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galaxy/tools/filters
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Dannon Baker c3605c7112 Merge remote-tracking branch 'upstream/release_21.09' into dev
2021-10-19 09:59:21 -04:00
..
gff
Check types of modules without type annotations in the their signatures on new modules.
2021-10-11 16:08:26 -04:00
__init__.py
Check types of modules without type annotations in the their signatures on new modules.
2021-10-11 16:08:26 -04:00
axt_to_concat_fasta.py
Fix import order and Python3 compatibility for tools/
2016-09-29 19:26:22 +01:00
axt_to_concat_fasta.xml
Add EDAM topics to unannotated tools
2020-10-30 17:59:45 +01:00
axt_to_fasta.py
Fixes for pycodestyle 2.2.0
2016-11-15 16:56:50 +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 all E201 and E202 style errors
2017-08-17 11:35:39 +01:00
axt_to_lav.py
Drop support for retired Python 3.5
2020-10-07 11:52:13 +01:00
axt_to_lav.xml
Annotate tools with edam_operations
2016-05-19 17:27:04 +02:00
bed2gff.xml
Fix tests for bed2gff
2019-05-08 17:45:10 +02:00
bed_to_bigbed.xml
Deprecate size attribute of <param/> and remove it from tools
2018-09-10 11:34:37 +01:00
bed_to_gff_converter.py
Add python requirement to CONVERTER_bed_to_gff_0
2020-02-09 16:44:20 +01:00
catWrapper.py
Fix all E722 errors and ignore E741
2017-10-24 11:29:09 +01:00
catWrapper.xml
Merge branch 'dev' into edam-tool-panel
2021-01-07 19:54:12 +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
Deprecate size attribute of <param/> and remove it from tools
2018-09-10 11:34:37 +01:00
commWrapper.pl
Fix script shebangs
2019-10-26 20:20:01 +01:00
commWrapper.xml
Add EDAM topics to unannotated tools
2020-10-30 17:59:45 +01:00
compare.xml
Add EDAM topics to unannotated tools
2020-10-30 17:59:45 +01:00
condense_characters.pl
Fix script shebangs
2019-10-26 20:20:01 +01:00
condense_characters.xml
Fix script shebangs
2019-10-26 20:20:01 +01:00
convert_characters.py
Fix errors reported by flake8 3.6.0
2018-10-24 23:22:19 +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
…
CreateInterval.xml
Deprecate size attribute of <param/> and remove it from tools
2018-09-10 11:34:37 +01:00
cutWrapper.pl
Fix script shebangs
2019-10-26 20:20:01 +01:00
cutWrapper.xml
Add EDAM topics to unannotated tools
2020-10-30 17:59:45 +01:00
fileGrep.xml
Add EDAM topics to unannotated tools
2020-10-30 17:59:45 +01:00
fixedValueColumn.pl
Fix script shebangs
2019-10-26 20:20:01 +01:00
fixedValueColumn.xml
Add EDAM topics to unannotated tools
2020-10-30 17:59:45 +01:00
gff2bed.xml
Annotate tools with edam_operations
2016-05-19 17:27:04 +02:00
gff_to_bed_converter.py
Use context manager in CONVERTER_gff_to_bed_0
2020-02-09 16:44:20 +01:00
grep_1.0.1.xml
Restore Grep1 version 1.0.1
2021-07-12 18:20:43 +02:00
grep.py
Fix linting in grep.py script
2021-07-12 18:29:26 +02:00
grep.xml
Fix patterns in Grep1 tool
2021-06-18 13:11:39 +02:00
gtf2bedgraph.xml
Annotate tools with edam_operations
2016-05-19 17:27:04 +02:00
gtf_to_bedgraph_converter.py
Fix all E722 errors and ignore E741
2017-10-24 11:29:09 +01:00
headWrapper.xml
Ignore sigpipe in Show beginning1 tool
2021-06-09 11:28:41 +02:00
join.py
Drop support for retired Python 3.5
2020-10-07 11:52:13 +01:00
joiner2.xml
dos2unix of tools/ directory. Some whitespace and PEP-8 fixes.
2015-05-15 12:40:52 +01:00
joiner.xml
XML fix for joiner.xml.
2020-02-19 13:13:08 -05:00
joinWrapper.py
py3: Fix comp1 tool
2018-09-05 17:43:53 +02:00
lav_to_bed_code.py
Fix all E722 errors and ignore E741
2017-10-24 11:29:09 +01:00
lav_to_bed.py
Drop support for retired Python 3.5
2020-10-07 11:52:13 +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
Drop support for retired Python 3.5
2020-10-07 11:52:13 +01:00
mergeCols.xml
…
pasteWrapper.pl
Fix script shebangs
2019-10-26 20:20:01 +01:00
pasteWrapper.xml
Lint some tools
2017-01-23 21:11:43 +00:00
random_lines_two_pass.py
Make str.join()s more efficient
2020-01-23 11:06:32 +00:00
randomlines.py
Drop support for retired Python 3.5
2020-10-07 11:52:13 +01:00
randomlines.xml
Deprecate size attribute of <param/> and remove it from tools
2018-09-10 11:34:37 +01:00
remove_beginning.pl
Fix script shebangs
2019-10-26 20:20:01 +01:00
remove_beginning.xml
Deprecate size attribute of <param/> and remove it from tools
2018-09-10 11:34:37 +01:00
secure_hash_message_digest.py
Swap all odicts for OrderedDicts, remove galaxy.util.odict
2019-08-18 19:25:44 +01:00
secure_hash_message_digest.xml
Make hash selection mandatory
2021-02-22 11:13:02 +01:00
sff_extract.py
Rev mypy.
2021-04-23 14:49:53 -04:00
sff_extractor.xml
Fix sffextractor tests by requiring python 2.7
2018-09-05 14:22:01 +02:00
sorter.py
Modernize sorter (sort1) tool:
2021-10-01 12:47:14 -04:00
sorter.xml
Modernize sorter (sort1) tool:
2021-10-01 12:47:14 -04:00
tailWrapper.xml
Apply suggestions from code review
2021-05-04 13:47:29 +02:00
trimmer.py
Drop support for retired Python 3.5
2020-10-07 11:52:13 +01:00
trimmer.xml
Fix and simplify built-in trim tool
2020-08-24 17:38:25 +02:00
ucsc_gene_bed_to_exon_bed.py
Fix all E722 errors and ignore E741
2017-10-24 11:29:09 +01:00
ucsc_gene_bed_to_exon_bed.xml
Python3: fix remaining print statements
2017-10-12 18:34:29 +01:00
ucsc_gene_bed_to_intron_bed.py
Fix all E722 errors and ignore E741
2017-10-24 11:29:09 +01:00
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 all E722 errors and ignore E741
2017-10-24 11:29:09 +01:00
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 errors reported by flake8 3.6.0
2018-10-24 23:22:19 +01:00
uniq.xml
Add python to Count1 tool requirements
2019-01-08 11:21:31 +01:00
wc_gnu.xml
Fix wc_gnu test 1; list comprehensions are function objects on py3 and can't access outer local namespace
2018-09-05 14:22:00 +02:00
wig_to_bigwig.xml
Deprecate size attribute of <param/> and remove it from tools
2018-09-10 11:34:37 +01:00
wiggle_to_simple.py
Move wiggle_to_interval out of GALAXY_LIB_TOOLS_UNVERSIONED
2020-02-12 09:47:36 +01:00
wiggle_to_simple.xml
Fix typo, other places that use wrong galaxy-util version
2020-02-19 09:56:02 +01:00