galaxy

bed_convert.xml

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

biomart_filter.py

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

biomart_test.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

biomart.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

echo.py

Moving james-wsgi branch to new trunk.

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

echo.xml

Moving james-wsgi branch to new trunk.

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

encode_db.xml

More width hints for data source tools.

2007-07-05 19:20:33 +00:00

encode_import_all_latest_datasets.xml

Modified tools using the <select_options> tag approach for dynamic options to use the new <select> tag approach. I modified the microbial import tool to use the older <select_options> approach last week and will modify it to use the new <select> approach next week. A few tools still use the oldest dynamic_options attribute approach, but modifying them to use the new <select> tag will be trivial. I'll do this when I return.

2007-11-21 18:48:37 +00:00

encode_import_chromatin_and_chromosomes.xml

Modified tools using the <select_options> tag approach for dynamic options to use the new <select> tag approach. I modified the microbial import tool to use the older <select_options> approach last week and will modify it to use the new <select> approach next week. A few tools still use the oldest dynamic_options attribute approach, but modifying them to use the new <select> tag will be trivial. I'll do this when I return.

2007-11-21 18:48:37 +00:00

encode_import_code.py

Enhancements to the way dynamic_options work in order to enable tools using dynemic_options to function in workdflow.

2007-10-19 20:42:11 +00:00

encode_import_gencode.xml

Modified tools using the <select_options> tag approach for dynamic options to use the new <select> tag approach. I modified the microbial import tool to use the older <select_options> approach last week and will modify it to use the new <select> approach next week. A few tools still use the oldest dynamic_options attribute approach, but modifying them to use the new <select> tag will be trivial. I'll do this when I return.

2007-11-21 18:48:37 +00:00

encode_import_genes_and_transcripts.xml

Modified tools using the <select_options> tag approach for dynamic options to use the new <select> tag approach. I modified the microbial import tool to use the older <select_options> approach last week and will modify it to use the new <select> approach next week. A few tools still use the oldest dynamic_options attribute approach, but modifying them to use the new <select> tag will be trivial. I'll do this when I return.

2007-11-21 18:48:37 +00:00

encode_import_multi-species_sequence_analysis.xml

Modified tools using the <select_options> tag approach for dynamic options to use the new <select> tag approach. I modified the microbial import tool to use the older <select_options> approach last week and will modify it to use the new <select> approach next week. A few tools still use the oldest dynamic_options attribute approach, but modifying them to use the new <select> tag will be trivial. I'll do this when I return.

2007-11-21 18:48:37 +00:00

encode_import_transcription_regulation.xml

Modified tools using the <select_options> tag approach for dynamic options to use the new <select> tag approach. I modified the microbial import tool to use the older <select_options> approach last week and will modify it to use the new <select> approach next week. A few tools still use the oldest dynamic_options attribute approach, but modifying them to use the new <select> tag will be trivial. I'll do this when I return.

2007-11-21 18:48:37 +00:00

encode_import.py

All of the stuff in /cache has been moved to /depot/data2.

2007-03-13 21:27:39 +00:00

encodedb_filter.py

Changed trans->app.

2007-05-31 20:31:28 +00:00

fetch.py

Moving james-wsgi branch to new trunk.

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

genbank.py

Moving james-wsgi branch to new trunk.

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

genbank.xml

Moving james-wsgi branch to new trunk.

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

hbvar_filter.py

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

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

Moving james-wsgi branch to new trunk.

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

import.xml

Moving james-wsgi branch to new trunk.

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

microbial_import_code.py

Modified tools using the <select_options> tag approach for dynamic options to use the new <select> tag approach. I modified the microbial import tool to use the older <select_options> approach last week and will modify it to use the new <select> approach next week. A few tools still use the oldest dynamic_options attribute approach, but modifying them to use the new <select> tag will be trivial. I'll do this when I return.

2007-11-21 18:48:37 +00:00

microbial_import.py

Moving james-wsgi branch to new trunk.

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

microbial_import.xml

Modified tools using the <select_options> tag approach for dynamic options to use the new <select> tag approach. I modified the microbial import tool to use the older <select_options> approach last week and will modify it to use the new <select> approach next week. A few tools still use the oldest dynamic_options attribute approach, but modifying them to use the new <select> tag will be trivial. I'll do this when I return.

2007-11-21 18:48:37 +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 support for gff3 datatype

2007-09-18 15:43:44 +00:00

ucsc_proxy.py

Moving james-wsgi branch to new trunk.

2006-11-15 16:28:21 +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

More width hints for data source tools.

2007-07-05 19:20:33 +00:00

ucsc_tablebrowser_code.py

Add the ability to define datatypes in the configuration file.

2007-06-01 19:25:19 +00:00

ucsc_tablebrowser_test.xml

More width hints for data source tools.

2007-07-05 19:20:33 +00:00

ucsc_tablebrowser.py

More friendly error message for when ucsc table browser is down.

2007-05-23 14:45:38 +00:00

ucsc_tablebrowser.xml

New layouts and style.

2007-07-05 18:39:36 +00:00

ucsc_testproxy.xml

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

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

upload_code.py

Enhanced upload utility to dynamically load the File Format select list using values from the registry's datatypes_by_extension dictionary.

2007-09-27 14:12:01 +00:00

upload.xml

Cleaned up functional tests, eliminating some redundant tests and unused test data files. Next step, add many missing tests.

2007-10-03 14:17:41 +00:00