galaxy

gff

Switch to_json_string/from_json_string in galaxy/tools.

2014-09-09 10:06:35 -04:00

axt_to_concat_fasta.py

Separate framework and tool environments.

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

axt_to_concat_fasta.xml

typo fixes for tools in folders A-M

2009-09-27 23:11:43 -04:00

axt_to_fasta.py

Separate framework and tool environments.

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

axt_to_fasta.xml

typo fixes for tools in folders A-M

2009-09-27 23:11:43 -04:00

axt_to_lav_code.py

Fix most of the db flushes to be compatibel with sqlalchemy 05. Add the _monkeypatch_query_method() back into assignmapper due to a single object.get() method in the MetadataCollection class since Metadata has no current hook into mapping.context ( the sqlalchemy session ). There a 4 flushes in metadata,py and 20 flushes in model.__init__.py that still use the _monkeypatch_session_method in assignmapper due to the same issue, but all other flushes are fixed.

2009-11-11 15:59:41 -05:00

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

Fix some bad paths (to /depot) in the axt_to_lav tool, which isn't actually used but I found it anyway, and the test data file for lav_to_bed.

2010-09-27 21:46:04 -04:00

bed2gff.xml

Replaced "query" with "dataset" in a number of tool definition XML files.

2013-01-14 16:13:54 -08:00

bed_to_bigbed.xml

Fix bed_to_bigBed test

2011-02-24 15:23:21 -05:00

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

Modified sort tool to fix backwards compatibility. Reverted catWrapper tool back to old version before recent changes (for backwards compatibility).

2009-09-24 13:54:12 -04:00

catWrapper.xml

First pass standardizing to 'dataaset' from 'query'.

2011-01-27 13:46:20 -05:00

changeCase.pl

Removed offending code from last checkin - sorry for the foul-up

2012-08-07 13:35:39 -04:00

changeCase.xml

Removed offending code from last checkin - sorry for the foul-up

2012-08-07 13:35:39 -04:00

commWrapper.pl

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

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

commWrapper.xml

First pass standardizing to 'dataaset' from 'query'.

2011-01-27 13:46:20 -05:00

compare.xml

First pass standardizing to 'dataaset' from 'query'.

2011-01-27 13:46:20 -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

Replaced "query" with "dataset" in a number of tool definition XML files.

2013-01-14 16:13:54 -08:00

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

Make stripping and condensing optional.

2014-10-28 16:57:49 +01:00

convert_characters.xml

Make stripping and condensing optional.

2014-10-28 16:57:49 +01:00

CreateInterval.pl

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

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

CreateInterval.xml

First pass standardizing to 'dataaset' from 'query'.

2011-01-27 13:46:20 -05:00

cutWrapper.pl

Add support for column ranges to Cut tool. Thank to John Chilton for this code.

2013-03-21 12:19:14 -04:00

cutWrapper.xml

Add support for column ranges to Cut tool. Thank to John Chilton for this code.

2013-03-21 12:19:14 -04:00

fileGrep.xml

Typos

2011-02-25 13:35:27 -05:00

fixedValueColumn.pl

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

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

fixedValueColumn.xml

First pass standardizing to 'dataaset' from 'query'.

2011-01-27 13:46:20 -05:00

gff2bed.xml

Replaced "query" with "dataset" in a number of tool definition XML files.

2013-01-14 16:13:54 -08:00

gff_to_bed_converter.py

Move gff_util.py from galaxy/tools/util to galaxy/datatypes/util because gff_utils are now used by the framework as well as tools.

2010-11-14 11:29:44 -05:00

grep.py

grep/select tool: fixed tab-delimiter matching for GNU version of grep

2013-04-02 15:18:22 -04:00

grep.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

gtf2bedgraph.xml

Add empty_field validator to gtf2bedgraph.xml

2014-06-27 22:21:37 +00:00

gtf_to_bedgraph_converter.py

Add track definition to bedgraph files generated by gtf2bedgraph.

2010-05-13 15:35:41 -04:00

headWrapper.pl

Fixed head/tail wrapper for Mac.

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

headWrapper.xml

First pass standardizing to 'dataaset' from 'query'.

2011-01-27 13:46:20 -05:00

join.py

Remove dependency on simplejson; convert everything over to using the json module in the python standard library.

2014-01-10 07:29:05 -05:00

joiner2.xml

First pass standardizing to 'dataaset' from 'query'.

2011-01-27 13:46:20 -05:00

joiner.xml

Remove dependency on simplejson; convert everything over to using the json module in the python standard library.

2014-01-10 07:29:05 -05:00

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

Use a literal tab character instead of the bash $'\t' syntax in the join and sort tools. This makes them compatible with bourne sh and dash.

2010-09-27 21:22:49 -04:00

lav_to_bed_code.py

Fix most of the db flushes to be compatibel with sqlalchemy 05. Add the _monkeypatch_query_method() back into assignmapper due to a single object.get() method in the MetadataCollection class since Metadata has no current hook into mapping.context ( the sqlalchemy session ). There a 4 flushes in metadata,py and 20 flushes in model.__init__.py that still use the _monkeypatch_session_method in assignmapper due to the same issue, but all other flushes are fixed.

2009-11-11 15:59:41 -05:00

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

Fix locations of cached data for tests

2010-02-25 12:27:07 -05:00

mergeCols.py

clean up

2009-02-10 10:43:21 -05:00

mergeCols.xml

First pass standardizing to 'dataaset' from 'query'.

2011-01-27 13:46:20 -05:00

pasteWrapper.pl

added space to paste tool, removed old solexa tool, fixes fastq stat test

2009-10-08 09:01:19 -04:00

pasteWrapper.xml

First pass standardizing to 'dataaset' from 'query'.

2011-01-27 13:46:20 -05:00

random_lines_two_pass.py

Some random lines tool tweaks.

2011-09-25 13:27:14 -04:00

randomlines.py

New tool to select N random lines from a file/dataset. Closes #238

2010-04-01 22:48:57 -04:00

randomlines.xml

Some random lines tool tweaks.

2011-09-25 13:27:14 -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

typo fixes for tools in folders A-M

2009-09-27 23:11:43 -04:00

secure_hash_message_digest.py

Add tool for calculating Secure Hashes / Message Digests of a dataset using the user selected algorithms.

2011-09-09 12:01:43 -04:00

secure_hash_message_digest.xml

Tool help updates.

2011-11-14 13:26:29 -05:00

sff_extract.py

Update sff extractor to version 0.2.10.

2011-10-20 16:38:14 -04:00

sff_extractor.xml

Update sff extractor to version 0.2.10.

2011-10-20 16:38:14 -04:00

sorter.py

sort: update log to browser

2013-03-08 12:10:19 -05:00

sorter.xml

Fix sorting of numbers in scientific notation.

2013-05-28 15:48:45 +02:00

tailWrapper.pl

Fixed head/tail wrapper for Mac.

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

tailWrapper.xml

First pass standardizing to 'dataaset' from 'query'.

2011-01-27 13:46:20 -05:00

trimmer.py

Adjusted trimming tool to include negative positions. Modified help and test.

2013-01-30 10:38:58 +01:00

trimmer.xml

Adjusted trimming tool to include negative positions. Modified help and test.

2013-01-30 10:38:58 +01:00

ucsc_gene_bed_to_exon_bed.py

fixed calculation of codon starts

2011-03-24 15:03:12 -04:00

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

uniq.xml edited online with Bitbucket

2014-10-23 16:42:15 +00:00

wc_gnu.xml

Tool help updates.

2011-11-14 13:26:29 -05:00

wig_to_bigwig.xml

Enable BedGraph to be used as input to wig-to-bigwig tool.

2013-01-24 17:06:51 -05:00

wiggle_to_simple.py

Adding back 'wiggle to interval' converter

2009-12-01 11:49:07 -05:00

wiggle_to_simple.xml

Backed out changeset 9532e80796ec

2013-11-07 13:02:22 -05:00