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2,488 Commits 72 Branches 243 Tags
4e6b7d1cffe90d801ddfab91ebad6d516886d699
Commit Graph
121 Commits
Author SHA1 Message Date
Greg Von Kuster 0090622f59 Add ability to share histories with multiple users, along with bug fixes and more functional test coverage for history features. 2009-06-05 11:15:25 -04:00
Greg Von Kuster e608f904ee Add tool config for GrameneMart data source. 2009-05-27 14:19:59 -04:00
Guruprasad Anada 24293166da MAQ mapping pipeline for SOLiD data 2009-05-13 21:54:45 -04:00
Guruprasad Anada 4f1a6fe60f Added SOLiD tool section with QC tools. 2009-05-05 22:44:30 -04:00
Anton Nekrutenko 7b5136a4c0 Changed taxonomyu to metagenomics 2009-03-02 14:52:59 -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 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
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
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
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
Greg Von Kuster 051a78bc39 Add new tool config for flymine production server. 2009-01-13 10:55:08 -05:00
Greg Von Kuster 42ca95a373 Enhance the tool panel, now supports following tags: 
<toolbox>
    <tool file="data_source/upload.xml"/>            # tools outside sections
    <label text="Basic Tools" id="basic_tools" />    # labels outside sections
    <workflow id="529fd61ab1c6cc36" />               # workflows outside sections
    <section name="Get Data" id="getext">            # sections
        <tool file="data_source/biomart.xml" />      # tools inside sections
        <label text="In Section" id="in_section" />  # labels inside sections
        <workflow id="adb5f5c93f827949" />           # workflows inside sections
    </section>
</toolbox>
 2008-12-18 16:35:26 -05:00
Greg Von Kuster dfd5e9827f Rename gbrowse_elegans to wormbase_test, add a config for the wormbase production server. 2008-12-15 10:37:39 -05:00
Greg Von Kuster 7b49309886 Add new EpiGRAPH tools that point to EpiGRAPH production server. 2008-10-28 11:27:42 -04:00
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
Greg Von Kuster b3b6c54247 Use only 1 underlying executable ( data_source.py ) for data source tools. A new tag set is added to the data source tool configs to handle tranlsation of request param names sent by remote apps ( something like <param_trans galaxy_name="dbkey" remote_name="GENOME" missing="?" /> ). 2008-10-07 15:21:46 -04:00
Greg Von Kuster c05f66d5ee Treat EpiGRAPH as a data source much like ucsc table browser. 2008-10-06 13:34:51 -04:00
Guruprasad Anada 0f1130e84a Adding tools to fetch microsatellites and estimate their mutabilities. 2008-09-24 18:20:39 -04:00
Greg Von Kuster b4890c1bbb Integrate with intermine ( data source ) and epigraph ( data destination ). Receiving data from epigraph coming soon. Data is sent to epigraph using a combination of DATA_URL and REDIRECT_URL tool params. This tool creates jobs, but does not queue them for execution. 2008-09-22 10:36:34 -04:00
Guruprasad Anada e2f4f46a75 Adding tools to compute Substitution rates. 2008-09-21 17:36:28 -04:00
Guruprasad Anada cb74e79f21 Adding a new set of toolss to perform multiple linear regression analysis. 2008-09-20 18:14:24 -04:00
Wen-Yu Chung 07118387a1 Fix a bug in shrimp_wrapper and add a tool for splitting paired-end reads. 
Update datatype/fastqsolexa so the number of sequences is correct.
 2008-09-19 12:02:13 -04:00
Guruprasad Anada 6b68878aec Forgot to update tool_conf.sample with the new tool details. 2008-09-17 17:14:59 -04:00
Wen-Yu Chung bca6ad57e1 add SHRiMP mapper for short reads analysis. 2008-09-15 15:04:41 -04:00
Anton Nekrutenko 74d5327978 Lastz with additional short read changes 2008-09-12 15:14:20 -04:00
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 051dc9ca94 A bit of cleanup, added FASTQ to FASTA converted to tool_conf.xml.sample. 2008-05-27 19:59:33 +00:00
Greg Von Kuster c32f87624f Added code for integration with C. Elegans / GBrowse test server. 2008-05-12 18:55:48 +00:00
Greg Von Kuster 185b4353c2 Deleted findcluster_mysql tool code. 2008-05-01 17:44:56 +00:00
Anton Nekrutenko a3ee9be735 More clean up and modification of FASTA tools 2008-04-29 14:36:04 +00:00
Greg Von Kuster 5657e61320 Misc tool cleanup: eliminated all references to python2.3 / python2.4, imported galaxy eggs in several missed tools. Commented Pattern Matching tool section from tool_conf.xml.sample since tool is not functional. Added job runner info for short read tools in universe_wsgi.ini.sample. 2008-04-25 13:04:55 +00:00
Daniel Blankenberg 7f89a78f35 Add tool for profiling locally cached annotations from the UCSC table browser. 2008-04-09 17:34:35 +00:00
Wen-Yu Chung b8265695d2 add a new tool (poisson2test) with funcitonal test data to taxonomy section. 2008-04-08 15:05:43 +00:00
Wen-Yu Chung 67986d25f6 sorry, hit the wrong button (want to click cancel but click ok instead). 
add two tools and functional test data for short reads.
update tool_conf.xml.sample.
 2008-03-31 19:29:00 +00:00
Wen-Yu Chung 163e4bc200 2008-03-31 19:24:56 +00:00
Wen-Yu Chung 598462643a update ucsc builds.txt. now blat tool should pass functional test. 
also update boxplot config file.
 2008-03-28 16:07:00 +00:00
Wen-Yu Chung 9adee0844d update short reads tools. add functional test data. 2008-03-27 22:11:18 +00:00
Daniel Blankenberg 3025531e0b Add a tool that allows species based concatenation of FASTA files. Useful for manipulating the results of MAF to FASTA conversion or stitching. 
This does not work on the results of the Extract Genomic DNA tool, since it uses a different header style.
 2008-03-27 17:58:47 +00:00
Anton Nekrutenko 41769817da more tax fixes 2008-03-21 15:15:11 +00:00
Anton Nekrutenko 2d14d029ea Added taxonomy to tool_comf.xml.sample 2008-03-20 19:54:32 +00:00
Guruprasad Anada 89bb493d3c Adding new tool to estimate insertion and deletion rates from 3-way alignments. 
Also, modified 'Fetch Indels' tool.
 2008-03-13 16:21:39 +00:00
Guruprasad Anada b032b71bc0 Adding tool to fetch closest upstream and downstream features for a given set of intervals. 
Added: Tool xml and py files, test data.
Modified: tool_conf.xml.sample.
 2008-03-05 20:08:01 +00:00
Greg Von Kuster 135c9a0377 Removed the remainder of the tool version subdirectories. 2008-03-03 18:38:57 +00:00
Greg Von Kuster 4dd1f044e1 Removed tool version directiories for some of the tools...the rest soon. 2008-03-03 16:14:06 +00:00
Greg Von Kuster 335ebef0af Restored version 1.1.0 of aggregate scores tool and moved the fixes to version 1.1.1. 2008-02-28 00:08:05 +00:00
Wen-Yu Chung 5b4e5a772b modify data structure used in short read tools. 
update functional test data.
 2008-02-25 18:42:39 +00:00
Anton Nekrutenko f607e77b6a Tool for changing case 2008-02-25 15:15:18 +00:00