John Chilton
f8bf5f4d8e
Merged in clayton_turner/galaxy-central (pull request #322 )
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Added "ignore lines starting with specific characters" to group tool
2014-02-20 10:35:58 -06:00
Aysam Guerler
ba0362aa8d
Add get data back to to tool panel (will be replaced by a placeholder soon)
2014-02-19 12:51:52 -05:00
Aysam Guerler
73e74f74c8
Upload: Hide former upload tool
2014-02-18 14:57:08 -05:00
Dave Bouvier
5f485f05b3
Remove tool that was migrated to the tool shed in 10719:c2f06b5cfba1. Remove test data that belonged to tools that were removed in 12288:401ee23dcf2f.
2014-02-17 13:05:00 -05:00
Dave Bouvier
ba17a35a99
Remove stats/wiggle_to_simple, which is an exact duplicate of filters/wiggle_to_simple.
2014-02-14 12:34:58 -05:00
Clayton Turner
fd85979a86
Fixed XML versioning and inputfile name
2014-02-14 12:25:20 -05:00
Clayton Turner
9e86f172bc
Merge from stable
2014-02-10 16:49:43 -05:00
Clayton Turner
7347d75a4a
Added ignore lines starting with specific characters to group tool
2014-02-10 16:00:30 -05:00
Daniel Blankenberg
040fb029f8
Update GenomeSpace import tools to use current working directory instead of __new_file_path__ for extrafiles created using multiple outputs technique. Should resolve issue on our public servers where only the first selected file was being imported to the history.
2014-02-05 13:44:32 -05:00
Dannon Baker
832d0c7985
Merged in nsoranzo/galaxy-central (pull request #312 )
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Remove unused imports and unused variables. Fix spacing.
2014-02-04 10:33:40 -05:00
Nate Coraor
9c64fc123e
Remove broken and/or obsolete tools.
2014-01-27 13:58:31 -05:00
Nicola Soranzo
3f103e2b38
Remove unused imports and unused variables. Fix spacing.
2014-01-27 19:51:46 +01:00
Dave Bouvier
448d9f55eb
Migrate 43 tools from the distribution to the tool shed.
2014-01-27 09:53:14 -05:00
Daniel Blankenberg
3dbcdacfab
Fix for aggregate_scores_in_intervals.py broken in 95bf71620d50c6d81248eef2001a7dc156ae1088.
2014-01-27 09:54:34 -05:00
Nate Coraor
da52ddb317
Merge security fix for filtering tools from stable/next-stable.
2013-11-04 14:56:57 -05:00
Nate Coraor
e8d81d72c5
Merge security fix for filtering tools from stable.
2013-11-04 14:56:17 -05:00
John Chilton
4fb2b89347
White-list expressions executed by filtering and dna_filtering tools.
2013-11-04 14:55:00 -05:00
John Chilton
32b07c04f3
Rev slightly the tool version of extract_genomic_dna.xml since output is slightly different.
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Update tool help to reflect new output format.
2013-10-25 00:06:14 -04:00
John Chilton
54a3dba91e
Update hg17 test case for extract_genomic_dna.xml tor reflect recent changes.
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Cannot delete or modify previous output file - it is used as input for another tool. Use assertion testing to weaken test case. As this tool is migrated to the tool shed the hg17 test cases should probably be eliminated completely.
2013-10-25 00:03:57 -04:00
Bjoern Gruening
f444f30235
bugfix and one test fix
2013-10-24 18:13:18 +02:00
Bjoern Gruening
11b74295d2
Add the value (nameCol) in a given BED file to the FASTA header.
2013-10-18 18:31:44 +02:00
Nicola Soranzo
7b386b14ed
Fix for "NotFound: cannot find 'cov_cutoff' while searching for 'expected.cov_cutoff'"
2013-10-17 12:46:13 +02:00
John Chilton
892912c02d
Merged in abrenner/galaxy-central (pull request #215 )
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histogram2 - RPY requires R - missing from requirements tag
Thanks for the contribution!
2013-10-16 22:12:40 -05:00
John Chilton
60488bf064
Merged in nsoranzo/galaxy-central-tools2 (pull request #234 )
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Bug fixes for 3 tools (rebased #222 )
2013-10-16 12:49:34 -05:00
Aysam Guerler
d9b284bf5e
Modify bowtie error handler
2013-10-16 11:03:51 -04:00
Ross Lazarus
c860c25f77
Remove unused test-data/rtestouts
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Remove references in converters to g2.bx.psu.edu
Note leaving rgenetics converters and datatypes - ped still used in genomic variation tools.
2013-10-14 21:43:32 +11:00
Nate Coraor
607fc002ea
Fix outdated usage of states in microbial dataset post-job hook.
2013-10-10 12:53:10 -04:00
Nate Coraor
705457f218
Convert DOS line endings.
2013-10-10 12:48:07 -04:00
Ross Lazarus
5d4e73cc1e
Proper removal of rgenetics deprecated tool wrappers
2013-10-08 16:30:54 +11:00
Ross Lazarus
b467ec50bb
Big cleanup - remove material in tools/rgenetics accidentally added in August when a push was made from a BakerIDI repository - apologies to all. This push will revert all those changes and also removes the old rgenetics SNP tools which are now deprecated.
2013-10-08 16:15:56 +11:00
Ross Lazarus
c1af859f90
revert bowtie2 and tophat2 wrappers
2013-10-08 13:34:54 +11:00
Ross Lazarus
4caf74eaa6
backout -r 10806
2013-10-08 10:54:45 +11:00
Ross Lazarus
070ee188fa
backout -r 10800
2013-10-08 10:52:21 +11:00
Ross Lazarus
eaaaa3cce7
backout -r 10799
2013-10-08 10:50:10 +11:00
Ross Lazarus
a17e071f38
hg backout -r 1092b0d
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backout unintended commits to tophat and bowtie2 wrappers
2013-10-08 10:24:59 +11:00
Ross Lazarus
87b1203b4a
branch merge
2013-10-05 09:56:05 +10:00
Ross Lazarus
7938d1fc81
local changes
2013-10-05 09:51:18 +10:00
Nicola Soranzo
f109dea17f
Fix for "syntax error near unexpected token `;;'".
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<command> should not end with a semicolon, otherwise
BaseJobRunner.build_command_line() would create a bash command containing
';;' when appending metadata setting commands.
2013-10-04 18:15:22 +02:00
Dave Bouvier
695aa8f44d
Migrate cuffcompare, cuffdiff, cufflinks, and cuffmerge from the distribution to the tool shed. Update the 'Review migration stages' layout.
2013-10-01 13:54:57 -04:00
Dave Bouvier
b0efe4ddea
Migrate tools from the distribution to the tool shed, including but not limited to samtools and fastx_toolkit tools.
2013-09-26 10:05:00 -04:00
Nicola Soranzo
3b5fc4077c
Fix reference to 'Fetch taxonomic representation' tool.
2013-09-18 14:44:42 +02:00
Nicola Soranzo
d7d1210111
Prevent no choice in multiple selections.
2013-09-18 14:43:59 +02:00
Adam Brenner
35d32232d4
histogram2.xml python module rpy requires R package.
2013-09-12 18:36:20 +00:00
Jeremy Goecks
81da436ec1
Merged in saketkc/galaxy-central (pull request #184 )
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VCFTools Incompatible with VCF4.1
2013-09-11 12:16:14 -04:00
John Chilton
0d3922850e
Add ucsc_tools requirement for extract_genomic_dna.xml tool.
2013-09-03 12:32:02 -05:00
Ross Lazarus
0890601616
Merged galaxy/galaxy-central into default
2013-08-29 13:36:22 +10:00
Saket Choudhary
8e2a20370a
Automated merge with ssh://bitbucket.org/galaxy/galaxy-central
2013-08-28 22:45:32 +05:30
Jeremy Goecks
bd8809e00d
Add version command information to Cuff* tools.
2013-08-23 10:49:06 -04:00
Ross Lazarus
7146ba9c38
tweaks. ready for branch merge
2013-08-12 13:04:57 +10:00
Ross Lazarus
a4622551de
branch merge with central
2013-08-08 15:38:10 +10:00
John Chilton