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114 Commits
Author SHA1 Message Date
Dave Bouvier 448d9f55eb Migrate 43 tools from the distribution to the tool shed. 2014-01-27 09:53:14 -05:00
Dave Bouvier 9402faf4fc Remove files from test-data that are not referenced in any tool test definition or functional test script. 2014-01-08 14:15:53 -05:00
Dave Bouvier bb25625d31 Restore files that were deleted due to a tool migration, but are still used in test/functiona/test_get_data.py. 2013-11-13 10:46:38 -05:00
Ross Lazarus c860c25f77 Remove unused test-data/rtestouts 
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
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
Jeremy Goecks ea8d337316 Add parameter to filtering tool to optionally skip header lines. Add test for new parameter usage as well. 2013-01-29 10:37:16 -05:00
Jeremy Goecks 9719bed6f9 Enable BedGraph to be used as input to wig-to-bigwig tool. 2013-01-24 17:06:51 -05:00
Dannon Baker 0b2e939d4d Remove blast tools and test data from the distribution, update tool_conf.xml.sample to reflect this. 2012-08-22 16:12:59 -04:00
Greg Von Kuster fb1f65a057 Eliminate teh emboss 5 functional test output data since it is now available in the emboss_5 repository in the tool shed. 2012-03-21 16:41:45 -04:00
Kanwei Li c0a1b39214 Add missing test files 2011-06-10 20:10:09 -04:00
Kanwei Li 34155271b3 [Peter Cock] Filtering tool: Only cast used columns. Fix valid lines and skipped info lines. [Kanwei] Add new testcases to test this behavior. Fixes #537. Fixes #535 2011-05-27 10:47:17 +02:00
Ross Lazarus 7859f56954 reverting reorder test outputs - PhiX reference used to generate them seems different from that on the buildbot 2011-05-13 21:24:03 -04:00
Ross Lazarus 5e25812f6f finally have picard reorder tests working 2011-05-13 17:12:19 -04:00
Kanwei Li af3f4a2ff9 More BLAST tests 2011-04-06 12:38:00 -04:00
Nate Coraor d765f607c4 Slight output difference on the buildbot for weblogo, hopefully the difference is static. 2011-03-23 16:42:14 -04:00
Greg Von Kuster 8ba7de4c8b Improved checking to determine if a bam file is sorted. If the version of samtools being used is 0.1.13 or newer, determination of bam sorting is now much more robust. Add a new functional test to the test_library_features script that tests uploading a library_dataset (where the file is an unsorted bam file) using a combination of 'upload_paths' and 'link_to_files'. Rename the test-data file previously named 3.bam to now be named 3unsorted.bam to clarify that it is an unsorted bam file. 2011-03-23 12:18:57 -04:00
Ross Lazarus 6646cfa80d Adding two new tool wrappers and tests - clustalw (http://www.clustal.org) for multiple alignments and a sequence motif generator based on weblogo3 (http://weblogo.berkeley.edu) which works on fasta files such as alignments from clustalw 2011-03-22 14:08:32 -04:00
Nate Coraor ea0e8ead22 Fix the qual_stats_boxplot and quality_score_distribution tests again, hopefully 2011-03-02 13:46:07 -05:00
Kelly Vincent 7d0ff14df9 Converted several tools to data table style of loc file handling (Bowtie, BWA, Lastz, Megablast, PerM, SRMA). Cleaned up several tool XML files, removing unnecessary None parameters. 2010-11-08 00:10:13 -05:00
Jeremy Goecks ccf07c72aa Enable filter tool to operate correctly on files with a variable number of columns (such as SAM files). Tool prepares and processes only columns up to and including the right-most column (i.e. column with the largest index) in the filtering condition, and subsequent columns are ignored. New functional test added for this functionality as well. 2010-11-04 16:30:34 -04:00
Nate Coraor dd09a19fc2 Updated test outputs for pdf/image output tools that differ slightly on updated dependencies. 2010-09-29 17:25:31 -04:00
Nate Coraor 8e05ce7817 Add test for bz2 file upload 2010-09-10 14:17:05 -04:00
Kelly Vincent 3b12bb72e9 Fixing buildbot tests: added missing column join test files; regenerated and enhanced BWA test files; sorted tophat_out1.sam and specified sort=True in test for it 2010-08-25 21:51:41 -04:00
Greg Von Kuster a7e30c4441 Apply patch from Brad Chapman providing support for detecting, uploading and displaying UCSC bigWig and bigBed. Add new functional tests for uploading and detecting bigbed and bigwig formats, and correct and clean up the test_get_data.py functional test script. 2010-08-19 13:58:10 -04:00
Nate Coraor 6e7427e8e2 Removed binseq.zip test and replace it with a zip test. 2010-07-01 08:59:26 -04:00
Jeremy Goecks eed5d297c3 Add GFF support to GOPS subtract tool and updated functional tests. Using the GFF-->BED converter is lossy as GFF has more attributes/features than BED, so it's necessary to directly support GFF. Basic approach used is to modify interval coordinates during reading and writing while not changing the middle, computational steps; this approach can be used to provide GFF support for any tool that uses bx-python to operate on intervals. 2010-06-07 16:28:46 -04:00
Daniel Blankenberg 183c2d3d13 Bug fix for handling 'spaces to tab' for non-binary composite datatype files. 
Add upload tests for testing 'space to tab' when uploading composite and non-composite datatypes.
 2010-06-07 15:34:20 -04:00
Ross Lazarus aae3898b4f Adding rg test outputs and updated tools 2010-03-26 14:42:15 -04:00
Kelly Vincent 710e9cfd07 Added new tabular/pileup join tool and associated test files. Also added pileup datatype. 2010-03-26 12:00:55 -04:00
Kelly Vincent 09fa3f0bf1 Updated Bowtie test files to handle new version (0.12.3) of Bowtie (bowtie_color_wrapper will fail until new version installed). Updated samtools tools test files. Removed version references from Bowtie and BWA tools. 2010-02-24 07:11:43 -05:00
Daniel Blankenberg 8082c6f36f Add a new FASTQ tool suite. Four FASTQ variants are supported: sanger, illumina, solexa and solid. 
Tools include:
	FASTQ Groomer convert between various FASTQ quality formats
	Combine FASTA and QUAL into FASTQ
	FASTQ joiner on paired end reads
	FASTQ splitter on joined paired end reads
	FASTQ to FASTA converter
	FASTQ Summary Statistics by column
	Filter FASTQ reads by quality score and length
	FASTQ Trimmer by column
	Manipulate FASTQ reads on various attributes
	Boxplot of quality statistics (Generic, with outliers)
 2010-02-23 16:48:07 -05:00
Greg Von Kuster 72e7836cbb Enhance functional test framework so that a boolean form field ( checkbox ) can have a false value ( be unchecked ). Add a 2nd test to gops_concat that uses this behavior. 2010-02-17 11:07:08 -05:00
Guruprasad Anada fb9147e83d Fixed functional tests for short_reads_figure_score tool. 2010-01-08 11:28:37 -05:00
Greg Von Kuster aa36d79d30 Update the output datasets for functional test for the quality_score_distribution tool due to a new version of R - update tool version as well. 2009-12-10 10:56:01 -05:00
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