John ChiltonandClaude Opus 5.5 382b9f80e3 Name workbook tests for the mapping they check, require dataDescription ...

Tests stop at the rule builder, so name them for the mapping, not an import.
Both callers pass dataDescription, so drop its unused default. Fix H3K4me27
to H3K27me3 in workbook_example_4.tsv.

Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>

2026-10-08 07:54:47 -04:00

..

bwa_mem2_index

Fix directory uploads, use `__FETCH_DATA__` api

2025-02-25 18:10:10 +01:00

exports

Legacy history export tests and infrastructure.

2019-03-11 10:56:25 -04:00

highdicom

Employ more diverse DICOM test data

2026-01-19 17:56:27 +01:00

library

Fix library security functional tests.

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

rules

Name workbook tests for the mapping they check, require dataDescription

2026-10-08 07:54:47 -04:00

users

Fix certain failing functional tests.

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

1.axt

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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

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1.bed.spaces

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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.csv

WIP: metadata validation.

2023-06-06 10:02:29 +02:00

1.ct

Add connectivity table test dataset

2022-11-18 18:24:54 -05:00

1.customtrack

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1.fasta

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1.fasta.gz

Add test-data

2019-04-07 23:15:35 +02:00

1.fastq

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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

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1.lav

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1.pileup

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1.RData

Add missing file from previous commit.

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

1.sam

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1.sam.gz

Configuration tests for the last few upload enhancements.

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

1.scf

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1.sff

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1.tabular

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1.tiff

Some more upload/sniff tests.

2018-05-24 10:31:28 -04:00

1.txt

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1.wig

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1.yaml

added sniffer for yaml

2021-09-20 13:07:20 -07:00

2.bed

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2.cram

Update pysam depedency to 0.20.0

2023-01-01 03:37:53 +00:00

2.csv

Use consistent naming for added test csv

2025-05-04 09:04:15 -04:00

2.fasta

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2.tabular

make 2nd column of 2.tabular test data unique values

2021-01-12 13:44:58 +01:00

2gen.fastq

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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

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3.maf

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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

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4.bed.bz2

Add test for bz2 file upload

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

4.bed.gz

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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

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5.gff

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5.gff3

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6.bed

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7.bed

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8.bed

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9.bed

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11.tabular

Test dumping multiple="false" data_column param as json

2018-06-30 09:11:42 -07:00

454Score.pdf

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454Score.png

Fix the qual_stats_boxplot and quality_score_distribution tests again, hopefully

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

a.tab

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a.txt

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asian_chars_1.txt

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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

bam_native_from_sam.bam

add new test file

2017-12-10 15:23:26 +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

Fix `metadata_bcf` framework test

2021-03-11 20:21:00 +00:00

biom1_metadata_test.txt

Add test for failing handling of BIOM1 metadata.

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

chebi_57262.v3k.mol

move test data for molecules converters

2021-06-29 14:06:39 +02:00

chopper.h5

Add support for visualizing HDF5 datasets. This contribution is split into two parts: the visualization plugin and backend changes. The client code integrates the h5web visualizer into Galaxy (https://h5web.panosc.eu). The backend changes add the ability to access the contents of a dataset without needing to read the whole dataset, which is essential for large files. It is based on the h5grove API (https://github.com/silx-kit/h5grove).

2023-05-04 20:48:15 -04:00

composite_output_expected_log

Improve composite output tool test.

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

drugbank_drugs.cml

move test data for molecules converters

2021-06-29 14:06:39 +02:00

drugbank_drugs.inchi

move test data for molecules converters

2021-06-29 14:06:39 +02:00

drugbank_drugs.mol

fix the to_inchi converter

2021-07-01 15:08:49 +02:00

drugbank_drugs.mol2

move test data for molecules converters

2021-06-29 14:06:39 +02:00

drugbank_drugs.sdf

move test data for molecules converters

2021-06-29 14:06:39 +02:00

drugbank_drugs.smi

move test data for molecules converters

2021-06-29 14:06:39 +02:00

empty.txt

add empty test file

2021-01-08 12:43:37 +01:00

example-bag.zip

Hierarchical upload API optimized for folders & collections.

2018-03-08 10:33:36 -05:00

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_in6.bed

add test case for fixed bug

2018-04-20 09:44:27 +02:00

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

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filter1_test2.bed

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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

filter1_test6.bed

add test case for fixed bug

2018-04-20 09:44:27 +02:00

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

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im1_uint8.png

Add functional test for image_diff

2024-02-27 19:22:33 +01:00

im1_uint8.tif

Add functional test for image_diff

2024-02-27 19:22:33 +01:00

im2_a.png

Add functional test for image_diff

2024-02-27 19:22:33 +01:00

im2_b.png

Add functional test for image_diff

2024-02-27 19:22:33 +01:00

im3_a.png

Fix bugs

2024-02-27 21:54:23 +01:00

im3_b_bool.tiff

Add test for content assertions with bool image

2026-01-03 11:59:13 +01:00

im3_b.tif

Fix bugs

2024-02-27 21:54:23 +01:00

im4_float.tif

Add float TIFF test case (fails with Pillow)

2024-03-19 22:03:34 +01:00

im5_uint8.tif

Add support for YXCS axes in asserts/image.py

2024-09-25 13:21:47 +02:00

im6_uint8.tif

Add test for ZCYX axes

2024-09-25 16:59:32 +02:00

im7_uint8.tif

Add test for ZYX axes

2024-09-25 17:11:26 +02:00

im8_uint16.tif

Make im8_uint16.tif tiled so we have a test for is_tiled=True

2025-03-25 14:36:42 +01:00

im9_multiseries.tif

Rename im9_multipage.tif -> im9_multiseries.tif

2025-03-25 14:36:42 +01:00

im_empty.tif

Add test for empty TIFF file (no metadata available)

2024-10-09 08:45:38 +02:00

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

matrix.cool

add test-data for new hdf5 based tool test

2019-02-05 04:23:13 +01:00

MTBLS6.zip

Start writing upload test for isa-tab.

2018-06-07 12:07:35 +01:00

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_3.txt

Fix linting and add test

2024-10-21 13:35:15 +02:00

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

new_tags_1.txt

add a bit of docs to the add tags tool

2021-04-21 11:45:07 +02:00

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

qname_sorted.bam

Add queryname sorted and input sorted datatypes

2018-02-22 19:59:55 +01:00

qualscores.qual454

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qualscores.qualsolid

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random-file

Configuration tests for the last few upload enhancements.

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

rgenetics.bed

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rgenetics.bim

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rgenetics.fam

…

rgenetics.map

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rgenetics.ped

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rocrate-test.zip

Replace GitHub raw content URLs with local mock HTTP server in tests

2026-03-13 12:19:55 +01:00

safe_relative_symlink.tar

Add test case and use assertRaises()

2019-04-12 12:41:48 +01:00

safetar_with_symlink.tar

Fix security problems when extracting untrusted tar files.

2018-10-04 11:32:52 -04:00

sam_with_header.sam

use unsorted sam file for tests

2017-12-10 15:23:26 +01:00

selenium-test-notebook.ipynb

Update ruff to 0.6.1

2024-08-17 18:58:38 +01:00

shrimp_cs_test1.csfasta

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simple_line_alternative.txt

Add missing newline at end of some test files

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

simple_line_no_newline.txt

Fix Galaxy tool/workflow staging and refactor for reuse in Planemo.

2020-08-01 10:34:46 -04:00

simple_line_x2_windows.txt

Display dataset source transform information.

2021-11-12 11:42:21 -05:00

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

sort_out1.bed

sort with header: add test-data for the state of art

2017-06-26 17:00:13 +02:00

sort_out2.bed

sort with header: add test-data for the state of art

2017-06-26 17:00:13 +02:00

sort_out3.tab

sort with header: add test-data for the state of art

2017-06-26 17:00:13 +02:00

sort_out4.sam

sort with header: done

2017-06-26 19:07:14 +02:00

test.vcf

Add VCF_BGZIP to VCF converter

2020-07-25 01:33:02 +01:00

test.vcf.gz

Added test file

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

testdir1.tar

SQUASH: Adding in other archive containers

2019-02-26 16:43:23 -07:00

testdir1.tar.gz

SQUASH: Adding in other archive containers

2019-02-26 16:43:23 -07:00

testdir1.zip

Hierarchical upload API optimized for folders & collections.

2018-03-08 10:33:36 -05:00

testdir.tar

Fix security problems when extracting untrusted tar files.

2018-10-04 11:32:52 -04:00

tinywga.bed

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tinywga.bim

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tinywga.fam

…

tinywga.map

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tinywga.ped

…

tinywga.ped.space_to_tab

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unsafe_relative_symlink.tar

Fix security problems when extracting untrusted tar files.

2018-10-04 11:32:52 -04:00

unsafe.tar

Fix security problems when extracting untrusted tar files.

2018-10-04 11:32:52 -04:00

unsafe.zip

Fix security problems when extracting untrusted tar files.

2018-10-04 11:32:52 -04:00