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galaxy/tools/filters
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John Davis f91693dc6e Merge pull request #16783 from SergeyYakubov/get-rid-of-filename-property 
Replace file_name property with get_file_name function
2023-11-08 17:19:40 -05:00
..
gff
Apply black to tools as well
2022-02-03 09:12:13 -05:00
__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
Apply black to tools as well
2022-02-03 09:12:13 -05:00
axt_to_concat_fasta.xml
Add EDAM topics to unannotated tools
2020-10-30 17:59:45 +01:00
axt_to_fasta.py
Apply black to tools as well
2022-02-03 09:12:13 -05:00
axt_to_fasta.xml
Annotate tools with edam_operations
2016-05-19 17:27:04 +02:00
axt_to_lav_code.py
Apply black to tools as well
2022-02-03 09:12:13 -05:00
axt_to_lav.py
Apply black to tools as well
2022-02-03 09:12:13 -05:00
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
Apply black to tools as well
2022-02-03 09:12:13 -05:00
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
Add missing requirements to perl tools
2023-09-29 15:22:09 +02:00
commWrapper.pl
Fix script shebangs
2019-10-26 20:20:01 +01:00
commWrapper.xml
Add missing requirements to perl tools
2023-09-29 15:22:09 +02:00
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
Add missing requirements to perl tools
2023-09-29 15:22:09 +02:00
convert_characters.py
FileInput no longer accept 'U' in the file mode
2023-09-16 18:33:07 +02:00
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
Add missing requirements to perl tools
2023-09-29 15:22:09 +02:00
cutWrapper.pl
Fix script shebangs
2019-10-26 20:20:01 +01:00
cutWrapper.xml
Add missing requirements to perl tools
2023-09-29 15:22:09 +02:00
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
Use format_source="input" instead of format="input"
2023-01-13 10:58:57 +01:00
gff2bed.xml
Annotate tools with edam_operations
2016-05-19 17:27:04 +02:00
gff_to_bed_converter.py
Apply black to tools as well
2022-02-03 09:12:13 -05:00
grep_1.0.1.xml
Restore Grep1 version 1.0.1
2021-07-12 18:20:43 +02:00
grep.py
Apply black to tools as well
2022-02-03 09:12:13 -05:00
grep.xml
bump version
2022-08-18 17:49:06 +02:00
gtf2bedgraph.xml
Annotate tools with edam_operations
2016-05-19 17:27:04 +02:00
gtf_to_bedgraph_converter.py
Apply black to tools as well
2022-02-03 09:12:13 -05:00
headWrapper.xml
Bump wrapper version and declare updates to it WF-safe
2022-10-31 23:03:32 +01:00
join.py
Apply black to tools as well
2022-02-03 09:12:13 -05:00
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
Apply black to tools as well
2022-02-03 09:12:13 -05:00
lav_to_bed_code.py
Replace file_name property with get_file_name function
2023-11-08 17:17:14 -05:00
lav_to_bed.py
Apply black to tools as well
2022-02-03 09:12:13 -05:00
lav_to_bed.xml
dos2unix of tools/ directory. Some whitespace and PEP-8 fixes.
2015-05-15 12:40:52 +01:00
mergeCols.py
Apply black to tools as well
2022-02-03 09:12:13 -05:00
mergeCols.xml
First pass standardizing to 'dataaset' from 'query'.
2011-01-27 13:46:20 -05:00
pasteWrapper.pl
Fix script shebangs
2019-10-26 20:20:01 +01:00
pasteWrapper.xml
Add missing requirements to perl tools
2023-09-29 15:22:09 +02:00
random_lines_two_pass.py
Apply black to tools as well
2022-02-03 09:12:13 -05:00
randomlines.py
Apply black to tools as well
2022-02-03 09:12:13 -05:00
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
Add missing requirements to perl tools
2023-09-29 15:22:09 +02:00
secure_hash_message_digest.py
Apply black to tools as well
2022-02-03 09:12:13 -05:00
secure_hash_message_digest.xml
Make hash selection mandatory
2021-02-22 11:13:02 +01:00
sff_extract.py
Fix new B018 errors raised by ruff 0.0.260
2023-04-13 16:53:01 +01:00
sff_extractor.xml
Fix `sff_extract` tool, drop type annotation
2022-03-16 15:24:55 +01:00
sorter.py
Fix missing grep input in sort1 tool
2023-10-24 15:14:50 +02:00
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
Apply black to tools as well
2022-02-03 09:12:13 -05:00
trimmer.xml
Fix and simplify built-in trim tool
2020-08-24 17:38:25 +02:00
ucsc_gene_bed_to_exon_bed.py
Apply black to tools as well
2022-02-03 09:12:13 -05:00
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
Apply black to tools as well
2022-02-03 09:12:13 -05:00
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
Apply black to tools as well
2022-02-03 09:12:13 -05:00
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
Apply black to tools as well
2022-02-03 09:12:13 -05:00
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
Apply black to tools as well
2022-02-03 09:12:13 -05:00
wiggle_to_simple.xml
Fix typo, other places that use wrong galaxy-util version
2020-02-19 09:56:02 +01:00