Daniel Blankenberg b9e242e4eb Add a new metadata type of Metadata Files. ...

These are now used to store the list of chromosomes for species as well as the index for MAF files.

MAF tools have been enhanced to make use of index files when available.

TODO: When datasets are purged from disk, these files should also be purged.

2008-10-22 13:49:22 -04:00

..

bed_convert.xml

Moving james-wsgi branch to new trunk.

2006-11-15 16:28:21 +00:00

biomart_test.xml

Use only 1 underlying executable ( data_source.py ) for data source tools. A new tag set is added to the data source tool configs to handle tranlsation of request param names sent by remote apps ( something like <param_trans galaxy_name="dbkey" remote_name="GENOME" missing="?" /> ).

2008-10-07 15:21:46 -04:00

biomart.xml

Use only 1 underlying executable ( data_source.py ) for data source tools. A new tag set is added to the data source tool configs to handle tranlsation of request param names sent by remote apps ( something like <param_trans galaxy_name="dbkey" remote_name="GENOME" missing="?" /> ).

2008-10-07 15:21:46 -04:00

data_source.py

Add a new metadata type of Metadata Files.

2008-10-22 13:49:22 -04:00

echo.py

Eliminated all Python2.4 references, added necessary assert statements to ensure minimum version of Python 2.4.

2008-03-28 15:24:50 +00:00

echo.xml

Moving james-wsgi branch to new trunk.

2006-11-15 16:28:21 +00:00

encode_db.xml

Change database schema to separate Dataset and HistoryDatasetAssociation. This is a significant change, be sure to follow the migration notes exactly.

2008-07-09 17:41:08 +00:00

encode_import_all_latest_datasets.xml

Rewrite of dynamic options for select lists. There are no more 'special cases' and new filters are much easier to incorporate, as neeeded.

2008-05-29 17:38:46 +00:00

encode_import_chromatin_and_chromosomes.xml

Rewrite of dynamic options for select lists. There are no more 'special cases' and new filters are much easier to incorporate, as neeeded.

2008-05-29 17:38:46 +00:00

encode_import_code.py

Change database schema to separate Dataset and HistoryDatasetAssociation. This is a significant change, be sure to follow the migration notes exactly.

2008-07-09 17:41:08 +00:00

encode_import_gencode.xml

Rewrite of dynamic options for select lists. There are no more 'special cases' and new filters are much easier to incorporate, as neeeded.

2008-05-29 17:38:46 +00:00

encode_import_genes_and_transcripts.xml

Rewrite of dynamic options for select lists. There are no more 'special cases' and new filters are much easier to incorporate, as neeeded.

2008-05-29 17:38:46 +00:00

encode_import_multi-species_sequence_analysis.xml

Rewrite of dynamic options for select lists. There are no more 'special cases' and new filters are much easier to incorporate, as neeeded.

2008-05-29 17:38:46 +00:00

encode_import_transcription_regulation.xml

Rewrite of dynamic options for select lists. There are no more 'special cases' and new filters are much easier to incorporate, as neeeded.

2008-05-29 17:38:46 +00:00

encode_import.py

Eliminated all Python2.4 references, added necessary assert statements to ensure minimum version of Python 2.4.

2008-03-28 15:24:50 +00:00

epigraph_import.xml

Use only 1 underlying executable ( data_source.py ) for data source tools. A new tag set is added to the data source tool configs to handle tranlsation of request param names sent by remote apps ( something like <param_trans galaxy_name="dbkey" remote_name="GENOME" missing="?" /> ).

2008-10-07 15:21:46 -04:00

fetch.py

Eliminated all Python2.4 references, added necessary assert statements to ensure minimum version of Python 2.4.

2008-03-28 15:24:50 +00:00

flymine.xml

Fixes for data_source tools, data.name, data.info, data.dbkey, and data.extension should now be properly set. Eliminated fastq data type from datatypes_conf.xml.sample since it is not a supported data type.

2008-10-17 10:46:29 -04:00

gbrowse_datasource.py

Revert 2715.

2008-06-04 13:02:15 +00:00

gbrowse_elegans.xml

Change C Elegans server URL to wormbase using GBrowse version 1.69.

2008-07-24 13:59:23 -04:00

gbrowse_filter_code.py

Fix for sniffing datatypes, sniff order is now retrieved from app.datatypes_registry rather than the default sniff_order list in the Registry class.

2008-05-28 21:20:15 +00:00

genbank.py

Eliminated all Python2.4 references, added necessary assert statements to ensure minimum version of Python 2.4.

2008-03-28 15:24:50 +00:00

genbank.xml

Moving james-wsgi branch to new trunk.

2006-11-15 16:28:21 +00:00

hbvar_filter.py

Revert 2715.

2008-06-04 13:02:15 +00:00

hbvar.xml

Changing all tools that use 'text' as file extension to now use 'txt'. We are eliminating the use of 'text' as a file extension within Galaxy and will now use only 'txt' for Text data types.

2007-09-27 12:24:27 +00:00

import.py

Eliminated all Python2.4 references, added necessary assert statements to ensure minimum version of Python 2.4.

2008-03-28 15:24:50 +00:00

import.xml

Moving james-wsgi branch to new trunk.

2006-11-15 16:28:21 +00:00

microbial_import_code.py

Change database schema to separate Dataset and HistoryDatasetAssociation. This is a significant change, be sure to follow the migration notes exactly.

2008-07-09 17:41:08 +00:00

microbial_import.py

Eliminated all Python2.4 references, added necessary assert statements to ensure minimum version of Python 2.4.

2008-03-28 15:24:50 +00:00

microbial_import.xml

Rewrite of dynamic options for select lists. There are no more 'special cases' and new filters are much easier to incorporate, as neeeded.

2008-05-29 17:38:46 +00:00

ucsc_archaea.xml

There has to be at least one tool named 'ucsc_proxy' for the proxies to work. They all use the same code with different urls, but they have to submit back to the tool_runner at the end. This closes ticket 121.

2007-05-30 15:47:59 +00:00

ucsc_filter.py

Added file_size column to dataset table, requires db schema alteration:

2008-01-08 16:19:25 +00:00

ucsc_proxy.py

Eliminated all Python2.4 references, added necessary assert statements to ensure minimum version of Python 2.4.

2008-03-28 15:24:50 +00:00

ucsc_proxy.xml

Update UCSC direct connection to use main ucsc site. Add direct test

2007-03-21 19:52:01 +00:00

ucsc_tablebrowser_archaea.xml

Fixes for data_source tools, data.name, data.info, data.dbkey, and data.extension should now be properly set. Eliminated fastq data type from datatypes_conf.xml.sample since it is not a supported data type.

2008-10-17 10:46:29 -04:00

ucsc_tablebrowser_test.xml

Fixes for data_source tools, data.name, data.info, data.dbkey, and data.extension should now be properly set. Eliminated fastq data type from datatypes_conf.xml.sample since it is not a supported data type.

2008-10-17 10:46:29 -04:00

ucsc_tablebrowser.xml

Fixes for data_source tools, data.name, data.info, data.dbkey, and data.extension should now be properly set. Eliminated fastq data type from datatypes_conf.xml.sample since it is not a supported data type.

2008-10-17 10:46:29 -04:00

ucsc_testproxy.xml

Update UCSC direct connection to use main ucsc site. Add direct test

2007-03-21 19:52:01 +00:00

upload.xml

Cleanup for fastqsolexa data type converters. We are currently supporting only the Solexa variant and will add support for other variants when the formats stabilize.

2008-06-09 20:15:04 +00:00