Greg Von Kuster
bcd6751cdf
Fix for uploading a Bam file that has not yet been sorted, the call to samtools sort has been moved from the sam_to_bam tool to the Bam()set_meta() method to ensure all Bam datasets are sorted prior to indexing. Added new functional tests to cover uploaing unsorted Bam files. Also cleaned up code in the upload tool for uploaing various binary data formats.
2009-12-07 16:04:33 -05:00
Daniel Blankenberg
f92b25d2f5
Enhance tool parameter sanitization. Sanitization rules can now be defined on a per input parameter basis. Resolves ticket #38 and #142 .
...
Sanitization now occurs as part of the InputValueWrapper logic. Previously sanitization occurred as soon as parameter values were provided by the user via form submits, causing the sanitized values to be stored in the database. Now the original user specified values are stored in the database and sanitation happens when str is called on the InputValueWrapper, i.e. during command-line generation and when generating configfiles.
Abstract out param name and value translations that are performed on data source tools. This changes some of the names of the tags used for these purposes (e.g. data_type_translation becomes value_translation) to reflect this generalization. The ToolConfigSyntax wiki page has been updated with these changes.
Future Enhancement:
Allow methods with arguments and keywords to be specified for sanitation and translation purposes.
2009-12-07 10:19:41 -05:00
Greg Von Kuster
08e0d5e532
Fixes for Bam data type's set_meta() and sam_to_bam tool, indexes will now be properly created for bam datasets. Fixes also for uploading Bam files, they will no longer be uncompressed on upload.
2009-12-04 19:51:46 -05:00
Greg Von Kuster
0e807f13f5
Add support for uploading BAM files.
2009-12-02 20:02:05 -05:00
Greg Von Kuster
20628e8381
First pass of the lastz tool wrapper that includes job splitting - works but needs polishing.
2009-11-27 10:53:50 -05:00
Greg Von Kuster
f5bf037191
Rename test files for taxonomy tools and set ftype for test's input datasets.
2009-11-20 15:35:30 -05:00
Ramkrishna Chakrabarty
702bad5d25
Added sff datatype
...
Also, made changes to upload.py to sniff sff binary files
2009-11-11 17:55:08 -05:00
Nate Coraor
7788be89ec
Update rg test data sample outputs to match the new versions Ross uploaded
2009-11-02 16:52:32 -05:00
Ross Lazarus
f471c7f0fe
updated rgenetics test files
2009-10-29 17:57:30 -04:00
Greg Von Kuster
9f6ceaef1c
Fixes and new functional tests for uploading multi-byte character files and fixes for displaying multi-byte character dataset peek.
2009-10-15 20:10:32 -04:00
Greg Von Kuster
98dc18756f
Add 2 rgenetics test files I missed for testing uploading composite data types.
2009-10-13 18:15:06 -04:00
Greg Von Kuster
f77e0e03f4
Add new functional tests for uploading composite data types lped and pbed - handles ticket # 173.
2009-10-13 16:37:20 -04:00
Kelly Vincent
7263afac9f
Added fastq (generic) datatype and deleted fastqsolexa datatype
2009-10-07 12:43:15 -04:00
Nate Coraor
87db3952d3
Real Job(tm) support for the library upload tool. Does not include iframe upload for the library side yet.
2009-09-25 14:36:12 -04:00
Kelly Vincent
52b8b0b667
Modified sort tool to fix backwards compatibility. Reverted catWrapper tool back to old version before recent changes (for backwards compatibility).
2009-09-24 13:54:12 -04:00
Kelly Vincent
eecf0af42b
Modified Concatenate queries tool to have two base files to concatenate and the option to add a third or more. Also removed to unnecessary sort1 test files.
2009-09-22 10:09:23 -04:00
Anton Nekrutenko
61c7d63087
Added pileup parser. Pardon the perl = used to its regexes too much
2009-09-04 10:23:37 -04:00
Kelly Vincent
6044060890
Added two new datatypes (sam and bam) and an associated test
2009-08-19 09:13:21 -04:00
Kelly Vincent
3bbac86312
Added fastqsanger data format and required bwa_wrapper to take only that format as input
2009-07-30 12:06:24 -04:00
Greg Von Kuster
2b6f2c946a
Fixes and functional tests for uploading directories of files from both the Admin view and the Libraries view ( requires new config setting ).
...
In addition to the config setting "library_import_dir" for the Admin view, the new config setting "user_library_import_dir" for the Libraries view will allow non-amin users to upload a directory of files.
The configured directory must contain sub-directories named the same as the non-admin user's Galaxy login ( email ). The non-admin user is restricted to uploading files or sub-directories of files contained in their directoy.
2009-06-16 09:55:15 -04:00
Guruprasad Anada
c072bd4b4a
Added functional tests for testing sniffing and metadata settings of qual454 and qualsolid datatypes.
2009-04-29 16:32:23 -04:00
Anton Nekrutenko
8e6f06d30b
restoring original files
2009-02-10 11:54:53 -05:00
Anton Nekrutenko
8624d6c974
Usability tweak for catWrapper
2009-02-10 11:01:54 -05:00
Wen-Yu Chung
05513833f5
fix for short read score distribution tool. restore test data. passed functional tests in scofield
2008-12-19 14:28:09 -05:00
Wen-Yu Chung
b31191d4bd
fix for short read score distribution tool. restore test data.
2008-12-19 14:25:43 -05:00
Wen-Yu Chung
1da324ffb5
fixed for short read build distribution tool. remove unused arrays.
2008-12-19 12:28:02 -05:00
Wen-Yu Chung
170f9d2d77
fixed for short read build distribution tool. remove unused arrays. also update test data output.
2008-12-19 12:25:52 -05:00
Greg Von Kuster
a8cd7a9118
Streamline the process of adding datasets to a library and then updating roles and permissions on them, improve admin GUI flow, more functional tests.
2008-11-18 17:10:16 -05:00
Greg Von Kuster
5331dee076
Add functioal test baseline support for the repeat construct, more work needed ( e.g., multiple repeat elements, refresh_on_change when the input to be refreshed is within a repeat construct ). Added functional tests for some tools that use this construct.
2008-11-10 14:22:01 -05:00
Wen-Yu Chung
0021c40c85
add shrimp_color_space mapping tool with functional test data.
...
add a new datatype called csfasta.
2008-10-13 15:06:42 -04:00
Anton Nekrutenko
f8915c416f
Forgot two test datasets
2008-09-14 14:58:50 -04:00
Guruprasad Anada
4c520e8ce2
Rewrote "convert delimiters to tab" tool in python.
...
Modified "Concatenate queries tail-to-head" tool to include multiple queries.
2008-07-02 19:43:08 +00:00
Greg Von Kuster
666de20b4d
Cleanup for fastqsolexa data type converters. We are currently supporting only the Solexa variant and will add support for other variants when the formats stabilize.
2008-06-09 20:15:04 +00:00
Greg Von Kuster
1a23f9e55d
Requires config modification - Add Fastq sniffer, add support for fastqsolexa data type, rename convert_fatsq2fasta tool to be fastq_to_fasta_qual, add functional tests for both fastq and fastqsolexa data types, misc code cleanup.
2008-05-29 19:12:36 +00:00
Greg Von Kuster
57fe2ba4b0
Cleaned up lav_to_bed a bit, added functional test. Removed old, unused tools from the ~/tools/filter directory.
2008-05-28 19:26:42 +00:00
Greg Von Kuster
f7806342fc
Requires change to Galaxy config - fixed the way the File Format select list in the upload tool is dynamically generated, now retrieved from the upload_file_formats in app.registry.
...
Fixed all references to 'qualityscore' file extensions to be 'qual', since that is the extension in the QualityScore class.
Added functional test to the fastq2fasta converter.
2008-05-28 16:01:29 +00:00
Wen-Yu Chung
50e24553ae
generate png file instead of pdf file in short read distribution tool.
...
add a fastq converting tool.
2008-05-27 18:51:34 +00:00
Wen-Yu Chung
bf61fee03f
update functional test for short read tools that generate pdf output.
2008-04-04 14:59:45 +00:00
Greg Von Kuster
1580ed8260
Functional tests will now properly handle output datasets in pdf format. Added functional tests for histogram and scatterplot. Fixed a bug where temporary files was not removed if functional test failed.
2008-04-04 14:45:29 +00:00
Wen-Yu Chung
9adee0844d
update short reads tools. add functional test data.
2008-03-27 22:11:18 +00:00
Wen-Yu Chung
78802fa73b
add scripts for preparing nt and wgs databases.
...
update blastdb location file, wgs is available now.
2008-03-27 17:41:40 +00:00
Wen-Yu Chung
5ba3755ad6
add functional test data for megablast xml parser.
...
the functional test is failed due to unknown reasons.
2008-03-25 22:09:54 +00:00
Anton Nekrutenko
a262ac1754
Finalizing taxonomy. Removed taxonomy processing from scripts. This does not require sqlite anymore. Script for fetching taxonomy now uses flat files directly and is much faster
2008-03-20 19:38:31 +00:00
Anton Nekrutenko
d25b346130
Changes to taxonomy fetches and two new datatypes: taxonomy and newick
2008-03-04 20:30:26 +00:00
Anton Nekrutenko
9dca050a79
Fisrt pass on taxonomic rank fetcher
2008-03-03 19:40:36 +00:00
Greg Von Kuster
71f25a7bfa
Fixes for bed_to_gff_converter.
2008-01-28 15:27:33 +00:00
Daniel Blankenberg
02a078da82
Decrease size of gops cluster test data.
2008-01-16 20:21:07 +00:00
Wen-Yu Chung
9f0f822deb
add a section: metagenomics
...
tools for running phred(need to change path later), trim sequence, generate boxplot and an array of length of the reads.
test data are added.
trim sequence and array of length passed functional test.
phred (2 ouput files) and boxplot (pdf file) didn't pass functional test yet.
2008-01-09 20:41:59 +00:00
Greg Von Kuster
8b0fe490b1
Reverting the test data for the gops_cluster tool to that which was originally used by Ian in rev 1636.
2008-01-07 13:02:10 +00:00
Greg Von Kuster
59416716eb
Deleted a huge emboss test data file that is not needed. Added binary, zipped and gzipped test data files.
2007-12-20 17:43:05 +00:00
Greg Von Kuster