1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/eb4dac39eed5/
changeset: eb4dac39eed5
user: dan
date: 2013-01-07 17:07:52
summary: Enhance Tool.check_and_update_param_values_helper() to check that the type of value provided is valid for the input parameter currently declared. Fixes issue where a server error would occur within workflows when parameter's type has changed to a non-compatible one: e.g. conditional group changed to dataset input.
affected #: 1 file
diff -r f93f509ca0c2a21acdf0ed17615d1caf839dcb98 -r eb4dac39eed53cc0ef1550ee63486358fd53ad59 lib/galaxy/tools/__init__.py
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -2181,7 +2181,12 @@
self.check_and_update_param_values_helper( input.cases[current].inputs, group_values, trans, messages, context, prefix )
else:
# Regular tool parameter, no recursion needed
- pass
+ try:
+ #this will fail when a parameter's type has changed to a non-compatible one: e.g. conditional group changed to dataset input
+ input.value_from_basic( values[ input.name ], trans.app, ignore_errors=False )
+ except:
+ messages[ input.name ] = "Value no longer valid for '%s%s', replaced with default" % ( prefix, input.label )
+ values[ input.name ] = input.get_initial_value( trans, context )
def handle_unvalidated_param_values( self, input_values, app ):
"""
Find any instances of `UnvalidatedValue` within input_values and
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/8fe64f73835c/
changeset: 8fe64f73835c
user: james_taylor
date: 2013-01-04 20:42:28
summary: remove trailing comma
affected #: 1 file
diff -r 312ba8a948a1c678bea807f4a0d3320af8363968 -r 8fe64f73835cd19274dcac65c935187d426b18ba templates/root/index.mako
--- a/templates/root/index.mako
+++ b/templates/root/index.mako
@@ -76,7 +76,7 @@
if( navigator.userAgent.match( /(iPhone|iPod|iPad)/i ) ) {
$("iframe").parent().css( {
"overflow": "scroll",
- "-webkit-overflow-scrolling": "touch",
+ "-webkit-overflow-scrolling": "touch"
})
}
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/8676b55d191c/
changeset: 8676b55d191c
user: jgoecks
date: 2013-01-04 18:07:38
summary: Improve wording for item sharing.
affected #: 1 file
diff -r ad04a8d066e7092fb73d5469f1935196923b8ab3 -r 8676b55d191c6742e6e7b8864e47918719314f78 templates/sharing_base.mako
--- a/templates/sharing_base.mako
+++ b/templates/sharing_base.mako
@@ -142,7 +142,7 @@
</form>
%else:
## User has a public username, so private sharing and publishing options.
- <h3>Making ${item_class_name} Accessible via Link and Publishing It</h3>
+ <h3>Make ${item_class_name} Accessible via Link and Publish It</h3><div>
%if item.importable:
@@ -214,7 +214,7 @@
##
## Sharing with Galaxy users.
##
- <h3>Sharing ${item_class_name} with Specific Users</h3>
+ <h3>Share ${item_class_name} with Individual Users</h3><div>
%if item.users_shared_with:
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/ad04a8d066e7/
changeset: ad04a8d066e7
user: inithello
date: 2013-01-04 17:30:11
summary: Tool shed functional tests for repositories with invalid tools, functional test enhancement for repositories with workflows.
affected #: 9 files
diff -r eb67f0b3555df7e249c2d8715d75c598dc25055b -r ad04a8d066e7092fb73d5469f1935196923b8ab3 test/tool_shed/base/twilltestcase.py
--- a/test/tool_shed/base/twilltestcase.py
+++ b/test/tool_shed/base/twilltestcase.py
@@ -97,7 +97,7 @@
Loop through each tool dictionary in the repository metadata associated with the received changeset_revision.
For each of these, check for a tools attribute, and load the tool metadata page if it exists, then display that tool's page.
'''
- repository_metadata = test_db_util.get_repository_metadata_by_repository_id_changeset_revision( repository.id, changeset_revision )
+ repository_metadata = self.get_repository_metadata_by_changeset_revision( repository, changeset_revision )
metadata = repository_metadata.metadata
if 'tools' not in metadata:
raise AssertionError( 'No tools in %s revision %s.' % ( repository.name, changeset_revision ) )
@@ -118,10 +118,9 @@
strings_not_displayed=[] )
def check_repository_invalid_tools_for_changeset_revision( self, repository, changeset_revision, strings_displayed=[], strings_not_displayed=[] ):
'''Load the invalid tool page for each invalid tool associated with this changeset revision and verify the received error messages.'''
- repository_metadata = test_db_util.get_repository_metadata_by_repository_id_changeset_revision( repository.id, changeset_revision )
+ repository_metadata = self.get_repository_metadata_by_changeset_revision( repository, changeset_revision )
metadata = repository_metadata.metadata
- if 'invalid_tools' not in metadata:
- return
+ assert 'invalid_tools' in metadata, 'Metadata for changeset revision %s does not define invalid tools' % changeset_revision
for tool_xml in metadata[ 'invalid_tools' ]:
self.load_invalid_tool_page( repository,
tool_xml=tool_xml,
@@ -396,9 +395,11 @@
def get_repository_metadata( self, repository ):
return [ metadata_revision for metadata_revision in repository.metadata_revisions ]
def get_repository_metadata_by_changeset_revision( self, repository, changeset_revision ):
- for metadata_revision in repository.metadata_revisions:
+ found = None
+ for metadata_revision in self.get_repository_metadata( repository ):
if metadata_revision.changeset_revision == changeset_revision:
- return metadata_revision
+ found = metadata_revision
+ return found
def get_repository_metadata_revisions( self, repository ):
return [ str( repository_metadata.changeset_revision ) for repository_metadata in repository.metadata_revisions ]
def get_repository_tip( self, repository ):
@@ -484,6 +485,8 @@
if not changeset_revision:
changeset_revision = self.get_repository_tip( repository )
metadata = self.get_repository_metadata_by_changeset_revision( repository, changeset_revision )
+ if not metadata:
+ raise AssertionError( 'Metadata not found for changeset revision %s.' % changeset_revision )
url = '/repository/generate_workflow_image?repository_metadata_id=%s&workflow_name=%s' % \
( self.security.encode_id( metadata.id ), tool_shed_encode( workflow_name ) )
self.visit_url( url )
diff -r eb67f0b3555df7e249c2d8715d75c598dc25055b -r ad04a8d066e7092fb73d5469f1935196923b8ab3 test/tool_shed/functional/test_0000_basic_repository_features.py
--- a/test/tool_shed/functional/test_0000_basic_repository_features.py
+++ b/test/tool_shed/functional/test_0000_basic_repository_features.py
@@ -2,8 +2,8 @@
import tool_shed.base.test_db_util as test_db_util
repository_name = 'filtering_0000'
-repository_description = "Galaxy's filtering tool"
-repository_long_description = "Long description of Galaxy's filtering tool"
+repository_description = "Galaxy's filtering tool for test 0000"
+repository_long_description = "Long description of Galaxy's filtering tool for test 0000"
class TestBasicRepositoryFeatures( ShedTwillTestCase ):
diff -r eb67f0b3555df7e249c2d8715d75c598dc25055b -r ad04a8d066e7092fb73d5469f1935196923b8ab3 test/tool_shed/functional/test_0060_workflows.py
--- a/test/tool_shed/functional/test_0060_workflows.py
+++ b/test/tool_shed/functional/test_0060_workflows.py
@@ -2,9 +2,8 @@
import tool_shed.base.test_db_util as test_db_util
repository_name = 'filtering_0060'
-repository_description = "Galaxy's filtering tool"
-repository_long_description = "Long description of Galaxy's filtering tool"
-workflow_repository_name = 'filtering_workflow_0060'
+repository_description="Galaxy's filtering tool for test 0060"
+repository_long_description="Long description of Galaxy's filtering tool for test 0060"
workflow_filename = 'Workflow_for_0060_filter_workflow_repository.ga'
workflow_name = 'Workflow for 0060_filter_workflow_repository'
@@ -54,6 +53,7 @@
'filtering/filtering_2.2.0.tar',
commit_message="Uploaded filtering 2.2.0",
remove_repo_files_not_in_tar='No' )
+# raise Exception( self.get_repository_tip( repository ) )
self.load_workflow_image_in_tool_shed( repository, workflow_name, strings_not_displayed=[ '#EBBCB2' ] )
def test_0025_verify_repository_metadata( self ):
'''Verify that resetting the metadata does not change it.'''
diff -r eb67f0b3555df7e249c2d8715d75c598dc25055b -r ad04a8d066e7092fb73d5469f1935196923b8ab3 test/tool_shed/functional/test_0070_invalid_tool.py
--- a/test/tool_shed/functional/test_0070_invalid_tool.py
+++ b/test/tool_shed/functional/test_0070_invalid_tool.py
@@ -1,12 +1,13 @@
from tool_shed.base.twilltestcase import ShedTwillTestCase, common, os
import tool_shed.base.test_db_util as test_db_util
-repository_name = 'freebayes_0070'
-repository_description = "Galaxy's freebayes tool"
-repository_long_description = "Long description of Galaxy's freebayes tool"
+repository_name = 'bismark_0070'
+repository_description = "Galaxy's bismark wrapper"
+repository_long_description = "Long description of Galaxy's bismark wrapper"
+category_name = 'Test 0070 Invalid Tool Revisions'
-class TestFreebayesRepository( ShedTwillTestCase ):
- '''Testing freebayes with tool data table entries, .loc files, and tool dependencies.'''
+class TestBismarkRepository( ShedTwillTestCase ):
+ '''Testing bismark with valid and invalid tool entries.'''
def test_0000_create_or_login_admin_user( self ):
"""Create necessary user accounts and login as an admin user."""
self.logout()
@@ -19,14 +20,11 @@
admin_user = test_db_util.get_user( common.admin_email )
assert admin_user is not None, 'Problem retrieving user with email %s from the database' % admin_email
admin_user_private_role = test_db_util.get_private_role( admin_user )
- def test_0005_create_category( self ):
- """Create a category for this test suite"""
- self.create_category( name='Test 0070 Repository With Invalid Tool', description='Tests for a repository with an invalid tool.' )
- def test_0010_create_test_repository_and_upload_tool_xml( self ):
- '''Create and populate a freebayes repository. After this test, it should contain one valid tool and one invalid tool.'''
+ def test_0005_create_category_and_repository( self ):
+ """Create a category for this test suite, then create and populate a bismark repository. It should contain at least one each valid and invalid tool."""
+ category = self.create_category( name=category_name, description='Tests for a repository with invalid tool revisions.' )
self.logout()
self.login( email=common.test_user_1_email, username=common.test_user_1_name )
- category = test_db_util.get_category_by_name( 'Test 0070 Repository With Invalid Tool' )
repository = self.get_or_create_repository( name=repository_name,
description=repository_description,
long_description=repository_long_description,
@@ -34,20 +32,18 @@
category_id=self.security.encode_id( category.id ),
strings_displayed=[] )
self.upload_file( repository,
- 'freebayes/freebayes.xml',
+ 'bismark/bismark.tar',
valid_tools_only=False,
strings_displayed=[],
- commit_message='Uploaded the tool xml.' )
+ commit_message='Uploaded the tool tarball.' )
+ self.display_manage_repository_page( repository, strings_displayed=[ 'Invalid tools' ] )
+ invalid_revision = self.get_repository_tip( repository )
self.upload_file( repository,
- 'filtering/filtering_1.1.0.tar',
- valid_tools_only=False,
+ 'bismark/bismark_methylation_extractor.xml',
+ valid_tools_only=False,
strings_displayed=[],
- commit_message='Uploaded the tool xml.',
- remove_repo_files_not_in_tar='No' )
- self.display_manage_repository_page( repository, strings_displayed=[ 'Valid tools', 'Invalid tools' ] )
- changeset_revision = self.get_repository_tip( repository )
- self.check_repository_tools_for_changeset_revision( repository, changeset_revision )
- self.check_repository_invalid_tools_for_changeset_revision( repository,
- changeset_revision,
- strings_displayed=[ 'requires an entry' ],
- strings_not_displayed=[] )
+ remove_repo_files_not_in_tar='No',
+ commit_message='Uploaded an updated tool xml.' )
+ valid_revision = self.get_repository_tip( repository )
+ self.check_repository_tools_for_changeset_revision( repository, valid_revision )
+ self.check_repository_invalid_tools_for_changeset_revision( repository, invalid_revision )
diff -r eb67f0b3555df7e249c2d8715d75c598dc25055b -r ad04a8d066e7092fb73d5469f1935196923b8ab3 test/tool_shed/functional/test_1060_install_repository_with_workflow.py
--- a/test/tool_shed/functional/test_1060_install_repository_with_workflow.py
+++ b/test/tool_shed/functional/test_1060_install_repository_with_workflow.py
@@ -2,8 +2,8 @@
import tool_shed.base.test_db_util as test_db_util
repository_name = 'filtering_0060'
-repository_description = "Galaxy's filtering tool"
-repository_long_description = "Long description of Galaxy's filtering tool"
+repository_description="Galaxy's filtering tool for test 0060",
+repository_long_description="Long description of Galaxy's filtering tool for test 0060",
workflow_filename = 'Workflow_for_0060_filter_workflow_repository.ga'
workflow_name = 'Workflow for 0060_filter_workflow_repository'
diff -r eb67f0b3555df7e249c2d8715d75c598dc25055b -r ad04a8d066e7092fb73d5469f1935196923b8ab3 test/tool_shed/functional/test_1070_invalid_tool.py
--- a/test/tool_shed/functional/test_1070_invalid_tool.py
+++ b/test/tool_shed/functional/test_1070_invalid_tool.py
@@ -1,9 +1,10 @@
from tool_shed.base.twilltestcase import ShedTwillTestCase, common, os
import tool_shed.base.test_db_util as test_db_util
-repository_name = 'freebayes_0070'
-repository_description = "Galaxy's freebayes tool"
-repository_long_description = "Long description of Galaxy's freebayes tool"
+repository_name = 'bismark_0070'
+repository_description = "Galaxy's bismark wrapper"
+repository_long_description = "Long description of Galaxy's bismark wrapper"
+category_name = 'Test 0070 Invalid Tool Revisions'
class TestFreebayesRepository( ShedTwillTestCase ):
'''Testing freebayes with tool data table entries, .loc files, and tool dependencies.'''
@@ -26,11 +27,11 @@
admin_user_private_role = test_db_util.get_private_role( admin_user )
def test_0005_ensure_existence_of_repository_and_category( self ):
'''Create freebayes repository and upload only freebayes.xml. This should result in an error message and invalid tool.'''
- self.create_category( name='Test 0070 Repository With Invalid Tool',
- description='Tests for a repository with an invalid tool.' )
+ self.create_category( name=category_name,
+ description='Test 1070 for a repository with an invalid tool.' )
self.logout()
self.login( email=common.test_user_1_email, username=common.test_user_1_name )
- category = test_db_util.get_category_by_name( 'Test 0070 Repository With Invalid Tool' )
+ category = test_db_util.get_category_by_name( category_name )
repository = self.get_or_create_repository( name=repository_name,
description=repository_description,
long_description=repository_long_description,
@@ -39,27 +40,29 @@
strings_displayed=[] )
if self.repository_is_new( repository ):
self.upload_file( repository,
- 'freebayes/freebayes.xml',
+ 'bismark/bismark.tar',
valid_tools_only=False,
- commit_message='Uploaded the invalid tool xml.' )
+ strings_displayed=[],
+ commit_message='Uploaded the tool tarball.' )
self.upload_file( repository,
- 'filtering/filtering_1.1.0.tar',
- valid_tools_only=False,
- commit_message='Uploaded the valid tool xml.',
- remove_repo_files_not_in_tar='No' )
+ 'bismark/bismark_methylation_extractor.xml',
+ valid_tools_only=False,
+ strings_displayed=[],
+ remove_repo_files_not_in_tar='No',
+ commit_message='Uploaded an updated tool xml.' )
def test_0010_browse_tool_shed( self ):
- """Browse the available tool sheds in this Galaxy instance and preview the freebayes repository."""
+ """Browse the available tool sheds in this Galaxy instance and preview the bismark repository."""
self.galaxy_logout()
self.galaxy_login( email=common.admin_email, username=common.admin_username )
- self.browse_tool_shed( url=self.url, strings_displayed=[ 'Test 0070 Repository With Invalid Tool' ] )
- category = test_db_util.get_category_by_name( 'Test 0070 Repository With Invalid Tool' )
+ self.browse_tool_shed( url=self.url, strings_displayed=[ category_name ] )
+ category = test_db_util.get_category_by_name( category_name )
self.browse_category( category, strings_displayed=[ repository_name ] )
self.preview_repository_in_tool_shed( repository_name, common.test_user_1_name, strings_displayed=[ repository_name ] )
def test_0015_install_freebayes_repository( self ):
'''Install the test repository without installing tool dependencies.'''
self.install_repository( repository_name,
common.test_user_1_name,
- 'Test 0070 Repository With Invalid Tool',
+ category_name,
install_tool_dependencies=False,
new_tool_panel_section='test_1070' )
installed_repository = test_db_util.get_installed_repository_by_name_owner( repository_name, common.test_user_1_name )
@@ -70,11 +73,9 @@
installed_repository.installed_changeset_revision ]
self.display_galaxy_browse_repositories_page( strings_displayed=strings_displayed )
self.display_installed_repository_manage_page( installed_repository,
- strings_displayed=[ 'simple expressions', 'Invalid tools' ],
- strings_not_displayed=[ 'variant detector' ] )
+ strings_displayed=[ 'methylation extractor', 'Invalid tools' ],
+ strings_not_displayed=[ 'bisulfite mapper' ] )
self.verify_tool_metadata_for_installed_repository( installed_repository )
self.update_installed_repository( installed_repository, strings_displayed=[ "there are no updates available" ] )
- assert 'invalid_tools' in installed_repository.metadata, 'No invalid tools were defined in %s.' % installed_repository.name
- def test_0020_verify_installed_repository_metadata( self ):
- '''Verify that resetting the metadata on an installed repository does not change the metadata.'''
- self.verify_installed_repository_metadata_unchanged( repository_name, common.test_user_1_name )
+ assert 'invalid_tools' in installed_repository.metadata, 'No invalid tools were defined in %s.' % \
+ installed_repository.name
diff -r eb67f0b3555df7e249c2d8715d75c598dc25055b -r ad04a8d066e7092fb73d5469f1935196923b8ab3 test/tool_shed/functional/test_1200_uninstall_and_reinstall_basic_repository.py
--- a/test/tool_shed/functional/test_1200_uninstall_and_reinstall_basic_repository.py
+++ b/test/tool_shed/functional/test_1200_uninstall_and_reinstall_basic_repository.py
@@ -27,8 +27,8 @@
self.logout()
self.login( email=common.test_user_1_email, username=common.test_user_1_name )
repository = self.get_or_create_repository( name='filtering_0000',
- description="Galaxy's filtering tool",
- long_description="Long description of Galaxy's filtering tool",
+ description="Galaxy's filtering tool for test 0000",
+ long_description="Long description of Galaxy's filtering tool for test 0000",
owner=common.test_user_1_name,
category_id=self.security.encode_id( category.id ) )
if self.repository_is_new( repository ):
@@ -56,8 +56,8 @@
installed_repository = test_db_util.get_installed_repository_by_name_owner( 'filtering_0000', common.test_user_1_name )
self.uninstall_repository( installed_repository, remove_from_disk=True )
strings_not_displayed = [ installed_repository.name,
- installed_repository.description,
- installed_repository.installed_changeset_revision ]
+ installed_repository.description,
+ installed_repository.installed_changeset_revision ]
self.display_galaxy_browse_repositories_page( strings_not_displayed=strings_not_displayed )
def test_0020_reinstall_filtering_repository( self ):
'''Reinstall the filtering repository.'''
@@ -77,8 +77,8 @@
installed_repository = test_db_util.get_installed_repository_by_name_owner( 'filtering_0000', common.test_user_1_name )
self.uninstall_repository( installed_repository, remove_from_disk=False )
strings_not_displayed = [ installed_repository.name,
- installed_repository.description,
- installed_repository.installed_changeset_revision ]
+ installed_repository.description,
+ installed_repository.installed_changeset_revision ]
self.display_galaxy_browse_repositories_page( strings_not_displayed=strings_not_displayed )
def test_0030_reactivate_filtering_repository( self ):
'''Reactivate the filtering repository and verify that it now shows up in the list of installed repositories.'''
diff -r eb67f0b3555df7e249c2d8715d75c598dc25055b -r ad04a8d066e7092fb73d5469f1935196923b8ab3 test/tool_shed/test_data/bismark/bismark.tar
Binary file test/tool_shed/test_data/bismark/bismark.tar has changed
diff -r eb67f0b3555df7e249c2d8715d75c598dc25055b -r ad04a8d066e7092fb73d5469f1935196923b8ab3 test/tool_shed/test_data/bismark/bismark_methylation_extractor.xml
--- /dev/null
+++ b/test/tool_shed/test_data/bismark/bismark_methylation_extractor.xml
@@ -0,0 +1,306 @@
+<tool id="bismark_methylation_extractor" name="Bismark" version="0.7.7.3">
+ <!-- Wrapper compatible with Bismark version 0.7.7 -->
+ <description>methylation extractor</description>
+ <!--<version_command>bismark_methylation_extractor version</version_command>-->
+ <requirements>
+ <requirement type="set_environment">SCRIPT_PATH</requirement>
+ <requirement type="package" version="0.12.8">bowtie</requirement>
+ <requirement type="package" version="2.0.0-beta7">bowtie2</requirement>
+ </requirements>
+ <parallelism method="basic"></parallelism>
+ <command interpreter="python">
+ bismark_methylation_extractor.py
+
+ --infile $input
+
+ --bismark_path \$SCRIPT_PATH
+
+ #if $singlePaired.sPaired == "single":
+ --single-end
+ #else:
+ --paired-end
+ $no_overlap
+ #end if
+
+ #if str($ignore_bps) != "0":
+ --ignore $ignore_bps
+ #end if
+
+ #if $report:
+ --report-file $o_report
+ #end if
+
+ #if $comprehensive:
+ --comprehensive
+ #end if
+
+ #if $merge_non_cpg:
+ --merge-non-cpg
+ #end if
+
+ #if $compress:
+ --compress $compressed_output
+ #else:
+ #if $comprehensive == False and $merge_non_cpg == False:
+ ##twelfe files
+ --cpg_ot $cpg_ot
+ --chg_ot $chg_ot
+ --chh_ot $chh_ot
+ --cpg_ctot $cpg_ctot
+ --chg_ctot $chg_ctot
+ --chh_ctot $chh_ctot
+ --cpg_ob $cpg_ob
+ --chg_ob $chg_ob
+ --chh_ob $chh_ob
+ --cpg_ctob $cpg_ctob
+ --chg_ctob $chg_ctob
+ --chh_ctob $chh_ctob
+ #elif $merge_non_cpg and $comprehensive:
+ ## two files
+ --non_cpg_context $non_cpg_context
+ --cpg_context $cpg_context
+ #elif $comprehensive:
+ ## three files
+ --cpg_context $cpg_context
+ --chg_context $chg_context
+ --chh_context $chh_context
+ #elif $merge_non_cpg:
+ ## eight files
+ --non_cpg_context_ctot $non_cpg_context_ctot
+ --non_cpg_context_ot $non_cpg_context_ot
+ --non_cpg_context_ob $non_cpg_context_ob
+ --non_cpg_context_ctob $non_cpg_context_ctob
+ --cpg_ot $cpg_ot
+ --cpg_ctot $cpg_ctot
+ --cpg_ob $cpg_ob
+ --cpg_ctob $cpg_ctob
+ #end if
+ ## end compress
+ #end if
+
+ </command>
+ <inputs>
+ <!-- Input Parameters -->
+ <param name="input" type="data" format="sam" label="SAM file from Bismark bisulfid mapper" />
+ <conditional name="singlePaired">
+ <param name="sPaired" type="select" label="Is this library mate-paired?">
+ <option value="single">Single-end</option>
+ <option value="paired">Paired-end</option>
+ </param>
+ <when value="single" />
+ <when value="paired">
+ <param name="no_overlap" type="boolean" truevalue="--no-overlap" falsevalue="" checked="False" label="This option avoids scoring overlapping methylation calls twice, in case of overlapping read one and read two" help="" />
+ </when>
+ </conditional>
+
+ <param name="ignore_bps" type="integer" value="0" label="Ignore the first N bp when processing the methylation call string" />
+ <param name="comprehensive" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Merge all four possible strand-specific methylation info
+into context-dependent output files" help="" />
+ <param name="merge_non_cpg" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Merge all non-CpG contexts into one file" help="This will produce eight strand-specific output files, or two output files in comprehensive mode." />
+ <param name="report" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Short methylation summary output" />
+ <param name="compress" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Compress all result files and output one single file" />
+
+ </inputs>
+ <outputs>
+ <!--
+ OT – original top strand
+ CTOT – complementary to original top strand
+ OB – original bottom strand
+ CTOB – complementary to original bottom strand
+ -->
+ <data format="tabular" name="o_report" label="${tool.name} on ${on_string}: Report file">
+ <filter> ( report is True ) </filter>
+ </data>
+
+ <!-- default output 12 files -->
+ <data format="tabular" name="cpg_ot" label="${tool.name} on ${on_string}: CpG original top strand">
+ <filter> ( compress == False and comprehensive == False and merge_non_CpG == False) </filter>
+ </data>
+ <data format="tabular" name="chg_ot" label="${tool.name} on ${on_string}: CHG original top strand">
+ <filter> ( compress == False and comprehensive == False and merge_non_CpG == False) </filter>
+ </data>
+ <data format="tabular" name="chh_ot" label="${tool.name} on ${on_string}: CHH original top strand">
+ <filter> ( compress == False and comprehensive == False and merge_non_CpG == False) </filter>
+ </data>
+ <data format="tabular" name="cpg_ctot" label="${tool.name} on ${on_string}: CpG complementary to top strand">
+ <filter> ( compress == False and comprehensive == False and merge_non_CpG == False) </filter>
+ </data>
+ <data format="tabular" name="chg_ctot" label="${tool.name} on ${on_string}: CHG complementary to top strand">
+ <filter> ( compress == False and comprehensive == False and merge_non_CpG == False) </filter>
+ </data>
+ <data format="tabular" name="chh_ctot" label="${tool.name} on ${on_string}: CHH complementary to top strand">
+ <filter> ( compress == False and comprehensive == False and merge_non_CpG == False) </filter>
+ </data>
+
+ <data format="tabular" name="cpg_ob" label="${tool.name} on ${on_string}: CpG original bottom strand">
+ <filter> ( compress == False and comprehensive == False and merge_non_CpG == False) </filter>
+ </data>
+ <data format="tabular" name="chg_ob" label="${tool.name} on ${on_string}: CHG original bottom strand">
+ <filter> ( compress == False and comprehensive == False and merge_non_CpG == False) </filter>
+ </data>
+ <data format="tabular" name="chh_ob" label="${tool.name} on ${on_string}: CHH original bottom strand">
+ <filter> ( compress == False and comprehensive == False and merge_non_CpG == False) </filter>
+ </data>
+ <data format="tabular" name="cpg_ctob" label="${tool.name} on ${on_string}: CpG complementary to bottom strand">
+ <filter> ( compress == False and comprehensive == False and merge_non_CpG == False) </filter>
+ </data>
+ <data format="tabular" name="chg_ctob" label="${tool.name} on ${on_string}: CHG complementary to bottom strand">
+ <filter> ( compress == False and comprehensive == False and merge_non_CpG == False) </filter>
+ </data>
+ <data format="tabular" name="chh_ctob" label="${tool.name} on ${on_string}: CHH complementary to bottom strand">
+ <filter> ( compress == False and comprehensive == False and merge_non_CpG == False) </filter>
+ </data>
+
+ <!-- Context-dependent methylation output files (comprehensive option) -->
+ <data format="tabular" name="cpg_context" label="${tool.name} on ${on_string}: CpG context dependent">
+ <filter> ( compress == False and comprehensive) </filter>
+ </data>
+ <data format="tabular" name="chg_context" label="${tool.name} on ${on_string}: CHG context dependent">
+ <filter> ( compress == False and comprehensive and merge_non_CpG == False) </filter>
+ </data>
+ <data format="tabular" name="chh_context" label="${tool.name} on ${on_string}: CHH context dependent">
+ <filter> ( compress == False and comprehensive and merge_non_CpG == False) </filter>
+ </data>
+
+ <data format="tabular" name="non_cpg_context" label="${tool.name} on ${on_string}: Non CpG context dependent">
+ <filter> ( compress == False and comprehensive and merge_non_cpg) </filter>
+ </data>
+
+ <data format="tabular" name="non_cpg_context_ot" label="${tool.name} on ${on_string}: Non CpG context dependent on original top strand">
+ <filter> ( compress == False and comprehensive == False and merge_non_cpg) </filter>
+ </data>
+ <data format="tabular" name="non_cpg_context_ctot" label="${tool.name} on ${on_string}: Non CpG context dependent on complementary to top strand">
+ <filter> ( compress == False and comprehensive == False and merge_non_cpg) </filter>
+ </data>
+ <data format="tabular" name="non_cpg_context_ob" label="${tool.name} on ${on_string}: Non CpG context dependent on bottom top strand">
+ <filter> ( compress == False and comprehensive == False and merge_non_cpg) </filter>
+ </data>
+ <data format="tabular" name="non_cpg_context_ctob" label="${tool.name} on ${on_string}: Non CpG context dependent on complementary to bottom strand">
+ <filter> ( compress == False and comprehensive == False and merge_non_cpg) </filter>
+ </data>
+
+ <data format="gzipped" name="compressed_output" label="${tool.name} on ${on_string}: Result archive.">
+ <filter> ( compress ) </filter>
+ </data>
+ </outputs>
+
+ <tests>
+ </tests>
+
+ <help>
+
+**What it does**
+
+The following is a brief description of all options to control the Bismark_
+methylation extractor. The script reads in a bisulfite read alignment results file
+produced by the Bismark bisulfite mapper and extracts the methylation information
+for individual cytosines. This information is found in the methylation call field
+which can contain the following characters:
+
+
+ - X = for methylated C in CHG context (was protected)
+ - x = for not methylated C CHG (was converted)
+ - H = for methylated C in CHH context (was protected)
+ - h = for not methylated C in CHH context (was converted)
+ - Z = for methylated C in CpG context (was protected)
+ - z = for not methylated C in CpG context (was converted)
+ - . = for any bases not involving cytosines
+
+
+The methylation extractor outputs result files for cytosines in CpG, CHG and CHH
+context (this distinction is actually already made in Bismark itself). As the methylation
+information for every C analysed can produce files which easily have tens or even hundreds of
+millions of lines, file sizes can become very large and more difficult to handle. The C
+methylation info additionally splits cytosine methylation calls up into one of the four possible
+strands a given bisulfite read aligned against:
+
+ - OT = original top strand
+ - CTOT = complementary to original top strand
+
+ - OB = original bottom strand
+ - CTOB = complementary to original bottom strand
+
+Thus, by default twelve individual output files are being generated per input file (unless
+--comprehensive is specified, see below). The output files can be imported into a genome
+viewer, such as SeqMonk, and re-combined into a single data group if desired (in fact
+unless the bisulfite reads were generated preserving directionality it doesn't make any
+sense to look at the data in a strand-specific manner). Strand-specific output files can
+optionally be skipped, in which case only three output files for CpG, CHG or CHH context
+will be generated. For both the strand-specific and comprehensive outputs there is also
+the option to merge both non-CpG contexts (CHG and CHH) into one single non-CpG context.
+
+
+.. _Bismark: http://www.bioinformatics.babraham.ac.uk/projects/bismark/
+
+
+It is developed by Krueger F and Andrews SR. at the Babraham Institute. Krueger F, Andrews SR. (2011) Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformatics, 27, 1571-2.
+
+-------
+
+**Bismark settings**
+
+All of the options have a default value. You can change any of them. If any Bismark function is missing please contact the tool author or your Galaxy admin.
+
+------
+
+**Outputs**
+
+The output files are in the following format (tab delimited)::
+
+
+ Column Description
+ -------- --------------------------------------------------------
+ 1 seq-ID
+ 2 strand
+ 3 chromosome
+ 4 position
+ 5 methylation call
+
+
+ * Methylated cytosines receive a '+' orientation,
+ * Unmethylated cytosines receive a '-' orientation.
+
+------
+
+**OPTIONS**
+
+Input::
+
+ -s/--single-end Input file(s) are Bismark result file(s) generated from single-end
+ read data. Specifying either --single-end or --paired-end is
+ mandatory.
+
+ -p/--paired-end Input file(s) are Bismark result file(s) generated from paired-end
+ read data. Specifying either --paired-end or --single-end is
+ mandatory.
+
+ --no_overlap For paired-end reads it is theoretically possible that read_1 and
+ read_2 overlap. This option avoids scoring overlapping methylation
+ calls twice. Whilst this removes a bias towards more methylation calls
+ towards the center of sequenced fragments it can de facto remove
+ a good proportion of the data.
+
+ --ignore INT Ignore the first INT bp at the 5' end of each read when processing the
+ methylation call string. This can remove e.g. a restriction enzyme site
+ at the start of each read.
+
+Output::
+
+ --comprehensive Specifying this option will merge all four possible strand-specific
+ methylation info into context-dependent output files. The default
+ contexts are:
+ - CpG context
+ - CHG context
+ - CHH context
+
+ --merge_non_CpG This will produce two output files (in --comprehensive mode) or eight
+ strand-specific output files (default) for Cs in
+ - CpG context
+ - non-CpG context
+
+ --report Prints out a short methylation summary as well as the paramaters used to run
+ this script.
+
+
+ </help>
+</tool>
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/564c49962741/
changeset: 564c49962741
user: greg
date: 2013-01-04 15:17:47
summary: Make sure metata is set for repositories in the tool shed that contain only invalid tools.
affected #: 1 file
diff -r 8d7d70348e526c64168392501922aa56f45d0a84 -r 564c49962741608b073e9c3fb87b57f7e8aa454b lib/galaxy/util/shed_util_common.py
--- a/lib/galaxy/util/shed_util_common.py
+++ b/lib/galaxy/util/shed_util_common.py
@@ -1056,6 +1056,7 @@
tool, valid, error_message = load_tool_from_config( app, full_path )
if tool is None:
if not valid:
+ invalid_tool_configs.append( name )
invalid_file_tups.append( ( name, error_message ) )
else:
invalid_files_and_errors_tups = check_tool_input_params( app, files_dir, name, tool, sample_file_copy_paths )
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
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changeset: 8d7d70348e52
user: jgoecks
date: 2013-01-04 04:07:55
summary: Fix bugs that prevented creating a Circster visualization from a dataset.
affected #: 1 file
diff -r d7475647cbb6a1c70218049fadc24ed1651d845a -r 8d7d70348e526c64168392501922aa56f45d0a84 lib/galaxy/webapps/galaxy/controllers/visualization.py
--- a/lib/galaxy/webapps/galaxy/controllers/visualization.py
+++ b/lib/galaxy/webapps/galaxy/controllers/visualization.py
@@ -725,12 +725,25 @@
Display a circster visualization.
"""
+ # Get dataset to add.
+ if dataset_id:
+ dataset = self.get_hda_or_ldda( trans, hda_ldda, dataset_id )
+
# Get/create vis.
if id:
# Display existing viz.
vis = self.get_visualization( trans, id, check_ownership=False, check_accessible=True )
else:
# Create new viz.
+ if not dbkey:
+ # If dbkey not specified, use dataset's dbkey.
+ dbkey = dataset.dbkey
+ if not dbkey or dbkey == '?':
+ # Circster requires a valid dbkey.
+ return trans.show_error_message( "You must set the dataset's dbkey to view it. You can set "
+ "a dataset's dbkey by clicking on the pencil icon and editing "
+ "its attributes.", use_panels=True )
+
vis = self.create_visualization( trans, type="genome", dbkey=dbkey, save=False )
# Get the vis config and work with it from here on out. Working with the
@@ -739,12 +752,10 @@
viz_config = self.get_visualization_config( trans, vis )
# Add dataset if specified.
- if dataset_id:
- dataset = self.get_hda_or_ldda( trans, hda_ldda, dataset_id )
+ if dataset:
viz_config[ 'tracks' ].append( self.get_new_track_config( trans, dataset ) )
# Get genome info.
- dbkey = viz_config[ 'dbkey' ]
chroms_info = self.app.genomes.chroms( trans, dbkey=dbkey )
genome = { 'dbkey': dbkey, 'chroms_info': chroms_info }
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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