Ross Lazarus
142c1c53c3
rg LD tool fixes
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rgHaploView.xml
path to haploview.jar in ${GALAXY_DATA_LIBRARY_FOLDER}/shared/jars
no need to separate rs with X in test
rgHaploView.py
fixes to map generation depending on whether a region or a list of rs has been supplied
repairs to tests and test output (re) generators
Regenerated all test output files since now changed slightly.
For the record, this was done as follows
using the supplied rgenetics utility test harness shell script
Be warned that rgtest.sh will recreate test outputs for all tools
# use rgtest_one_tool.sh
# 3 parameters: toolID, testsrc galaxy root, testout galaxy root
# first, test the tool to a neutral output directory
sudo sh tools/rgenetics/rgtest_one_tool.sh rgHaploView /opt/galaxy /tmp
# check contents
diff -r /opt/galaxy/test-data/rgtestouts/rgHaploView/* /tmp/test-data/rgtestouts/rgHaploView/*
# do it for real
sudo sh tools/rgenetics/rgtest_one_tool.sh rgHaploView /opt/galaxy /opt/galaxy
2010-09-06 17:00:16 -04:00
Dannon Baker
557396488e
Fix typo in Compute Motifs Frequency tool blurb.
2010-09-03 13:39:21 -04:00
Daniel Blankenberg
ebf8923704
Fix for tools/filters/wig_to_bigwig.xml when coordinates extend beyond chromosome boundaries and -clip was specified.
2010-09-01 19:26:25 -04:00
Daniel Blankenberg
e0b1f36bcd
Add a wig to bigWig converter tool.
2010-09-01 17:15:08 -04:00
Jeremy Goecks
a4d32927a9
Improved error checking for condition provided to tool 'gff_filter_by_feature_count.
2010-09-01 16:35:40 -04:00
Kelly Vincent
33bd292e41
Added BAM-to-SAM tool
2010-09-01 09:44:12 -04:00
Jeremy Goecks
e3dcfc89a7
Fix filenames problem in 'extract genomic dna' GFF functional tests that was introduced in 4200:291183d3896b .
2010-09-01 09:10:58 -04:00
Ross Lazarus
3c5e0416ca
Another small tweak - no idea what combination of plink and other dependencies
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will have on lines_diff at other sites...but buildbot seems fussy
Still missing scipy and haploview seems unhappy too.
2010-08-31 23:51:30 -04:00
Ross Lazarus
020333d1c1
Tweaks to lines_diff in 2 rg tests to account for different versions of R and plink
2010-08-31 20:30:08 -04:00
Ross Lazarus
ce431fd970
Fix for pdfnup blathering to stdout causing buildbot to barf
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Small adjustment to file size delta for rgManQQ
2010-08-31 08:25:44 -04:00
Ross Lazarus
1fe808274d
Fixes to some rgenetics tests and test outputs
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Some odd bugs in the new version of ggplot2 in R
Fixes to the Rrun function in rgutils
2010-08-31 02:27:33 -04:00
Kelly Vincent
6d2b2acf1b
Issue #380 : Properly handle -n and -v options in Bowtie
2010-08-31 01:04:32 -04:00
Jeremy Goecks
32b39c3805
Fix typo that prevented gff_filter_by_feature_count tool's output from being set correctly.
2010-08-27 12:54:00 -04:00
Kanwei Li
4f291405f6
trackster: Overview track, viz cloning, "Go-to" specific location, UI fixes
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- Each track now has an Overview checkbox that will set the initial chromosome-wide view of that track to become the overview
- Visualizations that users own or are shared with can now be cloned
- Go-to feature lets users go directly to a certain chrom (eg "chr1"), or chrom and position ("chr1:1-100,000,000")
- Fix double flushing when creating converter
- Line tracks display mode is now inline
- Use smaller font for tracks
- Fix web-kit bug where using scrollbar would also trigger viewport dragging
- Fix Line tracks jumping around when changing position
- Made default Line track height 80px from 100px
- Fix drag-zoom overlay appearing at top of header instead of Label track
- Minor grid refactoring
2010-08-26 12:12:32 -04:00
Jeremy Goecks
bcc1e7b76c
Add tool 'gff_filter_by_feature_count', create 'GFF' subheading under Tool Menu's Filter category for GFF filtering tools, and rename 'gff_filtering' tool 'gff_filter_by_attribute.'
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gff_filter_by_feature_count tool filters a GFF file using conditions based on transcripts' features counts; for example, it is possible to filter for transcripts that have a minimum number of exons or transcripts that have 3' UTRs.
Added GFF subheading to Tool Menu under Filtering and placed all GFF filtering tools under this heading.
2010-08-26 12:00:41 -04:00
Kelly Vincent
531c100548
Removing accidentally leftover test line from Tophat wrapper
2010-08-26 10:29:31 -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
Ramkrishna Chakrabarty
2c675b3743
Bug fixes and basic zoom feature for mutation viz tool
2010-08-25 16:47:39 -04:00
Ramkrishna Chakrabarty
c28eeafbd0
(no commit message)
2010-08-25 16:46:09 -04:00
Kelly Vincent
5e1ad9dc3b
Fixed another bug in column join so it will handle filling empty columns properly
2010-08-20 17:04:16 -04:00
Kelly Vincent
630211c330
Updated column join to handle situation when last column is a join column and a row is missing that column
2010-08-20 14:40:39 -04:00
Kelly Vincent
f6a3996d9b
Adding SRMA wrapper and all associated test files and index loc sample
2010-08-19 18:17:31 -04:00
Kanwei Li
2b7726fb02
Don't pipe errors for compute_q_values to a file so we can find out what the error is
2010-08-19 17:03:54 -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
Daniel Blankenberg
94c7417f37
Add BFAST Mapper tool and wrapper.
2010-08-18 16:52:06 -04:00
Nate Coraor
8a66864aee
Stop ignoring the sniff order set in the datatypes config file.
2010-08-18 14:56:10 -04:00
Jeremy Goecks
7fefc3de76
Enhance 'Fetch Closest Features' tool to use GFF files and added tests for new functionality.
2010-08-18 14:19:33 -04:00
Guruprasad Anada
12b9c486ea
Adding wavelet analysis tools made by Zaky from Makova lab.
2010-08-16 18:30:37 -04:00
Daniel Blankenberg
70a68cd688
Remove UCSC tablebrowser specific parameters from modmine.xml datasource tool.
2010-08-16 09:22:40 -04:00
Ramkrishna Chakrabarty
4dd21d2119
fixed the svgfig egg problem in mutation viz tool
2010-08-13 08:49:09 -04:00
Ramkrishna Chakrabarty
37ff568432
Mutation visualization tool
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Added svgfig egg
2010-08-12 14:21:59 -04:00
Kelly Vincent
108ca6e24a
Fixed bug in column join that mishandled trailing empty columns
2010-08-12 10:38:33 -04:00
Kelly Vincent
c7f29c9d4d
Fixed bug in column join that mishandled carriage returns
2010-08-12 09:54:15 -04:00
Daniel Blankenberg
b951bdd727
Add ToolOutputActions to set dbkey for BWA wrapper and remove no longer needed code file.
2010-08-10 11:36:50 -04:00
Jeremy Goecks
240fb5933e
Enhance GFF-to-BED converter to output block data. Added test for new functionality.
2010-08-09 22:37:43 -04:00
Daniel Blankenberg
b8d82b9f35
Enhance Cut tool to keep column assignments for Interval datatypes. All interval datatypes will become base interval type if User specified columns contain chromosome, start and end columns; in addition to the 3 required columns, name and strand will be set when possible.
2010-08-09 21:06:37 -04:00
Daniel Blankenberg
f97a380a56
Add ToolOutputActions to set dbkeys for LiftOver tool and both Bowtie wrappers; remove no longer needed code files.
2010-08-09 21:06:18 -04:00
Jeremy Goecks
c0ac1065b6
Update version numbers of cufflinks and tophat to reflect new tool installations.
2010-08-05 11:20:11 -04:00
Jeremy Goecks
6d9472e9be
Improvements to the GFF filtering tool.
2010-08-04 14:35:53 -04:00
Jeremy Goecks
44c69eca99
merge
2010-08-04 14:05:22 -04:00
Jeremy Goecks
508c61f532
Update gops_intersect and gops_subtract documentation to reflect that tools can accept both BED and GFF files.
2010-08-04 14:04:37 -04:00
James Taylor
6b95a1f7fd
Automated merge with https://bitbucket.org/galaxy/galaxy-central/
2010-08-04 14:01:39 -04:00
Kanwei Li
a1f9e6a572
Support for VCFv4.0 and misc VCF fixes [Brad Chapman]
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- Support for VCFv4.0, which should be identical to 3.3 support
- Correctly handle chromosome references when they start with 'chr' (instead of just numbers)
- Handle extra empty tabs on the header line which are present in GATK produced VCF and confuse the determination of how many sample states should be parsed.
2010-08-03 10:43:32 -04:00
Jeremy Goecks
f72c32dcf7
Added AttributeValueSplitterFilter to tool select parameter filters so that GFF attributes can be read and used as tool inputs. Updated gff_filtering tool to use this filter.
2010-07-29 17:41:46 -04:00
Guruprasad Anada
d40c580de6
Modified Group tool by adding Mode function to the list of aggregate operations.
2010-07-29 12:21:09 -04:00
Kelly Vincent
cfb23b85ec
Updated indel analysis tools: fixed counting bugs in indel_analysis and improved help section; standardized CIGAR regex across tools; updated test files for several tools
2010-07-21 16:25:46 -04:00
Daniel Blankenberg
36f7bcb0c8
Modify tools contributed by Chungoo Park (cxp440@psu.edu) for Linear Discriminant Analysis, and drawing Receiver Operating Characteristic plots; add a new tool to 'Generate A Matrix for using PC and LDA'; remove redundant 'Principal Component Analysis' tool.
2010-07-16 14:52:52 -04:00
Jeremy Goecks
e96e38e527
Fix bug so that fasta identifier produced by 'extract genomic dna' tool for GFF files is consistent with GFF coordinates.
2010-07-15 17:03:14 -04:00
Ross Lazarus
57b59ce905
Fixes for rgManQQ - manhattan and qqplot generator for
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interval pvalues
New qqplot image
Fixes to fix test output generators to only provide one set of pval columns
2010-07-15 04:58:08 -04:00
Daniel Blankenberg
5461c97a7b
Update vcf_to_mafcustomtrack tool to enforce a minimum of one dataset to be selected.
2010-07-14 12:18:24 -04:00
Ross Lazarus