||||
------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.test
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tools.wrappers module
|
||||
----------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.wrappers
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
|
||||
@@ -1,8 +1,5 @@
|
||||
search Package
|
||||
==============
|
||||
|
||||
:mod:`search` Package
|
||||
---------------------
|
||||
galaxy.tools.search package
|
||||
===========================
|
||||
|
||||
.. automodule:: galaxy.tools.search
|
||||
:members:
|
||||
|
||||
@@ -1,8 +1,5 @@
|
||||
filters Package
|
||||
===============
|
||||
|
||||
:mod:`filters` Package
|
||||
----------------------
|
||||
galaxy.tools.toolbox.filters package
|
||||
====================================
|
||||
|
||||
.. automodule:: galaxy.tools.toolbox.filters
|
||||
:members:
|
||||
|
||||
@@ -1,43 +1,44 @@
|
||||
lineages Package
|
||||
================
|
||||
|
||||
:mod:`lineages` Package
|
||||
-----------------------
|
||||
galaxy.tools.toolbox.lineages package
|
||||
=====================================
|
||||
|
||||
.. automodule:: galaxy.tools.toolbox.lineages
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`factory` Module
|
||||
---------------------
|
||||
Submodules
|
||||
----------
|
||||
|
||||
galaxy.tools.toolbox.lineages.factory module
|
||||
--------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.toolbox.lineages.factory
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`interface` Module
|
||||
-----------------------
|
||||
galaxy.tools.toolbox.lineages.interface module
|
||||
----------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.toolbox.lineages.interface
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`stock` Module
|
||||
-------------------
|
||||
galaxy.tools.toolbox.lineages.stock module
|
||||
------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.toolbox.lineages.stock
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`tool_shed` Module
|
||||
-----------------------
|
||||
galaxy.tools.toolbox.lineages.tool_shed module
|
||||
----------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.toolbox.lineages.tool_shed
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
|
||||
@@ -1,54 +1,11 @@
|
||||
toolbox Package
|
||||
===============
|
||||
|
||||
:mod:`toolbox` Package
|
||||
----------------------
|
||||
galaxy.tools.toolbox package
|
||||
============================
|
||||
|
||||
.. automodule:: galaxy.tools.toolbox
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`base` Module
|
||||
------------------
|
||||
|
||||
.. automodule:: galaxy.tools.toolbox.base
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`integrated_panel` Module
|
||||
------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.toolbox.integrated_panel
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`panel` Module
|
||||
-------------------
|
||||
|
||||
.. automodule:: galaxy.tools.toolbox.panel
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`tags` Module
|
||||
------------------
|
||||
|
||||
.. automodule:: galaxy.tools.toolbox.tags
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`watcher` Module
|
||||
---------------------
|
||||
|
||||
.. automodule:: galaxy.tools.toolbox.watcher
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Subpackages
|
||||
-----------
|
||||
|
||||
@@ -57,3 +14,47 @@ Subpackages
|
||||
galaxy.tools.toolbox.filters
|
||||
galaxy.tools.toolbox.lineages
|
||||
|
||||
Submodules
|
||||
----------
|
||||
|
||||
galaxy.tools.toolbox.base module
|
||||
--------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.toolbox.base
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tools.toolbox.integrated_panel module
|
||||
--------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.toolbox.integrated_panel
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tools.toolbox.panel module
|
||||
---------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.toolbox.panel
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tools.toolbox.tags module
|
||||
--------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.toolbox.tags
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tools.toolbox.watcher module
|
||||
-----------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.toolbox.watcher
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
|
||||
@@ -1,8 +1,5 @@
|
||||
galaxyops Package
|
||||
=================
|
||||
|
||||
:mod:`galaxyops` Package
|
||||
------------------------
|
||||
galaxy.tools.util.galaxyops package
|
||||
===================================
|
||||
|
||||
.. automodule:: galaxy.tools.util.galaxyops
|
||||
:members:
|
||||
|
||||
@@ -1,22 +1,11 @@
|
||||
util Package
|
||||
============
|
||||
|
||||
:mod:`util` Package
|
||||
-------------------
|
||||
galaxy.tools.util package
|
||||
=========================
|
||||
|
||||
.. automodule:: galaxy.tools.util
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`maf_utilities` Module
|
||||
---------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.util.maf_utilities
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Subpackages
|
||||
-----------
|
||||
|
||||
@@ -24,3 +13,15 @@ Subpackages
|
||||
|
||||
galaxy.tools.util.galaxyops
|
||||
|
||||
Submodules
|
||||
----------
|
||||
|
||||
galaxy.tools.util.maf_utilities module
|
||||
--------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tools.util.maf_utilities
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
|
||||
@@ -1,8 +1,5 @@
|
||||
importlib Package
|
||||
=================
|
||||
|
||||
:mod:`importlib` Package
|
||||
------------------------
|
||||
galaxy.util.backports.importlib package
|
||||
=======================================
|
||||
|
||||
.. automodule:: galaxy.util.backports.importlib
|
||||
:members:
|
||||
|
||||
@@ -1,8 +1,5 @@
|
||||
backports Package
|
||||
=================
|
||||
|
||||
:mod:`backports` Package
|
||||
------------------------
|
||||
galaxy.util.backports package
|
||||
=============================
|
||||
|
||||
.. automodule:: galaxy.util.backports
|
||||
:members:
|
||||
|
||||
@@ -1,19 +1,20 @@
|
||||
log Package
|
||||
===========
|
||||
|
||||
:mod:`log` Package
|
||||
------------------
|
||||
galaxy.util.log package
|
||||
=======================
|
||||
|
||||
.. automodule:: galaxy.util.log
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`fluent_log` Module
|
||||
------------------------
|
||||
Submodules
|
||||
----------
|
||||
|
||||
galaxy.util.log.fluent_log module
|
||||
---------------------------------
|
||||
|
||||
.. automodule:: galaxy.util.log.fluent_log
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
|
||||
@@ -1,27 +1,28 @@
|
||||
pastescript Package
|
||||
===================
|
||||
|
||||
:mod:`pastescript` Package
|
||||
--------------------------
|
||||
galaxy.util.pastescript package
|
||||
===============================
|
||||
|
||||
.. automodule:: galaxy.util.pastescript
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`loadwsgi` Module
|
||||
----------------------
|
||||
Submodules
|
||||
----------
|
||||
|
||||
galaxy.util.pastescript.loadwsgi module
|
||||
---------------------------------------
|
||||
|
||||
.. automodule:: galaxy.util.pastescript.loadwsgi
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`serve` Module
|
||||
-------------------
|
||||
galaxy.util.pastescript.serve module
|
||||
------------------------------------
|
||||
|
||||
.. automodule:: galaxy.util.pastescript.serve
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
|
||||
+270
-269
@@ -1,278 +1,11 @@
|
||||
util Package
|
||||
============
|
||||
|
||||
:mod:`util` Package
|
||||
-------------------
|
||||
galaxy.util package
|
||||
===================
|
||||
|
||||
.. automodule:: galaxy.util
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`aliaspickler` Module
|
||||
--------------------------
|
||||
|
||||
.. automodule:: galaxy.util.aliaspickler
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`biostar` Module
|
||||
---------------------
|
||||
|
||||
.. automodule:: galaxy.util.biostar
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`bunch` Module
|
||||
-------------------
|
||||
|
||||
.. automodule:: galaxy.util.bunch
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`dbkeys` Module
|
||||
--------------------
|
||||
|
||||
.. automodule:: galaxy.util.dbkeys
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`debugging` Module
|
||||
-----------------------
|
||||
|
||||
.. automodule:: galaxy.util.debugging
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`dictobj` Module
|
||||
---------------------
|
||||
|
||||
.. automodule:: galaxy.util.dictobj
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`directory_hash` Module
|
||||
----------------------------
|
||||
|
||||
.. automodule:: galaxy.util.directory_hash
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`expressions` Module
|
||||
-------------------------
|
||||
|
||||
.. automodule:: galaxy.util.expressions
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`hash_util` Module
|
||||
-----------------------
|
||||
|
||||
.. automodule:: galaxy.util.hash_util
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`heartbeat` Module
|
||||
-----------------------
|
||||
|
||||
.. automodule:: galaxy.util.heartbeat
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`inflection` Module
|
||||
------------------------
|
||||
|
||||
.. automodule:: galaxy.util.inflection
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`json` Module
|
||||
------------------
|
||||
|
||||
.. automodule:: galaxy.util.json
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`jstree` Module
|
||||
--------------------
|
||||
|
||||
.. automodule:: galaxy.util.jstree
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`lazy_process` Module
|
||||
--------------------------
|
||||
|
||||
.. automodule:: galaxy.util.lazy_process
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`lrucache` Module
|
||||
----------------------
|
||||
|
||||
.. automodule:: galaxy.util.lrucache
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`none_like` Module
|
||||
-----------------------
|
||||
|
||||
.. automodule:: galaxy.util.none_like
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`object_wrapper` Module
|
||||
----------------------------
|
||||
|
||||
.. automodule:: galaxy.util.object_wrapper
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`odict` Module
|
||||
-------------------
|
||||
|
||||
.. automodule:: galaxy.util.odict
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`permutations` Module
|
||||
--------------------------
|
||||
|
||||
.. automodule:: galaxy.util.permutations
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`plugin_config` Module
|
||||
---------------------------
|
||||
|
||||
.. automodule:: galaxy.util.plugin_config
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`properties` Module
|
||||
------------------------
|
||||
|
||||
.. automodule:: galaxy.util.properties
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`sanitize_html` Module
|
||||
---------------------------
|
||||
|
||||
.. automodule:: galaxy.util.sanitize_html
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`simplegraph` Module
|
||||
-------------------------
|
||||
|
||||
.. automodule:: galaxy.util.simplegraph
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`sleeper` Module
|
||||
---------------------
|
||||
|
||||
.. automodule:: galaxy.util.sleeper
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`sockets` Module
|
||||
---------------------
|
||||
|
||||
.. automodule:: galaxy.util.sockets
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`specs` Module
|
||||
-------------------
|
||||
|
||||
.. automodule:: galaxy.util.specs
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`sqlite` Module
|
||||
--------------------
|
||||
|
||||
.. automodule:: galaxy.util.sqlite
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`streamball` Module
|
||||
------------------------
|
||||
|
||||
.. automodule:: galaxy.util.streamball
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`submodules` Module
|
||||
------------------------
|
||||
|
||||
.. automodule:: galaxy.util.submodules
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`template` Module
|
||||
----------------------
|
||||
|
||||
.. automodule:: galaxy.util.template
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`topsort` Module
|
||||
---------------------
|
||||
|
||||
.. automodule:: galaxy.util.topsort
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`validation` Module
|
||||
------------------------
|
||||
|
||||
.. automodule:: galaxy.util.validation
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`xml_macros` Module
|
||||
------------------------
|
||||
|
||||
.. automodule:: galaxy.util.xml_macros
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Subpackages
|
||||
-----------
|
||||
|
||||
@@ -282,3 +15,271 @@ Subpackages
|
||||
galaxy.util.log
|
||||
galaxy.util.pastescript
|
||||
|
||||
Submodules
|
||||
----------
|
||||
|
||||
galaxy.util.aliaspickler module
|
||||
-------------------------------
|
||||
|
||||
.. automodule:: galaxy.util.aliaspickler
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.util.biostar module
|
||||
--------------------------
|
||||
|
||||
.. automodule:: galaxy.util.biostar
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.util.bunch module
|
||||
------------------------
|
||||
|
||||
.. automodule:: galaxy.util.bunch
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.util.dbkeys module
|
||||
-------------------------
|
||||
|
||||
.. automodule:: galaxy.util.dbkeys
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.util.debugging module
|
||||
----------------------------
|
||||
|
||||
.. automodule:: galaxy.util.debugging
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.util.dictobj module
|
||||
--------------------------
|
||||
|
||||
.. automodule:: galaxy.util.dictobj
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.util.directory_hash module
|
||||
---------------------------------
|
||||
|
||||
.. automodule:: galaxy.util.directory_hash
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.util.expressions module
|
||||
------------------------------
|
||||
|
||||
.. automodule:: galaxy.util.expressions
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.util.hash_util module
|
||||
----------------------------
|
||||
|
||||
.. automodule:: galaxy.util.hash_util
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.util.heartbeat module
|
||||
----------------------------
|
||||
|
||||
.. automodule:: galaxy.util.heartbeat
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.util.inflection module
|
||||
-----------------------------
|
||||
|
||||
.. automodule:: galaxy.util.inflection
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.util.json module
|
||||
-----------------------
|
||||
|
||||
.. automodule:: galaxy.util.json
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.util.jstree module
|
||||
-------------------------
|
||||
|
||||
.. automodule:: galaxy.util.jstree
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.util.lazy_process module
|
||||
-------------------------------
|
||||
|
||||
.. automodule:: galaxy.util.lazy_process
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.util.lrucache module
|
||||
---------------------------
|
||||
|
||||
.. automodule:: galaxy.util.lrucache
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.util.none_like module
|
||||
----------------------------
|
||||
|
||||
.. automodule:: galaxy.util.none_like
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.util.object_wrapper module
|
||||
---------------------------------
|
||||
|
||||
.. automodule:: galaxy.util.object_wrapper
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.util.odict module
|
||||
------------------------
|
||||
|
||||
.. automodule:: galaxy.util.odict
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.util.permutations module
|
||||
-------------------------------
|
||||
|
||||
.. automodule:: galaxy.util.permutations
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.util.plugin_config module
|
||||
--------------------------------
|
||||
|
||||
.. automodule:: galaxy.util.plugin_config
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.util.properties module
|
||||
-----------------------------
|
||||
|
||||
.. automodule:: galaxy.util.properties
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.util.sanitize_html module
|
||||
--------------------------------
|
||||
|
||||
.. automodule:: galaxy.util.sanitize_html
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.util.simplegraph module
|
||||
------------------------------
|
||||
|
||||
.. automodule:: galaxy.util.simplegraph
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.util.sleeper module
|
||||
--------------------------
|
||||
|
||||
.. automodule:: galaxy.util.sleeper
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.util.sockets module
|
||||
--------------------------
|
||||
|
||||
.. automodule:: galaxy.util.sockets
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.util.specs module
|
||||
------------------------
|
||||
|
||||
.. automodule:: galaxy.util.specs
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.util.sqlite module
|
||||
-------------------------
|
||||
|
||||
.. automodule:: galaxy.util.sqlite
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.util.streamball module
|
||||
-----------------------------
|
||||
|
||||
.. automodule:: galaxy.util.streamball
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.util.submodules module
|
||||
-----------------------------
|
||||
|
||||
.. automodule:: galaxy.util.submodules
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.util.template module
|
||||
---------------------------
|
||||
|
||||
.. automodule:: galaxy.util.template
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.util.topsort module
|
||||
--------------------------
|
||||
|
||||
.. automodule:: galaxy.util.topsort
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.util.validation module
|
||||
-----------------------------
|
||||
|
||||
.. automodule:: galaxy.util.validation
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.util.xml_macros module
|
||||
-----------------------------
|
||||
|
||||
.. automodule:: galaxy.util.xml_macros
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
|
||||
@@ -1,43 +1,44 @@
|
||||
phyloviz Package
|
||||
================
|
||||
|
||||
:mod:`phyloviz` Package
|
||||
-----------------------
|
||||
galaxy.visualization.data_providers.phyloviz package
|
||||
====================================================
|
||||
|
||||
.. automodule:: galaxy.visualization.data_providers.phyloviz
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`baseparser` Module
|
||||
------------------------
|
||||
Submodules
|
||||
----------
|
||||
|
||||
galaxy.visualization.data_providers.phyloviz.baseparser module
|
||||
--------------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.visualization.data_providers.phyloviz.baseparser
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`newickparser` Module
|
||||
--------------------------
|
||||
galaxy.visualization.data_providers.phyloviz.newickparser module
|
||||
----------------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.visualization.data_providers.phyloviz.newickparser
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`nexusparser` Module
|
||||
-------------------------
|
||||
galaxy.visualization.data_providers.phyloviz.nexusparser module
|
||||
---------------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.visualization.data_providers.phyloviz.nexusparser
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`phyloxmlparser` Module
|
||||
----------------------------
|
||||
galaxy.visualization.data_providers.phyloviz.phyloxmlparser module
|
||||
------------------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.visualization.data_providers.phyloviz.phyloxmlparser
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
|
||||
@@ -1,46 +1,11 @@
|
||||
data_providers Package
|
||||
======================
|
||||
|
||||
:mod:`data_providers` Package
|
||||
-----------------------------
|
||||
galaxy.visualization.data_providers package
|
||||
===========================================
|
||||
|
||||
.. automodule:: galaxy.visualization.data_providers
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`basic` Module
|
||||
-------------------
|
||||
|
||||
.. automodule:: galaxy.visualization.data_providers.basic
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`cigar` Module
|
||||
-------------------
|
||||
|
||||
.. automodule:: galaxy.visualization.data_providers.cigar
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`genome` Module
|
||||
--------------------
|
||||
|
||||
.. automodule:: galaxy.visualization.data_providers.genome
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`registry` Module
|
||||
----------------------
|
||||
|
||||
.. automodule:: galaxy.visualization.data_providers.registry
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Subpackages
|
||||
-----------
|
||||
|
||||
@@ -48,3 +13,39 @@ Subpackages
|
||||
|
||||
galaxy.visualization.data_providers.phyloviz
|
||||
|
||||
Submodules
|
||||
----------
|
||||
|
||||
galaxy.visualization.data_providers.basic module
|
||||
------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.visualization.data_providers.basic
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.visualization.data_providers.cigar module
|
||||
------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.visualization.data_providers.cigar
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.visualization.data_providers.genome module
|
||||
-------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.visualization.data_providers.genome
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.visualization.data_providers.registry module
|
||||
---------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.visualization.data_providers.registry
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
|
||||
@@ -1,8 +1,5 @@
|
||||
genome Package
|
||||
==============
|
||||
|
||||
:mod:`genome` Package
|
||||
---------------------
|
||||
galaxy.visualization.genome package
|
||||
===================================
|
||||
|
||||
.. automodule:: galaxy.visualization.genome
|
||||
:members:
|
||||
|
||||
@@ -1,43 +1,52 @@
|
||||
plugins Package
|
||||
===============
|
||||
galaxy.visualization.plugins package
|
||||
====================================
|
||||
|
||||
:mod:`config_parser` Module
|
||||
---------------------------
|
||||
.. automodule:: galaxy.visualization.plugins
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Submodules
|
||||
----------
|
||||
|
||||
galaxy.visualization.plugins.config_parser module
|
||||
-------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.visualization.plugins.config_parser
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`plugin` Module
|
||||
--------------------
|
||||
galaxy.visualization.plugins.plugin module
|
||||
------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.visualization.plugins.plugin
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`registry` Module
|
||||
----------------------
|
||||
galaxy.visualization.plugins.registry module
|
||||
--------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.visualization.plugins.registry
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`resource_parser` Module
|
||||
-----------------------------
|
||||
galaxy.visualization.plugins.resource_parser module
|
||||
---------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.visualization.plugins.resource_parser
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`utils` Module
|
||||
-------------------
|
||||
galaxy.visualization.plugins.utils module
|
||||
-----------------------------------------
|
||||
|
||||
.. automodule:: galaxy.visualization.plugins.utils
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
|
||||
@@ -1,22 +1,11 @@
|
||||
visualization Package
|
||||
=====================
|
||||
|
||||
:mod:`visualization` Package
|
||||
----------------------------
|
||||
galaxy.visualization package
|
||||
============================
|
||||
|
||||
.. automodule:: galaxy.visualization
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`genomes` Module
|
||||
---------------------
|
||||
|
||||
.. automodule:: galaxy.visualization.genomes
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Subpackages
|
||||
-----------
|
||||
|
||||
@@ -27,3 +16,15 @@ Subpackages
|
||||
galaxy.visualization.plugins
|
||||
galaxy.visualization.tracks
|
||||
|
||||
Submodules
|
||||
----------
|
||||
|
||||
galaxy.visualization.genomes module
|
||||
-----------------------------------
|
||||
|
||||
.. automodule:: galaxy.visualization.genomes
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
|
||||
@@ -1,8 +1,5 @@
|
||||
tracks Package
|
||||
==============
|
||||
|
||||
:mod:`tracks` Package
|
||||
---------------------
|
||||
galaxy.visualization.tracks package
|
||||
===================================
|
||||
|
||||
.. automodule:: galaxy.visualization.tracks
|
||||
:members:
|
||||
|
||||
@@ -1,11 +1,20 @@
|
||||
controllers Package
|
||||
===================
|
||||
galaxy.web.base.controllers package
|
||||
===================================
|
||||
|
||||
:mod:`admin` Module
|
||||
-------------------
|
||||
.. automodule:: galaxy.web.base.controllers
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Submodules
|
||||
----------
|
||||
|
||||
galaxy.web.base.controllers.admin module
|
||||
----------------------------------------
|
||||
|
||||
.. automodule:: galaxy.web.base.controllers.admin
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
|
||||
@@ -1,26 +1,7 @@
|
||||
base Package
|
||||
============
|
||||
galaxy.web.base package
|
||||
=======================
|
||||
|
||||
:mod:`controller` Module
|
||||
------------------------
|
||||
|
||||
.. automodule:: galaxy.web.base.controller
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`interactive_environments` Module
|
||||
--------------------------------------
|
||||
|
||||
.. automodule:: galaxy.web.base.interactive_environments
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`pluginframework` Module
|
||||
-----------------------------
|
||||
|
||||
.. automodule:: galaxy.web.base.pluginframework
|
||||
.. automodule:: galaxy.web.base
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
@@ -32,3 +13,31 @@ Subpackages
|
||||
|
||||
galaxy.web.base.controllers
|
||||
|
||||
Submodules
|
||||
----------
|
||||
|
||||
galaxy.web.base.controller module
|
||||
---------------------------------
|
||||
|
||||
.. automodule:: galaxy.web.base.controller
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.web.base.interactive_environments module
|
||||
-----------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.web.base.interactive_environments
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.web.base.pluginframework module
|
||||
--------------------------------------
|
||||
|
||||
.. automodule:: galaxy.web.base.pluginframework
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
|
||||
@@ -1,19 +1,20 @@
|
||||
helpers Package
|
||||
===============
|
||||
|
||||
:mod:`helpers` Package
|
||||
----------------------
|
||||
galaxy.web.framework.helpers package
|
||||
====================================
|
||||
|
||||
.. automodule:: galaxy.web.framework.helpers
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`grids` Module
|
||||
-------------------
|
||||
Submodules
|
||||
----------
|
||||
|
||||
galaxy.web.framework.helpers.grids module
|
||||
-----------------------------------------
|
||||
|
||||
.. automodule:: galaxy.web.framework.helpers.grids
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
|
||||
@@ -1,75 +1,76 @@
|
||||
middleware Package
|
||||
==================
|
||||
|
||||
:mod:`middleware` Package
|
||||
-------------------------
|
||||
galaxy.web.framework.middleware package
|
||||
=======================================
|
||||
|
||||
.. automodule:: galaxy.web.framework.middleware
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`error` Module
|
||||
-------------------
|
||||
Submodules
|
||||
----------
|
||||
|
||||
galaxy.web.framework.middleware.error module
|
||||
--------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.web.framework.middleware.error
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`profile` Module
|
||||
---------------------
|
||||
galaxy.web.framework.middleware.profile module
|
||||
----------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.web.framework.middleware.profile
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`remoteuser` Module
|
||||
------------------------
|
||||
galaxy.web.framework.middleware.remoteuser module
|
||||
-------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.web.framework.middleware.remoteuser
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`request_id` Module
|
||||
------------------------
|
||||
galaxy.web.framework.middleware.request_id module
|
||||
-------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.web.framework.middleware.request_id
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`sentry` Module
|
||||
--------------------
|
||||
galaxy.web.framework.middleware.sentry module
|
||||
---------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.web.framework.middleware.sentry
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`static` Module
|
||||
--------------------
|
||||
galaxy.web.framework.middleware.static module
|
||||
---------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.web.framework.middleware.static
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`translogger` Module
|
||||
-------------------------
|
||||
galaxy.web.framework.middleware.translogger module
|
||||
--------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.web.framework.middleware.translogger
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`xforwardedhost` Module
|
||||
----------------------------
|
||||
galaxy.web.framework.middleware.xforwardedhost module
|
||||
-----------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.web.framework.middleware.xforwardedhost
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
|
||||
@@ -1,54 +1,11 @@
|
||||
framework Package
|
||||
=================
|
||||
|
||||
:mod:`framework` Package
|
||||
------------------------
|
||||
galaxy.web.framework package
|
||||
============================
|
||||
|
||||
.. automodule:: galaxy.web.framework
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`base` Module
|
||||
------------------
|
||||
|
||||
.. automodule:: galaxy.web.framework.base
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`decorators` Module
|
||||
------------------------
|
||||
|
||||
.. automodule:: galaxy.web.framework.decorators
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`formbuilder` Module
|
||||
-------------------------
|
||||
|
||||
.. automodule:: galaxy.web.framework.formbuilder
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`openid_manager` Module
|
||||
----------------------------
|
||||
|
||||
.. automodule:: galaxy.web.framework.openid_manager
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`webapp` Module
|
||||
--------------------
|
||||
|
||||
.. automodule:: galaxy.web.framework.webapp
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Subpackages
|
||||
-----------
|
||||
|
||||
@@ -57,3 +14,47 @@ Subpackages
|
||||
galaxy.web.framework.helpers
|
||||
galaxy.web.framework.middleware
|
||||
|
||||
Submodules
|
||||
----------
|
||||
|
||||
galaxy.web.framework.base module
|
||||
--------------------------------
|
||||
|
||||
.. automodule:: galaxy.web.framework.base
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.web.framework.decorators module
|
||||
--------------------------------------
|
||||
|
||||
.. automodule:: galaxy.web.framework.decorators
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.web.framework.formbuilder module
|
||||
---------------------------------------
|
||||
|
||||
.. automodule:: galaxy.web.framework.formbuilder
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.web.framework.openid_manager module
|
||||
------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.web.framework.openid_manager
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.web.framework.webapp module
|
||||
----------------------------------
|
||||
|
||||
.. automodule:: galaxy.web.framework.webapp
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
|
||||
@@ -1,19 +1,20 @@
|
||||
proxy Package
|
||||
=============
|
||||
|
||||
:mod:`proxy` Package
|
||||
--------------------
|
||||
galaxy.web.proxy package
|
||||
========================
|
||||
|
||||
.. automodule:: galaxy.web.proxy
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`filelock` Module
|
||||
----------------------
|
||||
Submodules
|
||||
----------
|
||||
|
||||
galaxy.web.proxy.filelock module
|
||||
--------------------------------
|
||||
|
||||
.. automodule:: galaxy.web.proxy.filelock
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
|
||||
@@ -1,46 +1,11 @@
|
||||
web Package
|
||||
===========
|
||||
|
||||
:mod:`web` Package
|
||||
------------------
|
||||
galaxy.web package
|
||||
==================
|
||||
|
||||
.. automodule:: galaxy.web
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`buildapp` Module
|
||||
----------------------
|
||||
|
||||
.. automodule:: galaxy.web.buildapp
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`form_builder` Module
|
||||
--------------------------
|
||||
|
||||
.. automodule:: galaxy.web.form_builder
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`formatting` Module
|
||||
------------------------
|
||||
|
||||
.. automodule:: galaxy.web.formatting
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`params` Module
|
||||
--------------------
|
||||
|
||||
.. automodule:: galaxy.web.params
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Subpackages
|
||||
-----------
|
||||
|
||||
@@ -51,3 +16,39 @@ Subpackages
|
||||
galaxy.web.proxy
|
||||
galaxy.web.security
|
||||
|
||||
Submodules
|
||||
----------
|
||||
|
||||
galaxy.web.buildapp module
|
||||
--------------------------
|
||||
|
||||
.. automodule:: galaxy.web.buildapp
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.web.form_builder module
|
||||
------------------------------
|
||||
|
||||
.. automodule:: galaxy.web.form_builder
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.web.formatting module
|
||||
----------------------------
|
||||
|
||||
.. automodule:: galaxy.web.formatting
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.web.params module
|
||||
------------------------
|
||||
|
||||
.. automodule:: galaxy.web.params
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
|
||||
@@ -1,8 +1,5 @@
|
||||
security Package
|
||||
================
|
||||
|
||||
:mod:`security` Package
|
||||
-----------------------
|
||||
galaxy.web.security package
|
||||
===========================
|
||||
|
||||
.. automodule:: galaxy.web.security
|
||||
:members:
|
||||
|
||||
@@ -1,315 +1,324 @@
|
||||
galaxy.webapps.galaxy.api package
|
||||
=================================
|
||||
|
||||
:mod:`annotations` Module
|
||||
-------------------------
|
||||
.. automodule:: galaxy.webapps.galaxy.api
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Submodules
|
||||
----------
|
||||
|
||||
galaxy.webapps.galaxy.api.annotations module
|
||||
--------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.galaxy.api.annotations
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`authenticate` Module
|
||||
--------------------------
|
||||
galaxy.webapps.galaxy.api.authenticate module
|
||||
---------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.galaxy.api.authenticate
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`configuration` Module
|
||||
---------------------------
|
||||
galaxy.webapps.galaxy.api.configuration module
|
||||
----------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.galaxy.api.configuration
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`dataset_collections` Module
|
||||
---------------------------------
|
||||
galaxy.webapps.galaxy.api.dataset_collections module
|
||||
----------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.galaxy.api.dataset_collections
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`datasets` Module
|
||||
----------------------
|
||||
galaxy.webapps.galaxy.api.datasets module
|
||||
-----------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.galaxy.api.datasets
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`datatypes` Module
|
||||
-----------------------
|
||||
galaxy.webapps.galaxy.api.datatypes module
|
||||
------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.galaxy.api.datatypes
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`extended_metadata` Module
|
||||
-------------------------------
|
||||
galaxy.webapps.galaxy.api.extended_metadata module
|
||||
--------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.galaxy.api.extended_metadata
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`folder_contents` Module
|
||||
-----------------------------
|
||||
galaxy.webapps.galaxy.api.folder_contents module
|
||||
------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.galaxy.api.folder_contents
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`folders` Module
|
||||
---------------------
|
||||
galaxy.webapps.galaxy.api.folders module
|
||||
----------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.galaxy.api.folders
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`forms` Module
|
||||
-------------------
|
||||
galaxy.webapps.galaxy.api.forms module
|
||||
--------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.galaxy.api.forms
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`genomes` Module
|
||||
---------------------
|
||||
galaxy.webapps.galaxy.api.genomes module
|
||||
----------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.galaxy.api.genomes
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`group_roles` Module
|
||||
-------------------------
|
||||
galaxy.webapps.galaxy.api.group_roles module
|
||||
--------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.galaxy.api.group_roles
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`group_users` Module
|
||||
-------------------------
|
||||
galaxy.webapps.galaxy.api.group_users module
|
||||
--------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.galaxy.api.group_users
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`groups` Module
|
||||
--------------------
|
||||
galaxy.webapps.galaxy.api.groups module
|
||||
---------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.galaxy.api.groups
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`histories` Module
|
||||
-----------------------
|
||||
galaxy.webapps.galaxy.api.histories module
|
||||
------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.galaxy.api.histories
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`history_contents` Module
|
||||
------------------------------
|
||||
galaxy.webapps.galaxy.api.history_contents module
|
||||
-------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.galaxy.api.history_contents
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`item_tags` Module
|
||||
-----------------------
|
||||
galaxy.webapps.galaxy.api.item_tags module
|
||||
------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.galaxy.api.item_tags
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`job_files` Module
|
||||
-----------------------
|
||||
galaxy.webapps.galaxy.api.job_files module
|
||||
------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.galaxy.api.job_files
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`jobs` Module
|
||||
------------------
|
||||
galaxy.webapps.galaxy.api.jobs module
|
||||
-------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.galaxy.api.jobs
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`lda_datasets` Module
|
||||
--------------------------
|
||||
galaxy.webapps.galaxy.api.lda_datasets module
|
||||
---------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.galaxy.api.lda_datasets
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`libraries` Module
|
||||
-----------------------
|
||||
galaxy.webapps.galaxy.api.libraries module
|
||||
------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.galaxy.api.libraries
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`library_contents` Module
|
||||
------------------------------
|
||||
galaxy.webapps.galaxy.api.library_contents module
|
||||
-------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.galaxy.api.library_contents
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`metrics` Module
|
||||
---------------------
|
||||
galaxy.webapps.galaxy.api.metrics module
|
||||
----------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.galaxy.api.metrics
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`page_revisions` Module
|
||||
----------------------------
|
||||
galaxy.webapps.galaxy.api.page_revisions module
|
||||
-----------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.galaxy.api.page_revisions
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`pages` Module
|
||||
-------------------
|
||||
galaxy.webapps.galaxy.api.pages module
|
||||
--------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.galaxy.api.pages
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`provenance` Module
|
||||
------------------------
|
||||
galaxy.webapps.galaxy.api.provenance module
|
||||
-------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.galaxy.api.provenance
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`quotas` Module
|
||||
--------------------
|
||||
galaxy.webapps.galaxy.api.quotas module
|
||||
---------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.galaxy.api.quotas
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`remote_files` Module
|
||||
--------------------------
|
||||
galaxy.webapps.galaxy.api.remote_files module
|
||||
---------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.galaxy.api.remote_files
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`request_types` Module
|
||||
---------------------------
|
||||
galaxy.webapps.galaxy.api.request_types module
|
||||
----------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.galaxy.api.request_types
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`requests` Module
|
||||
----------------------
|
||||
galaxy.webapps.galaxy.api.requests module
|
||||
-----------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.galaxy.api.requests
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`roles` Module
|
||||
-------------------
|
||||
galaxy.webapps.galaxy.api.roles module
|
||||
--------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.galaxy.api.roles
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`samples` Module
|
||||
---------------------
|
||||
galaxy.webapps.galaxy.api.samples module
|
||||
----------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.galaxy.api.samples
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`search` Module
|
||||
--------------------
|
||||
galaxy.webapps.galaxy.api.search module
|
||||
---------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.galaxy.api.search
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`tool_data` Module
|
||||
-----------------------
|
||||
galaxy.webapps.galaxy.api.tool_data module
|
||||
------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.galaxy.api.tool_data
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`tool_shed_repositories` Module
|
||||
------------------------------------
|
||||
galaxy.webapps.galaxy.api.tool_shed_repositories module
|
||||
-------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.galaxy.api.tool_shed_repositories
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`tools` Module
|
||||
-------------------
|
||||
galaxy.webapps.galaxy.api.tools module
|
||||
--------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.galaxy.api.tools
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`users` Module
|
||||
-------------------
|
||||
galaxy.webapps.galaxy.api.users module
|
||||
--------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.galaxy.api.users
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`visualizations` Module
|
||||
----------------------------
|
||||
galaxy.webapps.galaxy.api.visualizations module
|
||||
-----------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.galaxy.api.visualizations
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`workflows` Module
|
||||
-----------------------
|
||||
galaxy.webapps.galaxy.api.workflows module
|
||||
------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.galaxy.api.workflows
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
|
||||
@@ -1,251 +1,252 @@
|
||||
controllers Package
|
||||
===================
|
||||
|
||||
:mod:`controllers` Package
|
||||
--------------------------
|
||||
galaxy.webapps.galaxy.controllers package
|
||||
=========================================
|
||||
|
||||
.. automodule:: galaxy.webapps.galaxy.controllers
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`admin` Module
|
||||
-------------------
|
||||
Submodules
|
||||
----------
|
||||
|
||||
galaxy.webapps.galaxy.controllers.admin module
|
||||
----------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.galaxy.controllers.admin
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`admin_toolshed` Module
|
||||
----------------------------
|
||||
galaxy.webapps.galaxy.controllers.admin_toolshed module
|
||||
-------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.galaxy.controllers.admin_toolshed
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`async` Module
|
||||
-------------------
|
||||
galaxy.webapps.galaxy.controllers.async module
|
||||
----------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.galaxy.controllers.async
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`biostar` Module
|
||||
---------------------
|
||||
galaxy.webapps.galaxy.controllers.biostar module
|
||||
------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.galaxy.controllers.biostar
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`cloudlaunch` Module
|
||||
-------------------------
|
||||
galaxy.webapps.galaxy.controllers.cloudlaunch module
|
||||
----------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.galaxy.controllers.cloudlaunch
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`data_manager` Module
|
||||
--------------------------
|
||||
galaxy.webapps.galaxy.controllers.data_manager module
|
||||
-----------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.galaxy.controllers.data_manager
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`dataset` Module
|
||||
---------------------
|
||||
galaxy.webapps.galaxy.controllers.dataset module
|
||||
------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.galaxy.controllers.dataset
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`error` Module
|
||||
-------------------
|
||||
galaxy.webapps.galaxy.controllers.error module
|
||||
----------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.galaxy.controllers.error
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`external_service` Module
|
||||
------------------------------
|
||||
galaxy.webapps.galaxy.controllers.external_service module
|
||||
---------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.galaxy.controllers.external_service
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`external_services` Module
|
||||
-------------------------------
|
||||
galaxy.webapps.galaxy.controllers.external_services module
|
||||
----------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.galaxy.controllers.external_services
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`forms` Module
|
||||
-------------------
|
||||
galaxy.webapps.galaxy.controllers.forms module
|
||||
----------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.galaxy.controllers.forms
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`history` Module
|
||||
---------------------
|
||||
galaxy.webapps.galaxy.controllers.history module
|
||||
------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.galaxy.controllers.history
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`library` Module
|
||||
---------------------
|
||||
galaxy.webapps.galaxy.controllers.library module
|
||||
------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.galaxy.controllers.library
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`library_admin` Module
|
||||
---------------------------
|
||||
galaxy.webapps.galaxy.controllers.library_admin module
|
||||
------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.galaxy.controllers.library_admin
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`library_common` Module
|
||||
----------------------------
|
||||
galaxy.webapps.galaxy.controllers.library_common module
|
||||
-------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.galaxy.controllers.library_common
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`mobile` Module
|
||||
--------------------
|
||||
galaxy.webapps.galaxy.controllers.mobile module
|
||||
-----------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.galaxy.controllers.mobile
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`page` Module
|
||||
------------------
|
||||
galaxy.webapps.galaxy.controllers.page module
|
||||
---------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.galaxy.controllers.page
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`request_type` Module
|
||||
--------------------------
|
||||
galaxy.webapps.galaxy.controllers.request_type module
|
||||
-----------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.galaxy.controllers.request_type
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`requests` Module
|
||||
----------------------
|
||||
galaxy.webapps.galaxy.controllers.requests module
|
||||
-------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.galaxy.controllers.requests
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`requests_admin` Module
|
||||
----------------------------
|
||||
galaxy.webapps.galaxy.controllers.requests_admin module
|
||||
-------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.galaxy.controllers.requests_admin
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`requests_common` Module
|
||||
-----------------------------
|
||||
galaxy.webapps.galaxy.controllers.requests_common module
|
||||
--------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.galaxy.controllers.requests_common
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`root` Module
|
||||
------------------
|
||||
galaxy.webapps.galaxy.controllers.root module
|
||||
---------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.galaxy.controllers.root
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`search` Module
|
||||
--------------------
|
||||
galaxy.webapps.galaxy.controllers.search module
|
||||
-----------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.galaxy.controllers.search
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`tag` Module
|
||||
-----------------
|
||||
galaxy.webapps.galaxy.controllers.tag module
|
||||
--------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.galaxy.controllers.tag
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`tool_runner` Module
|
||||
-------------------------
|
||||
galaxy.webapps.galaxy.controllers.tool_runner module
|
||||
----------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.galaxy.controllers.tool_runner
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`ucsc_proxy` Module
|
||||
------------------------
|
||||
galaxy.webapps.galaxy.controllers.ucsc_proxy module
|
||||
---------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.galaxy.controllers.ucsc_proxy
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`user` Module
|
||||
------------------
|
||||
galaxy.webapps.galaxy.controllers.user module
|
||||
---------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.galaxy.controllers.user
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`userskeys` Module
|
||||
-----------------------
|
||||
galaxy.webapps.galaxy.controllers.userskeys module
|
||||
--------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.galaxy.controllers.userskeys
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`visualization` Module
|
||||
---------------------------
|
||||
galaxy.webapps.galaxy.controllers.visualization module
|
||||
------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.galaxy.controllers.visualization
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`workflow` Module
|
||||
----------------------
|
||||
galaxy.webapps.galaxy.controllers.workflow module
|
||||
-------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.galaxy.controllers.workflow
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
|
||||
@@ -1,10 +1,7 @@
|
||||
galaxy Package
|
||||
==============
|
||||
galaxy.webapps.galaxy package
|
||||
=============================
|
||||
|
||||
:mod:`buildapp` Module
|
||||
----------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.galaxy.buildapp
|
||||
.. automodule:: galaxy.webapps.galaxy
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
@@ -17,3 +14,15 @@ Subpackages
|
||||
galaxy.webapps.galaxy.api
|
||||
galaxy.webapps.galaxy.controllers
|
||||
|
||||
Submodules
|
||||
----------
|
||||
|
||||
galaxy.webapps.galaxy.buildapp module
|
||||
-------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.galaxy.buildapp
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
|
||||
@@ -1,67 +1,68 @@
|
||||
controllers Package
|
||||
===================
|
||||
|
||||
:mod:`controllers` Package
|
||||
--------------------------
|
||||
galaxy.webapps.reports.controllers package
|
||||
==========================================
|
||||
|
||||
.. automodule:: galaxy.webapps.reports.controllers
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`jobs` Module
|
||||
------------------
|
||||
Submodules
|
||||
----------
|
||||
|
||||
galaxy.webapps.reports.controllers.jobs module
|
||||
----------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.reports.controllers.jobs
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`query` Module
|
||||
-------------------
|
||||
galaxy.webapps.reports.controllers.query module
|
||||
-----------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.reports.controllers.query
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`root` Module
|
||||
------------------
|
||||
galaxy.webapps.reports.controllers.root module
|
||||
----------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.reports.controllers.root
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`sample_tracking` Module
|
||||
-----------------------------
|
||||
galaxy.webapps.reports.controllers.sample_tracking module
|
||||
---------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.reports.controllers.sample_tracking
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`system` Module
|
||||
--------------------
|
||||
galaxy.webapps.reports.controllers.system module
|
||||
------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.reports.controllers.system
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`users` Module
|
||||
-------------------
|
||||
galaxy.webapps.reports.controllers.users module
|
||||
-----------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.reports.controllers.users
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`workflows` Module
|
||||
-----------------------
|
||||
galaxy.webapps.reports.controllers.workflows module
|
||||
---------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.reports.controllers.workflows
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
|
||||
@@ -1,38 +1,11 @@
|
||||
reports Package
|
||||
===============
|
||||
|
||||
:mod:`reports` Package
|
||||
----------------------
|
||||
galaxy.webapps.reports package
|
||||
==============================
|
||||
|
||||
.. automodule:: galaxy.webapps.reports
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`app` Module
|
||||
-----------------
|
||||
|
||||
.. automodule:: galaxy.webapps.reports.app
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`buildapp` Module
|
||||
----------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.reports.buildapp
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`config` Module
|
||||
--------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.reports.config
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Subpackages
|
||||
-----------
|
||||
|
||||
@@ -40,3 +13,31 @@ Subpackages
|
||||
|
||||
galaxy.webapps.reports.controllers
|
||||
|
||||
Submodules
|
||||
----------
|
||||
|
||||
galaxy.webapps.reports.app module
|
||||
---------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.reports.app
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.webapps.reports.buildapp module
|
||||
--------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.reports.buildapp
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.webapps.reports.config module
|
||||
------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.reports.config
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
|
||||
@@ -1,8 +1,5 @@
|
||||
webapps Package
|
||||
===============
|
||||
|
||||
:mod:`webapps` Package
|
||||
----------------------
|
||||
galaxy.webapps package
|
||||
======================
|
||||
|
||||
.. automodule:: galaxy.webapps
|
||||
:members:
|
||||
|
||||
@@ -1,59 +1,68 @@
|
||||
api Package
|
||||
===========
|
||||
galaxy.webapps.tool_shed.api package
|
||||
====================================
|
||||
|
||||
:mod:`authenticate` Module
|
||||
--------------------------
|
||||
.. automodule:: galaxy.webapps.tool_shed.api
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Submodules
|
||||
----------
|
||||
|
||||
galaxy.webapps.tool_shed.api.authenticate module
|
||||
------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.tool_shed.api.authenticate
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`categories` Module
|
||||
------------------------
|
||||
galaxy.webapps.tool_shed.api.categories module
|
||||
----------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.tool_shed.api.categories
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`groups` Module
|
||||
--------------------
|
||||
galaxy.webapps.tool_shed.api.groups module
|
||||
------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.tool_shed.api.groups
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`repositories` Module
|
||||
--------------------------
|
||||
galaxy.webapps.tool_shed.api.repositories module
|
||||
------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.tool_shed.api.repositories
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`repository_revisions` Module
|
||||
----------------------------------
|
||||
galaxy.webapps.tool_shed.api.repository_revisions module
|
||||
--------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.tool_shed.api.repository_revisions
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`tools` Module
|
||||
-------------------
|
||||
galaxy.webapps.tool_shed.api.tools module
|
||||
-----------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.tool_shed.api.tools
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`users` Module
|
||||
-------------------
|
||||
galaxy.webapps.tool_shed.api.users module
|
||||
-----------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.tool_shed.api.users
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
|
||||
@@ -1,67 +1,68 @@
|
||||
controllers Package
|
||||
===================
|
||||
|
||||
:mod:`controllers` Package
|
||||
--------------------------
|
||||
galaxy.webapps.tool_shed.controllers package
|
||||
============================================
|
||||
|
||||
.. automodule:: galaxy.webapps.tool_shed.controllers
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`admin` Module
|
||||
-------------------
|
||||
Submodules
|
||||
----------
|
||||
|
||||
galaxy.webapps.tool_shed.controllers.admin module
|
||||
-------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.tool_shed.controllers.admin
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`groups` Module
|
||||
--------------------
|
||||
galaxy.webapps.tool_shed.controllers.groups module
|
||||
--------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.tool_shed.controllers.groups
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`hg` Module
|
||||
----------------
|
||||
galaxy.webapps.tool_shed.controllers.hg module
|
||||
----------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.tool_shed.controllers.hg
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`repository` Module
|
||||
------------------------
|
||||
galaxy.webapps.tool_shed.controllers.repository module
|
||||
------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.tool_shed.controllers.repository
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`repository_review` Module
|
||||
-------------------------------
|
||||
galaxy.webapps.tool_shed.controllers.repository_review module
|
||||
-------------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.tool_shed.controllers.repository_review
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`upload` Module
|
||||
--------------------
|
||||
galaxy.webapps.tool_shed.controllers.upload module
|
||||
--------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.tool_shed.controllers.upload
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`user` Module
|
||||
------------------
|
||||
galaxy.webapps.tool_shed.controllers.user module
|
||||
------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.tool_shed.controllers.user
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
|
||||
@@ -1,27 +1,28 @@
|
||||
middleware Package
|
||||
==================
|
||||
|
||||
:mod:`middleware` Package
|
||||
-------------------------
|
||||
galaxy.webapps.tool_shed.framework.middleware package
|
||||
=====================================================
|
||||
|
||||
.. automodule:: galaxy.webapps.tool_shed.framework.middleware
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`hg` Module
|
||||
----------------
|
||||
Submodules
|
||||
----------
|
||||
|
||||
galaxy.webapps.tool_shed.framework.middleware.hg module
|
||||
-------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.tool_shed.framework.middleware.hg
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`remoteuser` Module
|
||||
------------------------
|
||||
galaxy.webapps.tool_shed.framework.middleware.remoteuser module
|
||||
---------------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.tool_shed.framework.middleware.remoteuser
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
|
||||
@@ -1,8 +1,5 @@
|
||||
framework Package
|
||||
=================
|
||||
|
||||
:mod:`framework` Package
|
||||
------------------------
|
||||
galaxy.webapps.tool_shed.framework package
|
||||
==========================================
|
||||
|
||||
.. automodule:: galaxy.webapps.tool_shed.framework
|
||||
:members:
|
||||
|
||||
@@ -1,11 +1,20 @@
|
||||
migrate Package
|
||||
===============
|
||||
galaxy.webapps.tool_shed.model.migrate package
|
||||
==============================================
|
||||
|
||||
:mod:`check` Module
|
||||
-------------------
|
||||
.. automodule:: galaxy.webapps.tool_shed.model.migrate
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Submodules
|
||||
----------
|
||||
|
||||
galaxy.webapps.tool_shed.model.migrate.check module
|
||||
---------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.tool_shed.model.migrate.check
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
|
||||
@@ -1,22 +1,11 @@
|
||||
model Package
|
||||
=============
|
||||
|
||||
:mod:`model` Package
|
||||
--------------------
|
||||
galaxy.webapps.tool_shed.model package
|
||||
======================================
|
||||
|
||||
.. automodule:: galaxy.webapps.tool_shed.model
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`mapping` Module
|
||||
---------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.tool_shed.model.mapping
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Subpackages
|
||||
-----------
|
||||
|
||||
@@ -24,3 +13,15 @@ Subpackages
|
||||
|
||||
galaxy.webapps.tool_shed.model.migrate
|
||||
|
||||
Submodules
|
||||
----------
|
||||
|
||||
galaxy.webapps.tool_shed.model.mapping module
|
||||
---------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.tool_shed.model.mapping
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
|
||||
@@ -1,38 +1,11 @@
|
||||
tool_shed Package
|
||||
=================
|
||||
|
||||
:mod:`tool_shed` Package
|
||||
------------------------
|
||||
galaxy.webapps.tool_shed package
|
||||
================================
|
||||
|
||||
.. automodule:: galaxy.webapps.tool_shed
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`app` Module
|
||||
-----------------
|
||||
|
||||
.. automodule:: galaxy.webapps.tool_shed.app
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`buildapp` Module
|
||||
----------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.tool_shed.buildapp
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`config` Module
|
||||
--------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.tool_shed.config
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Subpackages
|
||||
-----------
|
||||
|
||||
@@ -46,3 +19,31 @@ Subpackages
|
||||
galaxy.webapps.tool_shed.security
|
||||
galaxy.webapps.tool_shed.util
|
||||
|
||||
Submodules
|
||||
----------
|
||||
|
||||
galaxy.webapps.tool_shed.app module
|
||||
-----------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.tool_shed.app
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.webapps.tool_shed.buildapp module
|
||||
----------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.tool_shed.buildapp
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.webapps.tool_shed.config module
|
||||
--------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.tool_shed.config
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
|
||||
@@ -1,19 +1,28 @@
|
||||
search Package
|
||||
==============
|
||||
galaxy.webapps.tool_shed.search package
|
||||
=======================================
|
||||
|
||||
:mod:`repo_search` Module
|
||||
-------------------------
|
||||
.. automodule:: galaxy.webapps.tool_shed.search
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Submodules
|
||||
----------
|
||||
|
||||
galaxy.webapps.tool_shed.search.repo_search module
|
||||
--------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.tool_shed.search.repo_search
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`tool_search` Module
|
||||
-------------------------
|
||||
galaxy.webapps.tool_shed.search.tool_search module
|
||||
--------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.tool_shed.search.tool_search
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
|
||||
@@ -1,8 +1,5 @@
|
||||
security Package
|
||||
================
|
||||
|
||||
:mod:`security` Package
|
||||
-----------------------
|
||||
galaxy.webapps.tool_shed.security package
|
||||
=========================================
|
||||
|
||||
.. automodule:: galaxy.webapps.tool_shed.security
|
||||
:members:
|
||||
|
||||
@@ -1,27 +1,36 @@
|
||||
util Package
|
||||
============
|
||||
galaxy.webapps.tool_shed.util package
|
||||
=====================================
|
||||
|
||||
:mod:`hgweb_config` Module
|
||||
--------------------------
|
||||
.. automodule:: galaxy.webapps.tool_shed.util
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Submodules
|
||||
----------
|
||||
|
||||
galaxy.webapps.tool_shed.util.hgweb_config module
|
||||
-------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.tool_shed.util.hgweb_config
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`ratings_util` Module
|
||||
--------------------------
|
||||
galaxy.webapps.tool_shed.util.ratings_util module
|
||||
-------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.tool_shed.util.ratings_util
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`shed_statistics` Module
|
||||
-----------------------------
|
||||
galaxy.webapps.tool_shed.util.shed_statistics module
|
||||
----------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.tool_shed.util.shed_statistics
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
|
||||
@@ -1,11 +1,20 @@
|
||||
work Package
|
||||
============
|
||||
galaxy.work package
|
||||
===================
|
||||
|
||||
:mod:`context` Module
|
||||
---------------------
|
||||
.. automodule:: galaxy.work
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Submodules
|
||||
----------
|
||||
|
||||
galaxy.work.context module
|
||||
--------------------------
|
||||
|
||||
.. automodule:: galaxy.work.context
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
||||
|
||||
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Reference in New Issue
Block a user