Greg Von Kuster
987df32669
Fix for rendering tools / workflows in target frames, also elimnate the Workflow link in the tool panel as we're now using the menu bar.
2009-02-23 13:52:34 -05:00
Greg Von Kuster
377a5d8981
Add the Libraries tab to base panel and fix the access_libraries tool config for PrognosysBio.
2009-02-23 11:04:27 -05:00
Guruprasad Anada
6fd54350eb
Integration of Assaf Gordon's Solexa toolkit into Galaxy - (all tools except 3 are working fine).
2009-02-20 14:17:46 -05:00
Anton Nekrutenko
8e6f06d30b
restoring original files
2009-02-10 11:54:53 -05:00
Anton Nekrutenko
1839cde45a
Another typo
2009-02-10 11:31:15 -05:00
Anton Nekrutenko
8624d6c974
Usability tweak for catWrapper
2009-02-10 11:01:54 -05:00
Anton Nekrutenko
f6f3092347
clean up
2009-02-10 10:43:21 -05:00
Anton Nekrutenko
01d16b3883
modified mergeCols to take advantage of repeat tag. Looks foolproof now.
2009-02-10 10:06:17 -05:00
Anton Nekrutenko
19bb2c924c
A simple tool for merging columns. Surprisingly useful for some analyses and also requested by a user lest Friday
2009-02-09 23:57:41 -05:00
Nate Coraor
42cbc8d893
Set a width hint for the library browser
2009-02-06 14:34:57 -05:00
Ian Schenck
28016bd908
Using deprecated sha module in place of hashlib to keep compatibility with python2.4
2009-02-05 15:34:31 -05:00
Daniel Blankenberg
377c2427a7
Allow workflows that contain tools that had parameters added to them after the workflow was created to be edited. Workflows containing tools with added parameters can still not be run until after they are edited and saved. Default values are provided in the workflow building mode.
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Allow most MAF tools to allow limiting of output species. MAF tools which do not allow species limiting include Extract Pairwise MAF blocks, MAF Coverage stats, and Filter MAF blocks by Size.
The functionality of Filter MAF blocks by Species and Filter MAF blocks by Size is now available in Filter MAF by specified attributes. Unfortunately tests are still not able to be written for the Filter MAF by specified attributes tool.
2009-02-04 14:55:45 -05:00
Guruprasad Anada
7db6a54cf7
updating security from central
2009-02-03 18:36:50 -05:00
Guruprasad Anada
b45b74f3ec
Fixes to get functional tests working.
2009-02-03 18:34:27 -05:00
Guruprasad Anada
a691c492d9
updating security from central
2009-02-03 15:17:00 -05:00
Guruprasad Anada
41d1ce79c8
Removed lzo requirement from two tools- getIndels and qualityFilter.
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Also added validator to the regression tools.
2009-02-03 15:06:21 -05:00
Nate Coraor
f8ce6fc19d
merge
2009-01-30 11:39:29 -05:00
Nate Coraor
288d581b75
Fix annotation profiler interpreter to be python, not python2.4
2009-01-30 11:37:51 -05:00
Ian Schenck
937e568e19
Ironed out nasty exceptions thrown on invalid genetrack outputs. Still need a way to resolve the optional 2nd output (exported intervals), and ensure the user picks at least 1 coverage dataset or 1 feature dataset.
2009-01-27 17:10:30 -05:00
Guruprasad Anada
753c5466c1
Commit changes from central to SEcurity
2009-01-27 16:20:13 -05:00
Guruprasad Anada
1f62ffbb01
Adding modified hyphy functional test output files, which have changed as the new version of HYPHY is installed on Galaxy. Also changing version numbers for all the affected tools.
2009-01-27 16:17:22 -05:00
Nate Coraor
4f02a56abc
merge
2009-01-27 14:49:21 -05:00
Daniel Blankenberg
4279415d2a
Fix For MAF Filter tool.
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Looks like when grouping parameter types were updated to be recursively wrapped properly, this tool was not updated.
2009-01-26 14:48:45 -05:00
Nate Coraor
de2fff1df2
merge
2009-01-23 12:57:06 -05:00
Anton Nekrutenko
076398c821
Changed grouping output to tabular
2009-01-22 12:46:37 -05:00
Anton Nekrutenko
43891dced2
updated bar charter to use png instead of pdf
2009-01-22 12:06:29 -05:00
Greg Von Kuster
bb2b948557
merging from central
2009-01-22 08:51:48 -05:00
Greg Von Kuster
705994a0fc
Fixes for formatting end of line chars in html when displaying dataset.info. Also change the biomart tool version.
2009-01-22 08:50:52 -05:00
Greg Von Kuster
b11c63fb44
meging heads again
2009-01-21 17:07:52 -05:00
Greg Von Kuster
6dd5b31c0e
merging from central
2009-01-21 17:06:02 -05:00
Greg Von Kuster
7e21fb74a3
Fixes for Biomart and UCSC to better ensure the data type is correctly set. A data type of "tabular" is now the default, and data will be sniffed if this is the data type.
2009-01-21 17:03:39 -05:00
Ian Schenck
82d09f5824
Finally remerged changeset. Should be good now.
2009-01-21 16:48:54 -05:00
Nate Coraor
427bc02028
Backed out changeset 83a0c394a797
2009-01-21 16:03:59 -05:00
Ian Schenck
73d609cf31
Merged
2009-01-21 11:45:50 -05:00
Ian Schenck
b8e76a8ca6
Made Genetrack load only if the dependencies import
2009-01-21 11:45:30 -05:00
Anton Nekrutenko
42adeabbc9
Lca commit. The tool itself is written by guru with minor modification made by me.
2009-01-21 09:51:06 -05:00
Guruprasad Anada
84535eb6e8
Changes to exception handling in LCA.
2009-01-20 13:24:12 -05:00
Ian Schenck
7dc603afaf
Merged in changes from remote head
2009-01-19 17:46:23 -05:00
Ian Schenck
6a0aa166aa
Initial GeneTrack commit. Most parts are in, but dependencies will still be a problem.
2009-01-19 17:45:28 -05:00
Wen-Yu Chung
ba3fd2175d
remove hash tables.
2009-01-19 15:51:01 -05:00
Wen-Yu Chung
498fbac868
remove the usage of hast tables in the fasta-tools
2009-01-19 15:47:02 -05:00
Anton Nekrutenko
2c85c6fee9
Preliminary commity for lca. Still in progress.
2009-01-19 12:12:36 -05:00
Guruprasad Anada
1a6342308a
Push changes to Security from Central..
2009-01-16 13:32:13 -05:00
Guruprasad Anada
50b46e60e3
Removed an option from grouping tool, which is now part of the LCA tool under Taxonomy.
2009-01-16 13:30:01 -05:00
Guruprasad Anada
d4eef49e01
Updating security from central
2009-01-15 13:11:47 -05:00
Guruprasad Anada
ee8779987e
More changes to mutability tool.
2009-01-15 13:10:04 -05:00
Greg Von Kuster
19c0b7e30b
merging from central
2009-01-15 11:03:19 -05:00
Greg Von Kuster
b7aaa17bc3
Change History.copy() back to use datasets rather than active_datasets. Add checks in set_peek() to properly set peek on purged datasets. Fixes sharing a history that contains purged datasets.
2009-01-15 10:49:01 -05:00
Guruprasad Anada
918b4a8258
Push changeset from central to Security..
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G: Enter commit message. Lines beginning with 'HG:' are removed.
2009-01-15 10:46:17 -05:00
Guruprasad Anada
d46171ea21
Fixed a bug in microsatellite mutability tool.
2009-01-15 10:42:22 -05:00
Greg Von Kuster