galaxy

axt_to_concat_fasta.py

Separate framework and tool environments.

2008-04-11 20:11:21 +00:00

axt_to_concat_fasta.xml

Add descriptions to dynamic options filters.

2008-05-30 16:58:15 +00:00

axt_to_fasta.py

Separate framework and tool environments.

2008-04-11 20:11:21 +00:00

axt_to_fasta.xml

Add descriptions to dynamic options filters.

2008-05-30 16:58:15 +00:00

axt_to_lav_code.py

Removed tool version directiories for some of the tools...the rest soon.

2008-03-03 16:14:06 +00:00

axt_to_lav.py

Misc tool cleanup: eliminated all references to python2.3 / python2.4, imported galaxy eggs in several missed tools. Commented Pattern Matching tool section from tool_conf.xml.sample since tool is not functional. Added job runner info for short read tools in universe_wsgi.ini.sample.

2008-04-25 13:04:55 +00:00

axt_to_lav.xml

Move ucsc and gbrowse data from static to tool-data/shared.

2008-06-03 18:53:26 +00:00

bed2gff.xml

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

bed_to_gff_converter.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

catWrapper.py

Rewrote "convert delimiters to tab" tool in python.

2008-07-02 19:43:08 +00:00

catWrapper.xml

Add functioal test baseline support for the repeat construct, more work needed ( e.g., multiple repeat elements, refresh_on_change when the input to be refreshed is within a repeat construct ). Added functional tests for some tools that use this construct.

2008-11-10 14:22:01 -05:00

changeCase.pl

Enhancements to changeCase tool, user can now select columns to convert.

2008-04-11 15:01:56 +00:00

changeCase.xml

Enhancements to changeCase tool, user can now select columns to convert.

2008-04-11 15:01:56 +00:00

commWrapper.pl

Removed tool version directiories for some of the tools...the rest soon.

2008-03-03 16:14:06 +00:00

commWrapper.xml

Removed tool version directiories for some of the tools...the rest soon.

2008-03-03 16:14:06 +00:00

compare.xml

Bug fixes for compare, Group and filter tools.

2008-12-02 11:41:25 -05:00

condense_characters.pl

Removed tool version directiories for some of the tools...the rest soon.

2008-03-03 16:14:06 +00:00

condense_characters.xml

Removed tool version directiories for some of the tools...the rest soon.

2008-03-03 16:14:06 +00:00

convert_characters.pl

Removed tool version directiories for some of the tools...the rest soon.

2008-03-03 16:14:06 +00:00

convert_characters.py

Rewrote "convert delimiters to tab" tool in python.

2008-07-02 19:43:08 +00:00

convert_characters.xml

Rewrote "convert delimiters to tab" tool in python.

2008-07-02 19:43:08 +00:00

CreateInterval.pl

Removed tool version directiories for some of the tools...the rest soon.

2008-03-03 16:14:06 +00:00

CreateInterval.xml

Removed tool version directiories for some of the tools...the rest soon.

2008-03-03 16:14:06 +00:00

cutWrapper.pl

Fix for cutWrapper, should now properly parse column delimiters.

2008-04-04 12:30:09 +00:00

cutWrapper.xml

Removed tool version directiories for some of the tools...the rest soon.

2008-03-03 16:14:06 +00:00

fileGrep.xml

Removed tool version directiories for some of the tools...the rest soon.

2008-03-03 16:14:06 +00:00

fixedValueColumn.pl

Removed tool version directiories for some of the tools...the rest soon.

2008-03-03 16:14:06 +00:00

fixedValueColumn.xml

Corrected old directions on several tools.

2008-03-13 20:46:43 +00:00

gff2bed.xml

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

gff_to_bed_converter.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

grep.py

Removed tool version directiories for some of the tools...the rest soon.

2008-03-03 16:14:06 +00:00

grep.xml

Corrected old directions on several tools.

2008-03-13 20:46:43 +00:00

headWrapper.pl

Fixed head/tail wrapper for Mac.

2008-04-22 18:11:59 +00:00

headWrapper.xml

Removed tool version directiories for some of the tools...the rest soon.

2008-03-03 16:14:06 +00:00

join.py

Revert 2715.

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

joiner2.xml

Removed tool version directiories for some of the tools...the rest soon.

2008-03-03 16:14:06 +00:00

joiner.xml

More fixes for twill 0.9, the annotation profiler tests do not yet pass, but all else should work now, more tests coming soon.

2008-09-05 16:36:51 -04:00

joinWrapper.pl

long overdue join wrapper fix. Needs to be rewritten in python down the road

2008-06-25 16:27:17 +00:00

joinWrapper.py

Rewrote "Compare two queries" tool in Python.

2008-09-16 14:09:16 -04:00

lav_to_bed_code.py

Cleaned up lav_to_bed a bit, added functional test. Removed old, unused tools from the ~/tools/filter directory.

2008-05-28 19:26:42 +00:00

lav_to_bed.py

Cleaned up lav_to_bed a bit, added functional test. Removed old, unused tools from the ~/tools/filter directory.

2008-05-28 19:26:42 +00:00

lav_to_bed.xml

Cleaned up lav_to_bed a bit, added functional test. Removed old, unused tools from the ~/tools/filter directory.

2008-05-28 19:26:42 +00:00

pasteWrapper.pl

Removed tool version directiories for some of the tools...the rest soon.

2008-03-03 16:14:06 +00:00

pasteWrapper.xml

Add a change_format tag to output datasets in tools. This allows for dynamic switching of output datatype based upon input values.

2008-09-30 16:17:12 -04:00

remove_beginning.pl

Removed tool version directiories for some of the tools...the rest soon.

2008-03-03 16:14:06 +00:00

remove_beginning.xml

More changes plus modification requested by Madelaine Gogol

2008-04-28 16:08:30 +00:00

sorter.py

Use the more recent POSIX standard '-k 1...' option to *nix sort rather

2008-06-11 19:13:19 +00:00

sorter.xml

More changes plus modification requested by Madelaine Gogol

2008-04-28 16:08:30 +00:00

tailWrapper.pl

Fixed head/tail wrapper for Mac.

2008-04-22 18:11:59 +00:00

tailWrapper.xml

Removed tool version directiories for some of the tools...the rest soon.

2008-03-03 16:14:06 +00:00

ucsc_gene_bed_to_exon_bed.py

Misc tool cleanup: eliminated all references to python2.3 / python2.4, imported galaxy eggs in several missed tools. Commented Pattern Matching tool section from tool_conf.xml.sample since tool is not functional. Added job runner info for short read tools in universe_wsgi.ini.sample.

2008-04-25 13:04:55 +00:00

ucsc_gene_bed_to_exon_bed.xml

Removed tool version directiories for some of the tools...the rest soon.

2008-03-03 16:14:06 +00:00

ucsc_gene_bed_to_intron_bed.py

Misc tool cleanup: eliminated all references to python2.3 / python2.4, imported galaxy eggs in several missed tools. Commented Pattern Matching tool section from tool_conf.xml.sample since tool is not functional. Added job runner info for short read tools in universe_wsgi.ini.sample.

2008-04-25 13:04:55 +00:00

ucsc_gene_bed_to_intron_bed.xml

Removed tool version directiories for some of the tools...the rest soon.

2008-03-03 16:14:06 +00:00

ucsc_gene_table_to_intervals.py

Misc tool cleanup: eliminated all references to python2.3 / python2.4, imported galaxy eggs in several missed tools. Commented Pattern Matching tool section from tool_conf.xml.sample since tool is not functional. Added job runner info for short read tools in universe_wsgi.ini.sample.

2008-04-25 13:04:55 +00:00

ucsc_gene_table_to_intervals.xml

Removed tool version directiories for some of the tools...the rest soon.

2008-03-03 16:14:06 +00:00

uniq.py

Removed tool version directiories for some of the tools...the rest soon.

2008-03-03 16:14:06 +00:00

uniq.xml

Fix functional test for count tool and correct spelling errors in template.

2008-09-08 09:16:32 -04:00