Nicola Soranzo 857948c033 Update requirements of sort1 tool ...

Otherwise the conda environment for it fails to solve with the following
error:

```
Solving environment: failed

LibMambaUnsatisfiableError: Encountered problems while solving:
  - package grep-2.14-h470a237_2 is excluded by strict repo priority
```

This is due to the fact that grep 2.14 is only available on the bioconda
channel, while newer versions are on conda-forge, which has a higher
priority.

Reported by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/20876/files#r2336209775 .

2025-09-11 01:44:30 +01:00

..

gff

Fix skipping of empty lines in gtf_filter_by_attribute_values_list tool

2025-09-10 03:45:54 +01:00

__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

Enable flake8-comprehensions ruff rules

2024-03-09 19:11:20 +00:00

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

Drop unnecessary global statements

2025-04-05 09:55:42 +02:00

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

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

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

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

Fix type annotations

2025-02-09 01:54:55 +00:00

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

Fix incorrect test for Grep1 tool

2025-09-10 03:22:09 +01:00

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

Drop unnecessary global statements

2025-04-05 09:55:42 +02:00

sff_extractor.xml

Fix `sff_extract` tool, drop type annotation

2022-03-16 15:24:55 +01:00

sorter.xml

Update requirements of sort1 tool

2025-09-11 01:44:30 +01:00

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

hide wig_to_bigWig tool

2024-02-15 11:38:05 +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