John Chilton 60e0b3af62 Merge pull request #5273 from mvdbeek/sort_collection_from_file ...

Allow sorting collection elements based on file

2018-01-08 09:03:30 -05:00

..

library

Fix library security functional tests.

2014-04-25 15:29:56 -04:00

users

Fix certain failing functional tests.

2014-04-16 16:13:11 -04:00

1.axt

…

1.bam

Restore files that were deleted due to a tool migration, but are still used in test/functiona/test_get_data.py.

2013-11-13 10:46:38 -05:00

1.bed

…

1.bed.spaces

Bug fix for handling 'spaces to tab' for non-binary composite datatype files.

2010-06-07 15:34:20 -04:00

1.bedgraph

Enable BedGraph to be used as input to wig-to-bigwig tool.

2013-01-24 17:06:51 -05:00

1.bigbed

Apply patch from Brad Chapman providing support for detecting, uploading and displaying UCSC bigWig and bigBed. Add new functional tests for uploading and detecting bigbed and bigwig formats, and correct and clean up the test_get_data.py functional test script.

2010-08-19 13:58:10 -04:00

1.bigwig

Apply patch from Brad Chapman providing support for detecting, uploading and displaying UCSC bigWig and bigBed. Add new functional tests for uploading and detecting bigbed and bigwig formats, and correct and clean up the test_get_data.py functional test script.

2010-08-19 13:58:10 -04:00

1.customtrack

…

1.fasta

…

1.fastq

Added fastq (generic) datatype and deleted fastqsolexa datatype

2009-10-07 12:43:15 -04:00

1.fastqsanger

Add missing newline at end of some test files

2017-11-28 17:13:18 +00:00

1.fastqsanger.bz2

add fastq(*).bz2 datatypes and converters

2016-11-24 15:37:51 +01:00

1.fastqsanger.gz

Create a BaseFastq class and add test tools

2016-11-11 16:13:18 +01:00

1.fastqsolexa

Add missing newline at end of some test files

2017-11-28 17:13:18 +00:00

1.interval

…

1.lav

…

1.pileup

Added new tabular/pileup join tool and associated test files. Also added pileup datatype.

2010-03-26 12:00:55 -04:00

1.RData

Add missing file from previous commit.

2015-09-23 15:10:06 +01:00

1.sam

Added two new datatypes (sam and bam) and an associated test

2009-08-19 09:13:21 -04:00

1.sam.gz

Configuration tests for the last few upload enhancements.

2017-08-12 07:13:05 -04:00

1.scf

…

1.sff

Added sff datatype

2009-11-11 17:55:08 -05:00

1.tabular

…

1.txt

…

1.wig

…

2.bed

…

2.fasta

…

2.tabular

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

2gen.fastq

Added fastq (generic) datatype and deleted fastqsolexa datatype

2009-10-07 12:43:15 -04:00

3.bam

More fixes to 3.bam to make it valid stripped out secondary HD header and duplicated sequences chr10-16

2016-02-02 13:54:24 -05:00

3.bed

…

3.maf

…

3unsorted.bam

Restore files that were deleted due to a tool migration, but are still used in test/functiona/test_get_data.py.

2013-11-13 10:46:38 -05:00

4.bed

…

4.bed.bz2

Add test for bz2 file upload

2010-09-10 14:17:05 -04:00

4.bed.gz

…

4.bed.zip

Removed binseq.zip test and replace it with a zip test.

2010-07-01 08:59:26 -04:00

5_Ig-like.gff

Cope with GFF3 as well as legacy GFF.

2017-06-26 11:16:06 +01:00

5.bed

…

5.gff

…

5.gff3

…

6.bed

…

7.bed

…

8.bed

…

9.bed

…

454Score.pdf

…

454Score.png

Fix the qual_stats_boxplot and quality_score_distribution tests again, hopefully

2011-03-02 13:46:07 -05:00

a.tab

…

a.txt

…

asian_chars_1.txt

Fixes and new functional tests for uploading multi-byte character files and fixes for displaying multi-byte character dataset peek.

2009-10-15 20:10:32 -04:00

bad.html.gz

Configuration tests for the last few upload enhancements.

2017-08-12 07:13:05 -04:00

bam_from_sam.bam

Add sam-to-bam conversion test tool

2016-11-16 22:01:47 +01:00

bcf_index_metadata_test.bcf

Added test for bcf index creation.

2015-04-28 13:45:33 -04:00

bcf_index_metadata_test.txt

Added test for bcf index creation.

2015-04-28 13:45:33 -04:00

biom1_metadata_test.txt

Add test for failing handling of BIOM1 metadata.

2016-06-07 12:02:09 -04:00

cat_wrapper_out1.bed

Modified sort tool to fix backwards compatibility. Reverted catWrapper tool back to old version before recent changes (for backwards compatibility).

2009-09-24 13:54:12 -04:00

composite_output_expected_log

Improve composite output tool test.

2016-05-16 11:51:03 -04:00

filter1_in3.sam

Enable filter tool to operate correctly on files with a variable number of columns (such as SAM files). Tool prepares and processes only columns up to and including the right-most column (i.e. column with the largest index) in the filtering condition, and subsequent columns are ignored. New functional test added for this functionality as well.

2010-11-04 16:30:34 -04:00

filter1_in5.tab

Add parameter to filtering tool to optionally skip header lines. Add test for new parameter usage as well.

2013-01-29 10:37:16 -05:00

filter1_inbad.bed

[Peter Cock] Filtering tool: Only cast used columns. Fix valid lines and skipped info lines. [Kanwei] Add new testcases to test this behavior. Fixes #537. Fixes #535

2011-05-27 10:47:17 +02:00

filter1_test1.bed

…

filter1_test2.bed

…

filter1_test3.sam

Enable filter tool to operate correctly on files with a variable number of columns (such as SAM files). Tool prepares and processes only columns up to and including the right-most column (i.e. column with the largest index) in the filtering condition, and subsequent columns are ignored. New functional test added for this functionality as well.

2010-11-04 16:30:34 -04:00

filter1_test4.bed

[Peter Cock] Filtering tool: Only cast used columns. Fix valid lines and skipped info lines. [Kanwei] Add new testcases to test this behavior. Fixes #537. Fixes #535

2011-05-27 10:47:17 +02:00

filter1_test5.tab

Add parameter to filtering tool to optionally skip header lines. Add test for new parameter usage as well.

2013-01-29 10:37:16 -05:00

filter_labels_1.txt

Implement collection operation for filtering lists from a file.

2017-04-17 17:08:25 -04:00

GRCm38mm10_chr5_34761740-34912521.fa

Moved API tests to live under test/ rather than test/functional/. Removed test for DNAse flanked genes. Added test for UCSC table browser.

2014-04-30 15:35:57 -04:00

html_file.txt

…

input_taxonomy.biom1

Add test for failing handling of BIOM1 metadata.

2016-06-07 12:02:09 -04:00

joiner_header_in1.tab

join with header: add test

2017-06-26 15:11:51 +02:00

joiner_header_in2.tab

join with header: add test

2017-06-26 15:11:51 +02:00

joiner_out1.bed

join with header: add test-data output files

2017-06-26 15:11:39 +02:00

joiner_out2.bed

join with header: add test-data output files

2017-06-26 15:11:39 +02:00

joiner_out3.bed

join with header: add test-data output files

2017-06-26 15:11:39 +02:00

joiner_out4.bed

join with header: add test-data output files

2017-06-26 15:11:39 +02:00

joiner_out5.tab

join with header: add test

2017-06-26 15:11:51 +02:00

joiner_out6.tab

join with header: add a use case with a fill value

2017-06-26 15:12:21 +02:00

joiner_out7.tab

join with header: add a regression test

2017-06-26 15:12:15 +02:00

neostore.zip

added tests

2017-06-13 16:09:00 +02:00

new_element_sort_order.txt

Allow sorting collection elements based on file

2018-01-08 08:49:26 +01:00

new_labels_1.txt

Start work on a relabelling collection operation.

2017-04-13 23:11:49 -04:00

new_labels_2.txt

Add possibility to rename collection items from a tabular file

2017-04-13 23:11:49 -04:00

new_labels_bad_1.txt

Various improvements to relabel from file collection operation.

2017-04-13 23:15:56 -04:00

new_labels_bad_2.txt

Fix relabel_from_file collection operation error handling if duplicate identifiers.

2017-04-17 13:12:57 -04:00

phiX.fasta

Converted several tools to data table style of loc file handling (Bowtie, BWA, Lastz, Megablast, PerM, SRMA). Cleaned up several tool XML files, removing unnecessary None parameters.

2010-11-08 00:10:13 -05:00

qualscores.qual454

Added functional tests for testing sniffing and metadata settings of qual454 and qualsolid datatypes.

2009-04-29 16:32:23 -04:00

qualscores.qualsolid

Added functional tests for testing sniffing and metadata settings of qual454 and qualsolid datatypes.

2009-04-29 16:32:23 -04:00

random-file

Configuration tests for the last few upload enhancements.

2017-08-12 07:13:05 -04:00

rgenetics.bed

Update rg test data sample outputs to match the new versions Ross uploaded

2009-11-02 16:52:32 -05:00

rgenetics.bim

Update rg test data sample outputs to match the new versions Ross uploaded

2009-11-02 16:52:32 -05:00

rgenetics.fam

Update rg test data sample outputs to match the new versions Ross uploaded

2009-11-02 16:52:32 -05:00

rgenetics.map

Update rg test data sample outputs to match the new versions Ross uploaded

2009-11-02 16:52:32 -05:00

rgenetics.ped

Update rg test data sample outputs to match the new versions Ross uploaded

2009-11-02 16:52:32 -05:00

sam_with_header.sam

Add sam-to-bam conversion test tool

2016-11-16 22:01:47 +01:00

selenium-test-notebook.ipynb

Implement outline of Jupyter testing.

2017-10-02 09:50:37 -04:00

shrimp_cs_test1.csfasta

…

simple_line_alternative.txt

Add missing newline at end of some test files

2017-11-28 17:13:18 +00:00

simple_line_x2.txt

Rework test framework testing and tools.

2014-04-28 11:48:51 -05:00

simple_line_x3.txt

Rework test framework testing and tools.

2014-04-28 11:48:51 -05:00

simple_line_x5.txt

Rework test framework testing and tools.

2014-04-28 11:48:51 -05:00

simple_line.txt

Rework test framework testing and tools.

2014-04-28 11:48:51 -05:00

simple_lines_both.txt

Add framework test tool that has both data and data_collection param - with test case.

2014-05-07 15:39:03 -05:00

simple_lines_interleaved.txt

Add missing newline at end of some test files

2017-11-28 17:13:18 +00:00

simple.xml

added functional test for <is_valid_xml>

2017-02-01 21:17:07 -06:00

test.vcf.gz

Added test file

2017-07-07 18:29:05 +03:00

tinywga.bed

updated rgenetics test files

2009-10-29 17:57:30 -04:00

tinywga.bim

updated rgenetics test files

2009-10-29 17:57:30 -04:00

tinywga.fam

updated rgenetics test files

2009-10-29 17:57:30 -04:00

tinywga.map

updated rgenetics test files

2009-10-29 17:57:30 -04:00

tinywga.ped

updated rgenetics test files

2009-10-29 17:57:30 -04:00

tinywga.ped.space_to_tab

Bug fix for handling 'spaces to tab' for non-binary composite datatype files.

2010-06-07 15:34:20 -04:00