mvdbeek 8337f55e21 Fix tests for bed2gff ...

and use single-quotes for path, remove deprecated inpterpreter
attribute.
Fixes https://jenkins.galaxyproject.org/job/docker-main-tools-py3/248/

2019-05-08 17:45:10 +02:00

..

gff

Deprecate size attribute of <param/> and remove it from tools

2018-09-10 11:34:37 +01:00

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

Annotate tools with edam_operations

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

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

Fix all E722 errors and ignore E741

2017-10-24 11:29:09 +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

Remove GFF headers during conversion.

2019-05-08 17:44:52 +02:00

catWrapper.py

Fix all E722 errors and ignore E741

2017-10-24 11:29:09 +01:00

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

Deprecate size attribute of <param/> and remove it from tools

2018-09-10 11:34:37 +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 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

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

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

CreateInterval.xml

Deprecate size attribute of <param/> and remove it from tools

2018-09-10 11:34:37 +01:00

cutWrapper.pl

fix wrong path in error message

2018-05-24 09:38:03 +02:00

cutWrapper.xml

Fix command quoting and remove size from text input for Cut tool.

2015-10-14 10:11:21 -04:00

fileGrep.xml

Deprecate size attribute of <param/> and remove it from tools

2018-09-10 11:34:37 +01:00

fixedValueColumn.pl

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

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

fixedValueColumn.xml

Deprecate size attribute of <param/> and remove it from tools

2018-09-10 11:34:37 +01:00

gff2bed.xml

Annotate tools with edam_operations

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

gff_to_bed_converter.py

Fix all E722 errors and ignore E741

2017-10-24 11:29:09 +01:00

grep.py

Fix errors reported by flake8 3.6.0

2018-10-24 23:22:19 +01:00

grep.xml

Deprecate size attribute of <param/> and remove it from tools

2018-09-10 11:34:37 +01:00

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.pl

Fixed head/tail wrapper for Mac.

2008-04-22 18:11:59 +00:00

headWrapper.xml

Deprecate size attribute of <param/> and remove it from tools

2018-09-10 11:34:37 +01:00

join.py

Change all remaining old-style classes to new style

2018-09-17 12:26:07 +01:00

joiner2.xml

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

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

joiner.xml

update help of joiner two datasets tool

2018-11-13 15:40:51 -08:00

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

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

Fix all E201 and E202 style errors

2017-08-17 11:35:39 +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 all E722 errors and ignore E741

2017-10-24 11:29:09 +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

Lint some tools

2017-01-23 21:11:43 +00:00

random_lines_two_pass.py

Make random_lines1 consistent on py2 and py3 (again)

2018-08-10 22:21:21 +02:00

randomlines.py

Fix all E201 and E202 style errors

2017-08-17 11:35:39 +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

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

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

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

py3: fix secure_hash_message_digest.py

2018-09-05 14:21:59 +02:00

secure_hash_message_digest.xml

Tool help updates.

2011-11-14 13:26:29 -05:00

sff_extract.py

Fix "occured" typo everywhere

2019-01-24 12:09:57 +00:00

sff_extractor.xml

Fix sffextractor tests by requiring python 2.7

2018-09-05 14:22:01 +02:00

sorter.py

Restore check_call for sed

2019-04-09 20:26:27 +01:00

sorter.xml

Detect errors using exit_code for sort tool

2019-04-06 10:00:27 +02:00

tailWrapper.pl

Fixed head/tail wrapper for Mac.

2008-04-22 18:11:59 +00:00

tailWrapper.xml

Deprecate size attribute of <param/> and remove it from tools

2018-09-10 11:34:37 +01:00

trimmer.py

Fix all E201 and E202 style errors

2017-08-17 11:35:39 +01:00

trimmer.xml

Use detect_errors="exit_code" in Trim tool

2017-04-04 18:47:55 +01:00

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

Fix all E201 and E202 style errors

2017-08-17 11:35:39 +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