galaxy

gff

Remove remaining references to galaxy.eggs . flake8 some files in tools/ .

2015-10-26 19:29:13 +00:00

axt_to_concat_fasta.py

Remove remaining references to galaxy.eggs . flake8 some files in tools/ .

2015-10-26 19:29:13 +00:00

axt_to_concat_fasta.xml

Make tool version explicit (Job runner would assume 1.0.0)

2015-03-09 15:21:48 +00:00

axt_to_fasta.py

Remove remaining references to galaxy.eggs . flake8 some files in tools/ .

2015-10-26 19:29:13 +00:00

axt_to_fasta.xml

Make tool version explicit (Job runner would assume 1.0.0)

2015-03-09 15:21:48 +00:00

axt_to_lav_code.py

dos2unix of tools/ directory. Some whitespace and PEP-8 fixes.

2015-05-15 12:40:52 +01:00

axt_to_lav.py

Remove remaining references to galaxy.eggs . flake8 some files in tools/ .

2015-10-26 19:29:13 +00:00

axt_to_lav.xml

dos2unix of tools/ directory. Some whitespace and PEP-8 fixes.

2015-05-15 12:40:52 +01:00

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

Remove remaining references to galaxy.eggs . flake8 some files in tools/ .

2015-10-26 19:29:13 +00:00

catWrapper.xml

dos2unix of tools/ directory. Some whitespace and PEP-8 fixes.

2015-05-15 12:40:52 +01:00

changeCase.pl

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

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

changeCase.xml

dos2unix of tools/ directory. Some whitespace and PEP-8 fixes.

2015-05-15 12:40:52 +01:00

commWrapper.pl

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

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

commWrapper.xml

Make tool version explicit (Job runner would assume 1.0.0)

2015-03-09 15:21:48 +00:00

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

dos2unix of tools/ directory. Some whitespace and PEP-8 fixes.

2015-05-15 12:40:52 +01:00

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 tool version explicit (Job runner would assume 1.0.0)

2015-03-09 15:21:48 +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

Make tool version explicit (Job runner would assume 1.0.0)

2015-03-09 15:21:48 +00:00

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

Fix command quoting and remove size from text input for Cut tool.

2015-10-14 10:11:21 -04:00

fileGrep.xml

Make tool version explicit (Job runner would assume 1.0.0)

2015-03-09 15:21:48 +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

Make tool version explicit (Job runner would assume 1.0.0)

2015-03-09 15:21:48 +00:00

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

Remove remaining references to galaxy.eggs . flake8 some files in tools/ .

2015-10-26 19:29:13 +00:00

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

Make tool version explicit (Job runner would assume 1.0.0)

2015-03-09 15:21:48 +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

dos2unix of tools/ directory. Some whitespace and PEP-8 fixes.

2015-05-15 12:40:52 +01:00

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

dos2unix of tools/ directory. Some whitespace and PEP-8 fixes.

2015-05-15 12:40:52 +01:00

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

dos2unix of tools/ directory. Some whitespace and PEP-8 fixes.

2015-05-15 12:40:52 +01:00

lav_to_bed.py

Remove remaining references to galaxy.eggs . flake8 some files in tools/ .

2015-10-26 19:29:13 +00:00

lav_to_bed.xml

dos2unix of tools/ directory. Some whitespace and PEP-8 fixes.

2015-05-15 12:40:52 +01:00

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

dos2unix of tools/ directory. Some whitespace and PEP-8 fixes.

2015-05-15 12:40:52 +01:00

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

dos2unix of tools/ directory. Some whitespace and PEP-8 fixes.

2015-05-15 12:40:52 +01:00

secure_hash_message_digest.py

Remove remaining references to galaxy.eggs . flake8 some files in tools/ .

2015-10-26 19:29:13 +00:00

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

dos2unix of tools/ directory. Some whitespace and PEP-8 fixes.

2015-05-15 12:40:52 +01:00

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

Make tool version explicit (Job runner would assume 1.0.0)

2015-03-09 15:21:48 +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

Make tool version explicit (Job runner would assume 1.0.0)

2015-03-09 15:21:48 +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

dos2unix of tools/ directory. Some whitespace and PEP-8 fixes.

2015-05-15 12:40:52 +01:00

uniq.py

Add sorting option to Count1 (tools/filters/uniq.xml)

2015-03-13 16:43:02 -04:00

uniq.xml

Add sorting option to Count1 (tools/filters/uniq.xml)

2015-03-13 16:43:02 -04:00

wc_gnu.xml

Make tool version explicit (Job runner would assume 1.0.0)

2015-03-09 15:21:48 +00:00

wig_to_bigwig.xml

wig_to_bigwig: Add error message for wrongly formatted data

2015-11-05 19:15:51 +01:00

wiggle_to_simple.py

Remove remaining references to galaxy.eggs . flake8 some files in tools/ .

2015-10-26 19:29:13 +00:00

wiggle_to_simple.xml

Make tool version explicit (Job runner would assume 1.0.0)

2015-03-09 15:21:48 +00:00