galaxy

maf

Added functional tests for sniffing and metadata settings on file upload. Fixed a test in the 'Filter Maf Blocks by size' tool. Added new test data. Commited the bug fix I really wanted in Axt.sniff().

2007-10-05 18:02:33 +00:00

aggTrack.pl

added get_flanks plus two additional tools for a David Gilmore: srg2wig and aggTrack. These two are for demo only and should not go to main

2007-02-15 15:11:08 +00:00

aggTrack.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

axt_to_concat_fasta.py

Moving james-wsgi branch to new trunk.

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

axt_to_concat_fasta.xml

Few of cosmetic changes

2007-05-25 20:40:15 +00:00

axt_to_fasta_code.py

Moving james-wsgi branch to new trunk.

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

axt_to_fasta.py

Moving james-wsgi branch to new trunk.

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

axt_to_fasta.xml

Few of cosmetic changes

2007-05-25 20:40:15 +00:00

axt_to_lav_code.py

Moving james-wsgi branch to new trunk.

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

axt_to_lav.py

Moving james-wsgi branch to new trunk.

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

axt_to_lav.xml

Few of cosmetic changes

2007-05-25 20:40:15 +00:00

bed2gff.pl

Moving james-wsgi branch to new trunk.

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

bed2gff.xml

More interface work for converters and feature extractors

2007-07-17 03:13:40 +00:00

BedLike2Text.pl

Moving james-wsgi branch to new trunk.

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

BedLike2Text.xml

Moving james-wsgi branch to new trunk.

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

catWrapper.xml

interface and help edits for text manipulation tools

2007-07-31 21:24:24 +00:00

commWrapper.pl

Moving james-wsgi branch to new trunk.

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

commWrapper.xml

Moving james-wsgi branch to new trunk.

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

compare.xml

Few of cosmetic changes

2007-05-25 20:40:15 +00:00

condense_characters.pl

Moving james-wsgi branch to new trunk.

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

condense_characters.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

convert_characters.pl

TRUNK:More fixes for uniq and STDERR printout

2006-12-20 19:15:54 +00:00

convert_characters.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

countColumns.py

for Trunk: Updated gops text; added links to screencasts; made join and compare smarter so they look up column numbers from datasets

2006-12-18 21:35:43 +00:00

CreateInterval.pl

Moving james-wsgi branch to new trunk.

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

CreateInterval.xml

interface and help edits for text manipulation tools

2007-07-31 21:24:24 +00:00

cutWrapper.pl

TRUNK:More cut changes

2006-12-20 02:44:02 +00:00

cutWrapper.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

fileGrep.xml

Moving james-wsgi branch to new trunk.

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

fixedValueColumn.pl

Moving james-wsgi branch to new trunk.

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

fixedValueColumn.xml

interface and help edits for text manipulation tools

2007-07-31 21:24:24 +00:00

gff2bed.pl

Moving james-wsgi branch to new trunk.

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

gff2bed.xml

specify the ftype for testing data

2007-09-10 16:16:38 +00:00

grep.py

Moving james-wsgi branch to new trunk.

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

grep.xml

More functional test cleanup, eliminated redundant tests, unused test data, and renamed some test data files.

2007-10-04 14:14:15 +00:00

headWrapper.pl

TRUNK:More fixes for uniq and STDERR printout

2006-12-20 19:15:54 +00:00

headWrapper.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

Interval2BedLike.pl

Moving james-wsgi branch to new trunk.

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

Interval2BedLike.xml

Moving james-wsgi branch to new trunk.

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

joiner2.py

for Trunk: Updated gops text; added links to screencasts; made join and compare smarter so they look up column numbers from datasets

2006-12-18 21:35:43 +00:00

joiner2.xml

for Trunk: Updated gops text; added links to screencasts; made join and compare smarter so they look up column numbers from datasets

2006-12-18 21:35:43 +00:00

joiner.xml

More functional test cleanup, eliminated redundant tests, unused test data, and renamed some test data files.

2007-10-04 14:14:15 +00:00

joinWrapper.pl

Moving james-wsgi branch to new trunk.

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

lav_to_bed_code.py

Some items that were not copied over to trunk.

2006-12-21 00:14:11 +00:00

lav_to_bed.py

Some items that were not copied over to trunk.

2006-12-21 00:14:11 +00:00

lav_to_bed.xml

Some items that were not copied over to trunk.

2006-12-21 00:14:11 +00:00

pasteWrapper_code.py

Add the ability to define datatypes in the configuration file.

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

pasteWrapper.pl

Moving james-wsgi branch to new trunk.

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

pasteWrapper.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

random_lines.py

Moving james-wsgi branch to new trunk.

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

random_lines.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

remove_beginning.pl

Moving james-wsgi branch to new trunk.

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

remove_beginning.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

sorter.py

Better error handling for tools that use columnlist tool parameter.

2007-09-19 14:49:02 +00:00

sorter.xml

More functional test cleanup, eliminated redundant tests, unused test data, and renamed some test data files.

2007-10-04 14:14:15 +00:00

srg2wig.pl

added get_flanks plus two additional tools for a David Gilmore: srg2wig and aggTrack. These two are for demo only and should not go to main

2007-02-15 15:11:08 +00:00

srg2wig.xml

added get_flanks plus two additional tools for a David Gilmore: srg2wig and aggTrack. These two are for demo only and should not go to main

2007-02-15 15:11:08 +00:00

tailWrapper.pl

TRUNK:More fixes for uniq and STDERR printout

2006-12-20 19:15:54 +00:00

tailWrapper.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

Text2BedLike.pl

Moving james-wsgi branch to new trunk.

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

Text2BedLike.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

ucsc_gene_bed_to_exon_bed.py

Modified "Gene Bed to Exon/Intron/Codon BED" tool to handle codons falling in the boundary of two consecutive exons.

2007-10-10 15:08:16 +00:00

ucsc_gene_bed_to_exon_bed.xml

Modified "Gene Bed to Exon/Intron/Codon BED" tool to handle codons falling in the boundary of two consecutive exons.

2007-10-10 15:08:16 +00:00

ucsc_gene_bed_to_intron_bed.py

new tool: gene bed to intron bed

2007-02-19 16:22:28 +00:00

ucsc_gene_bed_to_intron_bed.xml

change keyword 'value' to 'file' for test_toolbox

2007-03-13 15:20:46 +00:00

ucsc_gene_table_to_intervals.py

Moving james-wsgi branch to new trunk.

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

ucsc_gene_table_to_intervals.xml

Moving james-wsgi branch to new trunk.

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

uniq.py

Better error handling for tools that use columnlist tool parameter.

2007-09-19 14:49:02 +00:00

uniq.xml

Miscellaneous tool bug fixes.

2007-10-09 18:51:50 +00:00