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Author SHA1 Message Date
Guruprasad Anada 45cffbb8ed Added a new tool set for performing multivariate statistical analyses 2010-03-04 11:48:10 -05:00
Jeremy Goecks a6a86d0085 Provide minimum width for columns in published items grids so that tags/annotations do not squish other columns too much. 2010-03-03 17:05:56 -05:00
Greg Von Kuster dfe5db6cd1 Fix for sharing histories that include restricted datasets. 2010-03-03 17:00:50 -05:00
Kelly Vincent 7403f4301b Updated Bowtie wrapper for new fastqcssanger datatype, and added equCab2 to builds.txt so sam_to_bam and sam_pileup will pass 2010-03-03 15:37:43 -05:00
Daniel Blankenberg 1b973215f3 Update tool_conf.xml.main to use the new FASTQ tools. Minor updates to help text for a few of the FASTQ tools. 2010-03-03 15:18:09 -05:00
Daniel Blankenberg b0f458bf16 Changes for some FASTQ tools. Move several options of the Groomer tool under an advanced options conditional. Update help for groomer, filter and manipulation tools. 2010-03-03 14:34:31 -05:00
Daniel Blankenberg e835df2063 Enhance change_format tag of tool outputs to allow the use of Grouping Constructs. Objects can be accessed using the previously accepted bare name or using the same style as used within templates (e.g. the tool command tag). 
e.g.

  <outputs>
    <data name="output_file" format="fastqsanger">
      <change_format>
        <when input="input_type" value="cssanger" format="fastqcssanger" />
        <when input="options_type.output_type" value="solexa" format="fastqsolexa" />
        <when input="options_type.output_type" value="illumina" format="fastqillumina" />
        <when input="options_type.output_type" value="sanger" format="fastqsanger" />
        <when input="options_type.output_type" value="cssanger" format="fastqcssanger" />
      </change_format>
    </data>
  </outputs>

or

  <outputs>
    <data name="output_file" format="fastqsanger">
      <change_format>
        <when input="$input_type" value="cssanger" format="fastqcssanger" />
        <when input="${options_type.output_type}" value="solexa" format="fastqsolexa" />
        <when input="${options_type.output_type}" value="illumina" format="fastqillumina" />
        <when input="${options_type.output_type}" value="sanger" format="fastqsanger" />
        <when input="${options_type.output_type}" value="cssanger" format="fastqcssanger" />
      </change_format>
    </data>
  </outputs>

where 'options_type' is the name of the grouping parameter and 'output_type' is the name of a parameter found in this group and 'input_type' is the name of a parameter not found within a group.
 2010-03-03 14:30:32 -05:00
Ramkrishna Chakrabarty 9f28113081 Fixed broken functional tests 2010-03-03 13:51:29 -05:00
Greg Von Kuster 527e00dcd7 Error conditions will skip lines instead of stopping the tool for the lastz paired reads, and clean up the tool pages for both lastz tools. 2010-03-03 13:40:26 -05:00
Ramkrishna Chakrabarty 1e2bcf90f1 lims: 
- Fixed a bug in saving the data folder for dataset transfer
- UI tweaks
- renamed request state 'Submitted' to 'In Progress'
 2010-03-03 12:07:39 -05:00
Greg Von Kuster 6b67729784 First pass of the new lastz paired reads tool. Tool page help and info needs to be corrected for this version of the tool. 2010-03-02 16:40:40 -05:00
Anton Nekrutenko 175c63e0fd Modifications to pileup_parser 2010-03-02 16:35:21 -05:00
Nate Coraor 1391119d56 Fix SGE bug reported in issue #281 2010-03-02 13:20:47 -05:00
Jeremy Goecks 43d65adf35 Fix comment and indentation. 2010-03-02 12:32:44 -05:00
Nate Coraor 4a0c9b3175 I am having a bad day 2010-03-02 12:10:43 -05:00
Nate Coraor 1b8bcabd1e pbs_python 2.9.8 doesn't work 2010-03-02 12:08:01 -05:00
Nate Coraor 9b912184d0 Scratch that, just upgrade pbs_python instead 2010-03-02 11:52:16 -05:00
Nate Coraor a0bd85dbb3 Use the old method for fixing pbs_python's version 2010-03-02 11:37:55 -05:00
Jeremy Goecks 7f418fa411 Fix bug that prevents new Galaxy visitors from viewing an accessible/published workflow. Viewing an accessible/published workflow requires a history because rendering parameters require a history, so a history is now created for visitors that do not already have one. 2010-03-02 11:17:05 -05:00
Daniel Blankenberg a19ae79b85 Change color space FASTA file type from fastqsolid to fastqcssanger. 
Cripple accepted tool input formats for many of the FASTQ tools to only allow only fastqsanger and fastqcssanger to be used.
 2010-03-02 10:47:23 -05:00
Jeremy Goecks fa9367ed72 Fix bug that prevented tags with capital letters from being deleted. 2010-03-02 09:51:05 -05:00
Nate Coraor 9a8c5f6711 psycopg2 scramble fix 2010-03-02 00:38:57 -05:00
James Taylor 31a4f80604 [mq] workflow-invocation: Track workflow invocations in database, provide a view of the history grouped by workflow and job 2010-02-11 00:17:04 -05:00
Kanwei Li ab11e28bce Fix uploads not working 2010-03-01 17:47:28 -05:00
Greg Von Kuster 3aa2fc3601 Passwords are no longer changed ( sanitized ) as part of processing the request. Enhanced functional tests to cover the scenario where passwords include chars that break in sanitization. 2010-03-01 16:07:54 -05:00
Nate Coraor 2db1dbc5a9 update GeneTrack egg 2010-03-01 16:00:26 -05:00
Nate Coraor 006716f53a Egg support overhaul, introduces a number of fixes to the ABI recognition, better build scripts, a rewrite of the eggs library and eliminition of the need for python -ES 2010-03-01 15:41:30 -05:00
James Taylor a33a746dd8 UI tweaks 2010-03-01 13:30:37 -05:00
James Taylor a5f6a3dfb0 Page editor: use Galaxy styles for drop downs in menubar 2010-03-01 12:46:54 -05:00
James Taylor 4b4178c643 Ran optipng on sprite images 2010-03-01 12:14:04 -05:00
James Taylor ae1167251e fix: menu border opacity 2010-03-01 12:09:38 -05:00
James Taylor c99f487f5f 1) Jquery 1.4 again, with fixed tooltips; 2) Style changes for history, icons and editable text areas. 2010-03-01 12:01:50 -05:00
Jeremy Goecks b1a90dc158 Clean up pages: 
-remove unused code;
-show annotation field when creating a page;
-fix bug when filtering pages by sharing status.
 2010-02-28 22:19:56 -05:00
Kelly Vincent d091640cb5 Fixed dbkey's in sam_pileup and sam_to_bam tools in tests so they will pass 2010-02-25 23:20:19 -05:00
Ramkrishna Chakrabarty 300b34494c lims: bar code related state change bug fixed 2010-02-25 14:59:43 -05:00
Nate Coraor 0bfa58679b Fix locations of cached data for tests 2010-02-25 12:27:07 -05:00
Ramkrishna Chakrabarty 3df11a4257 lims: deactivate the enter key in requests page so that the scanner can be used to enter barcodes for each sample 2010-02-25 11:28:14 -05:00
Kanwei Li d64501f412 Fix workflow bug where "Layout" changes would not be saved, and "Save and Close" did not save 2010-02-24 18:55:30 -05:00
Daniel Blankenberg 77c4785eb7 Update Combine FASTA and QUAL tool to allow the quality score file to be optional. 
When not provided, the output will be fastqsanger or fastqsolid (when a csfasta is provided) with each quality score being the maximal allowed value (93).
 2010-02-24 16:50:06 -05:00
Daniel Blankenberg f11e459fbd Update test framework to allow not setting a value for optional DataToolParameter inputs. 2010-02-24 16:48:22 -05:00
Nate Coraor 6e9996f89a Fix for set metadata tests when setting metadata externally 2010-02-24 15:54:52 -05:00
Daniel Blankenberg 1dcf92edde Move FASTA classes in galaxy_utils from fastq.py to fasta.py. 2010-02-24 11:57:35 -05:00
Ramkrishna Chakrabarty 6b45a2c1f9 lims: 
- code cleanup
- cleanup tmp files after data transfer
 2010-02-24 10:42:36 -05:00
Ramkrishna Chakrabarty dd4757f20a lims: 
- added error msg when dataset transfer is started for samples with no library
- fixed typos
- now dataset transfer does not affect sample state
- request completion logic restored.
 2010-02-24 10:04:03 -05:00
Kelly Vincent d0e44fe520 Adding missing sam_merge test files 2010-02-24 08:44:22 -05:00
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 a28313bb46 FASTQ Manupulation tool no longer considers @ when matching or translating sequence identifiers. 2010-02-23 23:17:09 -05:00
Daniel Blankenberg 4cb98d8b5f Add gnuplot requirement tag to boxplot tool. 2010-02-23 19:54:54 -05:00
Kanwei Li e555f74b3b Refactor grid_base.mako and Fixes #285 2010-02-23 17:58:44 -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