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08fb160b38fbcd9bcdfd776bb75ae5c92ca002d1
galaxy/tools/filters
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Martin Cech a27e86786a wrap bare str raises with generic Exception() 
as Pyton 2.7 does not support bare str
2016-05-26 16:45:31 -04:00
..
gff
Fix the remaining 2180 flake8 errors in tools/ .
2016-02-10 18:46:03 +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
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 16:45:31 -04:00
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
Fix the remaining 2180 flake8 errors in tools/ .
2016-02-10 18:46:03 +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
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
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
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
Make tool version explicit (Job runner would assume 1.0.0)
2015-03-09 15:21:48 +00:00
gtf_to_bedgraph_converter.py
Fix the remaining 2180 flake8 errors in tools/ .
2016-02-10 18:46:03 +00:00
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 the remaining 2180 flake8 errors in tools/ .
2016-02-10 18:46:03 +00:00
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
Fix the remaining 2180 flake8 errors in tools/ .
2016-02-10 18:46:03 +00:00
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
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
Fix the remaining 2180 flake8 errors in tools/ .
2016-02-10 18:46:03 +00:00
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 the remaining 2180 flake8 errors in tools/ .
2016-02-10 18:46:03 +00:00
sff_extractor.xml
Update sff extractor to version 0.2.10.
2011-10-20 16:38:14 -04:00
sorter.py
Fix the remaining 2180 flake8 errors in tools/ .
2016-02-10 18:46:03 +00:00
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
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
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
Refactor galaxy.tools.exception_handling...
2016-01-21 14:31:41 +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