Nicola Soranzo
f865e8359f
Deprecate size attribute of <param/> and remove it from tools
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Also:
- dos2unix test/functional/tools/for_workflows/head.xml
- Single-quote text and data params in `<command/>`
- Remove deprecated `interpreter` attribute of `<command />`
2018-09-10 11:34:37 +01:00
Nicola Soranzo
2515267ca5
Add version attribute to tool requirements
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instead of relying on `lib/galaxy/tools/deps/resolvers/default_conda_mapping.yml` .
Follow-up on https://github.com/galaxyproject/galaxy/pull/5544 .
See https://github.com/galaxyproject/galaxy/pull/5544/files#r183909746 for
an explanation why that's preferrable for future-proof reproducibility.
Also, small fixes to `tools/evolution/codingSnps.xml` .
2018-04-25 15:50:35 +01:00
John Chilton
7712f69b69
Rev tool versions for tools with updated ucsc tool requirements.
2018-04-24 14:40:28 -04:00
Nate Coraor
4b09027ebb
Update all tools/converters using UCSC binaries to depend only on the
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binary they are using.
2018-02-15 10:54:04 -05:00
mvdbeek
3dbdf7d474
Make liftover tool use data table
2017-09-19 16:09:36 +02:00
yhoogstrate
6a38e0bda7
Update liftOver_wrapper.xml
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version++
2015-08-12 10:57:42 +02:00
youri
83bc5b74ff
liftOver.loc was not accessible from local data
2015-08-11 10:58:06 +02:00
Nicola Soranzo
22d4a1d8c3
dos2unix of tools/ directory. Some whitespace and PEP-8 fixes.
2015-05-15 12:40:52 +01:00
John Chilton
77b167bbd1
Comment out broken liftOver tests.
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liftOver loc file handling is problematic (https://trello.com/c/A6I6zQvF ). If it weren't this wouldn't be a problem. I could fix the API functional test framework to mimic the older form driven approach but it would take a week and would be rendered moot by fixing liftOver. Unfortunately, fixing liftOver would likely break a lot of existing workflows and tool reruns so I am not fixing that either.
Only option left, admittedly a crappy one, is to comment out the tests.
2015-02-23 23:09:19 -05:00
Dave Clements
f706f34948
Replaced "query" with "dataset" in a number of tool definition XML files.
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I got tired of coming across "query" when doing workshops.
2013-01-14 16:13:54 -08:00
Guruprasad Anada
feb0b91aba
Added additional options to the liftOver tool. It now supports GFF and GTF formats and allows multiple output regions and related options.
2011-07-26 16:14:31 -04:00
Nate Coraor
e05f11bc73
Convert a bunch of binary requirement tags to package requirements, and change the sputnik tool to call 'sputnik' instead of 'bx-sputnik'.
2010-10-07 16:23:57 -04:00
Daniel Blankenberg
f97a380a56
Add ToolOutputActions to set dbkeys for LiftOver tool and both Bowtie wrappers; remove no longer needed code files.
2010-08-09 21:06:18 -04:00
Kelly Vincent
44fb42f6a0
Fix try-except-finally bug to be compatible with Python 2.4 in several tools and twilltestcase.py. Updated liftOver test to replace hard-coded (incorrect) path and modified code file to allow for new path. Improved bowtie error handling.
2010-03-10 11:51:00 -05:00
Nate Coraor
0bfa58679b
Fix locations of cached data for tests
2010-02-25 12:27:07 -05:00
Guruprasad Anada
22b3dfa1c2
Added functional tests for a couple of my tools with multiple outputs/pdf outputs.
2010-02-03 13:53:16 -05:00
Greg Von Kuster
527e1258f1
Change the version of the liftOver tool due to the application of Brad Chapman's patch in change set 3021.
2009-11-13 14:20:03 -05:00
Ramkrishna Chakrabarty
468a631370
Applied patch provided by Brad Chapman in the liftOver tool to support BED files that contain track or browser lines. Resolves bitbucket issue 201.
2009-11-12 13:20:19 -05:00
Guruprasad Anada
167ce59b29
Bug fixes for histogram liftover and grouping tools.
2009-05-29 11:07:18 -04:00
Guruprasad Anada
d0c13d7ec4
Added a new option to specify minimum match value in the liftOver tool.
2009-04-03 13:25:01 -04:00
Guruprasad Anada
d6d59f7431
Added Validator to a bunch of tools..
2008-10-17 13:02:26 -04:00
Guruprasad Anada
f27ef3634f
Changing liftOver input from BED to Interval in order to preserve the contents of columns other than the chromosome, start and end columns. This information was previously being lost during Interval to BED conversion.
2008-06-08 19:28:45 +00:00
Daniel Blankenberg
11a2c767c3
Rewrite of dynamic options for select lists. There are no more 'special cases' and new filters are much easier to incorporate, as neeeded.
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MAF tool interfaces now support the use of index species and all species existing in cached alignment sets.
Until main is updated and the old maf_location files can be overwritten, these symbolic links are required:
maf_index.loc -> /depot/data2/galaxy/maf_index_new.loc
maf_pairwise.loc -> /depot/data2/galaxy/maf_pairwise_new.loc
2008-05-29 17:38:46 +00:00
Nate Coraor
f53cb1d7f1
Added tool dependencies to xml.
2008-04-25 19:40:16 +00:00
Greg Von Kuster
cd52cabd48
Eliminated hard-codes paths to locally cached data from tools, requires developers to add softlinks to development environments.
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Galaxy developers should execute the following commands in their $UNIVERSE_HOME/tool-data directories:
ln -s /depot/data2/galaxy/alignseq.loc alignseq.loc
ln -s /depot/data2/galaxy/binned_scores.loc binned_scores.loc
ln -s /depot/data2/galaxy/blastdb.loc blastdb.loc
ln -s /depot/data2/galaxy/encode_datasets.loc encode_datasets.loc
ln -s /depot/data2/galaxy/liftOver.loc liftOver.loc
ln -s /depot/data2/galaxy/maf_index.loc maf_index.loc
ln -s /depot/data2/galaxy/maf_pairwise.loc maf_pairwise.loc
ln -s /depot/data2/galaxy/microbes/microbial_data.loc microbial_data.loc
ln -s /depot/data2/galaxy/phastOdds.loc phastOdds.loc
ln -s /depot/data2/galaxy/quality_scores.loc quality_scores.loc
ln -s /depot/data2/galaxy/regions.loc regions.loc
ln -s /depot/data2/galaxy/twobit.loc twobit.loc
2008-03-21 18:31:39 +00:00
Guruprasad Anada
a57d78cd9b
Changes to liftOver tool: Modified the liftOver.loc file and changed the script files as required.
2008-03-21 15:51:40 +00:00
Greg Von Kuster
365a87fd90
Various tool improvements.
2008-03-18 20:42:57 +00:00
Greg Von Kuster
4dd1f044e1
Removed tool version directiories for some of the tools...the rest soon.
2008-03-03 16:14:06 +00:00
Greg Von Kuster
cabde35b99
Added tool version directory hierarchy for encode and extract tool directories.
2008-02-22 14:18:41 +00:00
Guruprasad Anada
82760a4c4b
Modified Lift-Over tool. The "TO" build-list will now be dynamically generated based on the input dataset's build.
2008-02-06 19:17:02 +00:00
Guruprasad Anada
987e2c7c4e
Adding liftOver tool. Test section is commented as the functinal test module doesn't handle multiple outputs yet. I've downloaded liftOver mapping files from UCSC for all the genomes for which we have sequences. I've added a function in get_ucsc_scores.pl file (which contains functions to fetch sequences and alignments) to fetch liftOver mappings too.
2008-01-17 19:24:34 +00:00
Nicola Soranzo