Nicola Soranzo d1974a42e5 Use detect_errors="exit_code" in Trim tool ...

Prevent job failures due to spurious messages on stderr from the cluster
scheduler.

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

..

gff

Remove seemingly unused file sort_gtf.py.

2016-12-23 10:21:15 -05:00

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 import order and Python3 compatibility for tools/

2016-09-29 19:26:22 +01:00

axt_to_lav.py

Fix import order and Python3 compatibility for tools/

2016-09-29 19:26:22 +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

Fixes for pycodestyle 2.2.0

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

catWrapper.py

Fixes for pycodestyle 2.2.0

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

catWrapper.xml

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

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

changeCase.pl

…

changeCase.xml

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

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

commWrapper.pl

…

commWrapper.xml

…

compare.xml

…

condense_characters.pl

…

condense_characters.xml

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

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

convert_characters.pl

…

convert_characters.py

Fixes for pycodestyle 2.2.0

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

convert_characters.xml

…

CreateInterval.pl

…

CreateInterval.xml

…

cutWrapper.pl

…

cutWrapper.xml

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

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

fileGrep.xml

…

fixedValueColumn.pl

…

fixedValueColumn.xml

…

gff2bed.xml

Annotate tools with edam_operations

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

gff_to_bed_converter.py

Fixes for pycodestyle 2.2.0

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

grep.py

Fixes for pycodestyle 2.2.0

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

grep.xml

…

gtf2bedgraph.xml

Annotate tools with edam_operations

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

gtf_to_bedgraph_converter.py

Fixes for pycodestyle 2.2.0

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

headWrapper.pl

…

headWrapper.xml

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

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

join.py

Fixes for pycodestyle 2.2.0

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

joiner2.xml

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

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

joiner.xml

…

joinWrapper.pl

…

joinWrapper.py

Fixes for pycodestyle 2.2.0

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

lav_to_bed_code.py

Fix import order and Python3 compatibility for tools/

2016-09-29 19:26:22 +01:00

lav_to_bed.py

Fixes for pycodestyle 2.2.0

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

lav_to_bed.xml

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

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

mergeCols.py

Fixes for pycodestyle 2.2.0

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

mergeCols.xml

…

pasteWrapper.pl

…

pasteWrapper.xml

Lint some tools

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

random_lines_two_pass.py

Fixes for pycodestyle 2.2.0

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

randomlines.py

Fixes for pycodestyle 2.2.0

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

randomlines.xml

…

remove_beginning.pl

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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

Fixes for pycodestyle 2.2.0

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

secure_hash_message_digest.xml

…

sff_extract.py

Fix import order and Python3 compatibility for tools/

2016-09-29 19:26:22 +01:00

sff_extractor.xml

…

sorter.py

Fixes for pycodestyle 2.2.0

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

sorter.xml

…

tailWrapper.pl

…

tailWrapper.xml

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

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

trimmer.py

Use detect_errors="exit_code" in Trim tool

2017-04-04 18:47:55 +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

Fixes for pycodestyle 2.2.0

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

ucsc_gene_bed_to_exon_bed.xml

…

ucsc_gene_bed_to_intron_bed.py

Fixes for pycodestyle 2.2.0

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

ucsc_gene_bed_to_intron_bed.xml

…

ucsc_gene_table_to_intervals.py

Fixes for pycodestyle 2.2.0

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

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

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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

Fixes for pycodestyle 2.2.0

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

wiggle_to_simple.xml

…