galaxy

access_libraries.xml

2011-01-31 16:41:03 -05:00

bed_convert.xml

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biomart_test.xml

Enhance tool parameter sanitization. Sanitization rules can now be defined on a per input parameter basis. Resolves ticket #38 and #142 .

2009-12-07 10:19:41 -05:00

biomart.xml

Enhance tool parameter sanitization. Sanitization rules can now be defined on a per input parameter basis. Resolves ticket #38 and #142 .

2009-12-07 10:19:41 -05:00

cbi_rice_mart.xml

Add the CBI Rice Mart data source tool to the distribution.

2010-06-04 15:49:58 -04:00

data_source.py

Handle non-ascii unicode in data source tools. Add util.is_binary() method that returns true when provided string contains a null byte.

2012-08-28 19:23:39 -04:00

ebi_sra.xml

Change EBI SRA tool to use auto detect for format determination now that they are providing additional formats. Fixes issue seen when sending SFF files.

2013-06-26 11:57:51 -04:00

echo.py

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echo.xml

Change History.copy() back to use datasets rather than active_datasets. Add checks in set_peek() to properly set peek on purged datasets. Fixes sharing a history that contains purged datasets.

2009-01-15 10:49:01 -05:00

eupathdb.xml

pdate EuPathDB datasource configuration file. Contributed by Mark Heiges.

2011-08-22 14:03:57 -04:00

fetch.py

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fly_modencode.xml

Some reworking of data_source tools and the standard data_source.py script. Remove hard-coded special-case handling of UCSC Table Browser and GBrowse datasource tools; functionality remains, but is now a part of the individual tools' XML configuration files. Auto-detect is now available by providing data_type=auto parameters.

2011-04-21 13:12:10 -04:00

flymine_test.xml

Re-add InterMine tools removed in 401ee23dcf2f70d4be0e975bb3e00a43ae1dfdd0.

2014-06-27 14:44:55 -04:00

flymine.xml

Re-add InterMine tools removed in 401ee23dcf2f70d4be0e975bb3e00a43ae1dfdd0.

2014-06-27 14:44:55 -04:00

genbank.py

Deprecated code corrections for supporting Python 2.6. Many of the Python 2.6 eggs are still throwing DeprecationWarning messages, so some things still won't work. Eggs for 2.6 need to be re-scrambled after corrections are made.

2009-08-14 15:37:31 -04:00

genbank.xml

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gramene_mart.xml

Enhance tool parameter sanitization. Sanitization rules can now be defined on a per input parameter basis. Resolves ticket #38 and #142 .

2009-12-07 10:19:41 -05:00

hapmapmart.xml

adding hapmapmart.xml to tools/data_source

2010-11-18 10:30:27 -05:00

hbvar_filter.py

Better approach to altering initial content of output dataset if necessary. The upload tool will now call the data type's groom_output_dataset() method ( a better name than before_setting_metadata since it is not related to metadata ). This will now also run on the cluster.

2009-12-08 11:46:13 -05:00

hbvar.xml

Rewrite HbVar datasource tool.

2012-05-04 15:35:51 -04:00

import.py

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import.xml

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metabolicmine.xml

Re-add InterMine tools removed in 401ee23dcf2f70d4be0e975bb3e00a43ae1dfdd0.

2014-06-27 14:44:55 -04:00

microbial_import_code.py

Fix outdated usage of states in microbial dataset post-job hook.

2013-10-10 12:53:10 -04:00

microbial_import.py

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microbial_import.xml

Fix old wiki links.

2014-04-10 20:00:45 +02:00

modmine.xml

Re-add InterMine tools removed in 401ee23dcf2f70d4be0e975bb3e00a43ae1dfdd0.

2014-06-27 14:44:55 -04:00

mousemine.xml

Re-add InterMine tools removed in 401ee23dcf2f70d4be0e975bb3e00a43ae1dfdd0.

2014-06-27 14:44:55 -04:00

ratmine.xml

Re-add InterMine tools removed in 401ee23dcf2f70d4be0e975bb3e00a43ae1dfdd0.

2014-06-27 14:44:55 -04:00

ucsc_archaea.xml

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ucsc_filter.py

Call set_size() before set_peek() on datasets, changes to set_peek() to not read entire files for some datatypes.

2008-12-02 10:50:54 -05:00

ucsc_proxy.py

Deprecated code corrections for supporting Python 2.6. Many of the Python 2.6 eggs are still throwing DeprecationWarning messages, so some things still won't work. Eggs for 2.6 need to be re-scrambled after corrections are made.

2009-08-14 15:37:31 -04:00

ucsc_proxy.xml

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ucsc_tablebrowser_archaea.xml

Some reworking of data_source tools and the standard data_source.py script. Remove hard-coded special-case handling of UCSC Table Browser and GBrowse datasource tools; functionality remains, but is now a part of the individual tools' XML configuration files. Auto-detect is now available by providing data_type=auto parameters.

2011-04-21 13:12:10 -04:00

ucsc_tablebrowser_test.xml

Some reworking of data_source tools and the standard data_source.py script. Remove hard-coded special-case handling of UCSC Table Browser and GBrowse datasource tools; functionality remains, but is now a part of the individual tools' XML configuration files. Auto-detect is now available by providing data_type=auto parameters.

2011-04-21 13:12:10 -04:00

ucsc_tablebrowser.xml

Backed out changeset 48bbe32beefe which introduced a whole bunch of unintended reversions from a broken hg repository

2011-07-06 09:44:56 +10:00

ucsc_testproxy.xml

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upload.py

Bugfix: Fix shutil.move for converted files in upload.py.

2014-06-10 09:36:28 -05:00

upload.xml

Hiding UUID input for upload tool

2014-08-18 16:37:30 -07:00

worm_modencode.xml

Some reworking of data_source tools and the standard data_source.py script. Remove hard-coded special-case handling of UCSC Table Browser and GBrowse datasource tools; functionality remains, but is now a part of the individual tools' XML configuration files. Auto-detect is now available by providing data_type=auto parameters.

2011-04-21 13:12:10 -04:00

wormbase_test.xml

Some reworking of data_source tools and the standard data_source.py script. Remove hard-coded special-case handling of UCSC Table Browser and GBrowse datasource tools; functionality remains, but is now a part of the individual tools' XML configuration files. Auto-detect is now available by providing data_type=auto parameters.

2011-04-21 13:12:10 -04:00

wormbase.xml

Update WormBase datasource tool to use WormBase 2.

2012-05-02 17:04:33 -04:00

yeastmine.xml

Re-add InterMine tools removed in 401ee23dcf2f70d4be0e975bb3e00a43ae1dfdd0.

2014-06-27 14:44:55 -04:00