Nicola Soranzo 2cd95c48f6 Fix import order everywhere ...

- Add flake8-import-order to flake8 Pipfile and remove py27-lint-imports
  and py27-lint-imports-include-list tox envs
- Fix most E201 and E202 errors reported by flake8-import-order v0.15,
  but pin flake8-import-order to v0.14.3 until
  https://github.com/PyCQA/flake8-import-order/issues/123
  is fixed

This let us drop 2 jobs on Travis per each job.

2017-11-14 19:42:39 +00:00

..

gff

Fix import order everywhere

2017-11-14 19:42:39 +00:00

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

Annotate tools with edam_operations

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

bed_to_bigbed.xml

Annotate tools with edam_operations

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

bed_to_gff_converter.py

Fix all E722 errors and ignore E741

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

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

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 all E722 errors and ignore E741

2017-10-24 11:29:09 +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

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

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 all E201 and E202 style errors

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

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

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

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

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

join.py

Fix all E722 errors and ignore E741

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

joiner2.xml

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

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

joiner.xml

Fix joiner tool to inherit datatype, restoring previous behavior.

2017-10-03 14:49:42 -04:00

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 all E201 and E202 style errors

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

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

Fix all E201 and E202 style errors

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

randomlines.py

Fix all E201 and E202 style errors

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

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

Fix all E201 and E202 style errors

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

secure_hash_message_digest.xml

Tool help updates.

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

sff_extract.py

Fix all E722 errors and ignore E741

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

sff_extractor.xml

Update sff extractor to version 0.2.10.

2011-10-20 16:38:14 -04:00

sorter.py

Fix all E201 and E202 style errors

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

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 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

Fixes for pycodestyle 2.2.0

2016-11-15 16:56:50 +00:00

uniq.xml

Add sorting option to Count1 (tools/filters/uniq.xml)

2015-03-13 16:43:02 -04:00

wc_gnu.xml

Single quote file names

2017-06-26 13:56:56 +02:00

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

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