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
Katrin Leinweber
f99f8667bc
Hyperlink DOIs against preferred resolver
2018-05-30 16:49:21 +01:00
John Chilton
88239abf5c
Add more distribution tool citations.
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xref #361 .
2015-10-05 15:16:50 +01:00
John Chilton
162e4de0e1
Enhance bfast to utilize GALAXY_SLOTS configuration when available.
2013-11-05 13:46:06 -06:00
Kelly Vincent
0017486eaa
Sam header suppression made optional in BFAST and default set to off for BFAST and Bowtie. Fixed dbkey setting on outputs for for BFAST, Bowtie, Mosaik. Fixed sorting of built-in builds for these tools so ordered by pretty name.
2011-05-09 12:11:54 -04:00
Daniel Blankenberg
4eb1b0a79f
Better determination in tests if a provided input is a DataToolParameter to better handle .gz and .zip uploads and allowing uploads from a sub-directory of test-data/.
2011-02-28 12:16:28 -05:00
Kelly Vincent
c0726bfb23
Fixed BFAST functional tests (corrected problem with chromosome names in test files)
2011-02-17 13:46:40 -05:00
Kelly Vincent
64553e62fa
Removed errant right parenthesis from BFAST wrapper command
2011-01-14 00:23:15 -05:00
Daniel Blankenberg
0adf8f72c3
Change method of accessing additional fields by name for dynamically generated select lists which was added in 4784:7be369e7cc6f.
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Access now takes the form similar to ${param.fields.path}.
2011-01-05 14:57:05 -05:00
Daniel Blankenberg
93925d842e
Update bfast wrapper to use $param.get_field( "path" ) method instead of previous hack to access path when building the command-line.
2011-01-03 10:38:00 -05:00
Daniel Blankenberg
7ad8a9a446
Remove erroneous "Unmapped Reads" label from bfast output which appeared in 4696:3b3b7f382ee2.
2010-12-20 15:58:31 -05:00
Kelly Vincent
f61d147034
Added --max and --un file output options to Bowtie and modified tests to test for them.
...
Made Bowtie test files longer (more than one test read).
Added explanation of canonical and full reference genome variants to BWA and Bowtie.
Added informative labels to output files for NGS tools.
2010-12-01 10:54:35 -05:00
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
94c7417f37
Add BFAST Mapper tool and wrapper.
2010-08-18 16:52:06 -04:00
Nicola Soranzo