galaxy

gff

Python 3: use "as" instead of comma in except clause

2016-05-17 23:53:16 +01:00

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

Annotate tools with edam_operations

2016-05-19 17:27:04 +02:00

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

Annotate tools with edam_operations

2016-05-19 17:27:04 +02:00

axt_to_lav_code.py

Fix the remaining 2180 flake8 errors in tools/ .

2016-02-10 18:46:03 +00:00

axt_to_lav.py

wrap bare str raises with generic Exception()

2016-05-26 13:14:22 -04:00

axt_to_lav.xml

Annotate tools with edam_operations

2016-05-19 17:27:04 +02:00

bed2gff.xml

Annotate tools with edam_operations

2016-05-19 17:27:04 +02:00

bed_to_bigbed.xml

Annotate tools with edam_operations

2016-05-19 17:27:04 +02:00

bed_to_gff_converter.py

Python3: Use open() instead of file()

2016-05-17 23:53:16 +01:00

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

Fix the remaining 2180 flake8 errors in tools/ .

2016-02-10 18:46:03 +00:00

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

Annotate tools with edam_operations

2016-05-19 17:27:04 +02:00

gff_to_bed_converter.py

Python3: Use open() instead of file()

2016-05-17 23:53:16 +01:00

grep.py

Fix the remaining 2180 flake8 errors in tools/ .

2016-02-10 18:46:03 +00:00

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

Annotate tools with edam_operations

2016-05-19 17:27:04 +02:00

gtf_to_bedgraph_converter.py

Python 3: use "as" instead of comma in except clause

2016-05-17 23:53:16 +01:00

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

Fix more E203 flake8 errors

2016-05-17 23:53:16 +01:00

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

Python 3: use "as" instead of comma in except clause

2016-05-17 23:53:16 +01:00

lav_to_bed_code.py

Fix the remaining 2180 flake8 errors in tools/ .

2016-02-10 18:46:03 +00:00

lav_to_bed.py

Python 3: use "as" instead of comma in except clause

2016-05-17 23:53:16 +01:00

lav_to_bed.xml

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

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

mergeCols.py

Fix more E203 flake8 errors

2016-05-17 23:53:16 +01:00

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

Fix the remaining 2180 flake8 errors in tools/ .

2016-02-10 18:46:03 +00:00

randomlines.py

Fix the remaining 2180 flake8 errors in tools/ .

2016-02-10 18:46:03 +00:00

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

Fix two errors in sff_extract.py detected by flake8 -- either of these code paths would have thrown an exception and failed prior to this.

2016-06-16 16:10:36 -04:00

sff_extractor.xml

Update sff extractor to version 0.2.10.

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

sorter.py

Python 3: use "as" instead of comma in except clause

2016-05-17 23:53:16 +01:00

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

Fix the remaining 2180 flake8 errors in tools/ .

2016-02-10 18:46:03 +00:00

trimmer.xml

Quote some parameters in Trim tool command

2016-04-25 19:48:06 +01:00

ucsc_gene_bed_to_exon_bed.py

Fix the remaining 2180 flake8 errors in tools/ .

2016-02-10 18:46:03 +00:00

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

Fix the remaining 2180 flake8 errors in tools/ .

2016-02-10 18:46:03 +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

Fix the remaining 2180 flake8 errors in tools/ .

2016-02-10 18:46:03 +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

Fix the remaining 2180 flake8 errors in tools/ .

2016-02-10 18:46:03 +00:00

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

Python 3: use "as" instead of comma in except clause

2016-05-17 23:53:16 +01:00

wiggle_to_simple.xml

Make tool version explicit (Job runner would assume 1.0.0)

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