4ba6f972a4
Limit input files format of Emboss tools to fasta.
2007-05-10 19:37:12 +00:00
059a63ece7
Allow gencode partitioning to work across the cluster.
2007-05-09 18:18:02 +00:00
bf5bfd7cb1
Limit input files format of tool msbar, needle, newcpgseek to fasta
2007-05-08 18:36:31 +00:00
39f811eff7
Added new Subtract Whole Query tool. Also some miscellaneous code clean-up.
2007-05-07 18:59:15 +00:00
f5e9f7735f
Limit input files format of EMBOSS tools to fasta
2007-05-04 19:42:41 +00:00
4d78666988
Some cleanup to Aggregate Scores tool.
2007-05-04 14:27:44 +00:00
4d720d63c6
Removed tmp and files from svn, now automatically created via run.sh
2007-05-02 19:23:00 +00:00
c8b6b006ee
change input ftype to 'wig'
2007-05-02 15:01:58 +00:00
1cff7712dc
Fasta extractor fix
2007-05-02 01:18:23 +00:00
061adc675d
Eliminated "require" for numpy.
2007-04-30 13:57:13 +00:00
fcd23e8376
Unsequenced genome for May
2007-04-30 00:46:15 +00:00
c26293b312
Remodelled "Get Flanks" tool on the lines of other "Operate on genomic intervals" tools. It now gets the chr num, start/stop positions and strand info from the input dataset's metadata.
2007-04-27 20:28:37 +00:00
c6d633a85a
Enhanced the tools to use Interval metadata for defining chrom, start and stop columns, among other tweaks. Added more useful info to the tool XML pages.
2007-04-27 20:23:51 +00:00
1a16bf28f1
Refactoring redundant code from GenomeBuildParameter, fixing bug where it
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was ignore passed in value (this causes problems with validation) and adding
unit tests (!!!).
2007-04-27 17:21:39 +00:00
3e78eb9107
Data fix to correct the failure of the aggregate_scores tests within the functional tests.
2007-04-27 14:57:19 +00:00
9e65adc861
Fix for correctly assigning .wig extension to wiggle files uploaded from UCSC. These files will now be 'format: wig' rather than 'format: tabular' in history items.
2007-04-26 15:24:32 +00:00
0f88b51cc3
Fix due to python nested scope issues.
2007-04-26 02:46:42 +00:00
8a6af19ee2
Parent/child fixes, child datasets will now appear in data parameter inputs.
2007-04-26 02:25:24 +00:00
17c53a41d7
change parameter for functional test of aggregate_binned_scores_in_intervals
2007-04-23 19:08:56 +00:00
7339fe6d9b
change parameter for functional test
2007-04-23 16:25:09 +00:00
4b087ffdd6
changes related to check_genome_build
2007-04-20 15:20:20 +00:00
e15d34fbf5
2007-04-20 14:32:35 +00:00
401e30e2c5
Requires db schema change. Enhance upload tool to default to the last build used in the "current" history.
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Database changes required:
alter table history add genome_build varchar(40);
There is now a new tool ToolParameter named GenomeBuildParameter which should be useful in several existing tools.
Also took care of some other miscellaneous items.
2007-04-19 20:53:16 +00:00
071d75df77
change the database server name
2007-04-19 14:06:35 +00:00
182d5bd027
update data for nj_tree_newrick aggregate test
2007-04-18 19:54:12 +00:00
66bc21458d
fix for sequence extract This was a munumentally stupid bug
2007-04-18 02:27:06 +00:00
35a472d31b
add picture for findcluster
2007-04-17 19:42:43 +00:00
98d5a86f39
small modifications on the findcluster tool
2007-04-17 19:39:37 +00:00
813233242b
small change of findcluster_pygre.py
2007-04-17 15:25:23 +00:00
240801fecf
small change of parameters
2007-04-16 19:13:27 +00:00
d533ed82e1
change for upload tool: keep the original format of the file
2007-04-16 15:37:49 +00:00
f2bf096005
add a new section and a new tool, find-cluster
2007-04-13 21:08:22 +00:00
af5615424f
add a new section, pattern-matching, and a new tool, find-cluster
2007-04-13 21:04:32 +00:00
192f2af527
Made necessary modifications to /lib/galaxy/tools/__init__.py and added the test input and output files for "Display customtrack at UCSC" tool.
2007-04-13 15:58:39 +00:00
012e460482
Adding tool "Display customtracks at UCSC" under Graph/Display data tab. I've added new param attributes called repeat (to repeat the param a certain number of times) and condition (to display or not display the param) and have added dynamic_options for type "data" in order to facilitate multiple data selection. These changes required certain modifications in the framework (/lib/galaxy/tools/__init__.py and parameters.py , /lib/galaxy/datatypes/interval.py and in templates/tool_form.tmpl). I ran functional tests and found no errors in any of the tools due to these modifications. There were the usual assertion errors and database errors.
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Modified get_flanks.py and get_flanks.xml files. Better exception handling and tool tips.
Also moved GMAJ and LAJ tools to Graph/Display data section.
2007-04-12 16:52:39 +00:00
027b85f612
Add Gene bed and maf to fasta tool.
2007-04-10 16:11:04 +00:00
c2d1d0189f
Some corrections for tracking referrals. Eliminated the referer column from the event table as it is not needed.
2007-04-10 16:07:53 +00:00
d3553be251
Requires db schema change. Changes to allow for tracking of referrals.
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Database changes required:
alter table galaxy_session add referer varchar(255);
alter table event add referer varchar(255);
2007-04-06 18:56:13 +00:00
3927948418
Fix for uploading interval files which lack a strand column.
2007-04-06 15:04:07 +00:00
323041dba0
HYPHY nj tree builder now also makes species-only-labeled trees as well
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as others.
2007-04-06 13:58:24 +00:00
bddbe4a68b
Update the description of Aggregate datapoints based on the changes of the output.
2007-04-06 13:45:03 +00:00
18b25d241f
Corrected behavior of upload tool under 2 conditions: 1) if user clicks execute button with no posted data or URL and 2) if user uploads an empty file.
2007-04-05 19:57:58 +00:00
6ea6c7bad1
Fix some tiny bugs in the xml file of tool Aggregate datapoints.
2007-04-05 19:34:28 +00:00
3b0852ee01
Add a tool to select maf blocks by number.
2007-04-05 18:26:44 +00:00
baacb7c67c
Enhanced security measures for condition entered as free text - should make tool more useful and reduce job errors.
2007-04-05 18:24:47 +00:00
fe136cdefa
Add tool to compute maf alignment coverage.
2007-04-05 17:57:16 +00:00
ab8bef0acc
change cf_maf_limit_to_species.dat
2007-04-05 15:39:59 +00:00
6d7d82cd93
Add a tool to allow filtering by MAF block size.
2007-04-05 14:55:05 +00:00
f8cd6433d2
Clean up comment.
2007-04-04 15:57:44 +00:00
5f1b12b56e
Add neighbor joining tree building via HYPHY.
2007-04-04 15:44:37 +00:00
Yi Zhang