Ross Lazarus b4d4cf0f14 Updates to FastQC wrapper ...

1) improvement suggested by bwlang to pass the history file name in as the file name to fastqc so it appears in the outputs instead of the previously unhelpful internal galaxy filename
2) lack of html output from fastqc or return of non-zero error code now triggers job failure - outputs may still be there but at least it goes red.

2012-02-10 10:40:00 +11:00

..

listFiles.py

Adding rg test outputs and updated tools

2010-03-26 14:42:15 -04:00

plinkbinJZ.py

Adding rg test outputs and updated tools

2010-03-26 14:42:15 -04:00

rgCaCo.py

minor tweaks to rgCaCo.py

2011-03-27 19:50:50 -04:00

rgCaCo.xml

Revised rgenetics tools to remove post job hooks

2011-03-25 13:12:21 -04:00

rgClean.py

Adding rg test outputs and updated tools

2010-03-26 14:42:15 -04:00

rgClean.xml

Revised rgenetics tools to remove post job hooks

2011-03-25 13:12:21 -04:00

rgClustalw.py

python wrapper for clustalw tool

2011-03-23 19:14:14 -04:00

rgClustalw.xml

still having a problem with getting clustalw2 to print sequence indices - test does not cover so passes

2011-03-23 19:32:32 -04:00

rgEigPCA.py

Removed redundant code from rgEigPCA.py now that it takes a pre-converted ldindep dataset.

2010-05-20 12:41:51 -04:00

rgEigPCA.xml

Revised rgenetics tools to remove post job hooks

2011-03-25 13:12:21 -04:00

rgfakePed.py

removed python2.4 from rgfakePed.py

2011-05-16 10:03:47 -04:00

rgfakePed.xml

repairs to rgfakePed tool for generating null genotype data - since removing the _code.py trick of renaming composite file components means all of the parts (eg map and ped) acquire the default name of RgeneticsData, that's what the tool has to create - rather than sensibly named components based on the title - since only way to fix this wart is to reintroduce a bigger wart using the post execution hook, decided to just go with that default base_name to make things more sustanable in the long term

2011-05-16 09:12:19 -04:00

rgfakePhe.py

Adjust image links in tools to work with a proxy prefix [Brad Chapman]. Fixes #141

2010-12-14 14:22:13 -05:00

rgfakePhe.xml

fix for missing html ref in picard_reordersam and for data index srma_indexes in gcbias

2011-04-28 16:25:09 -04:00

rgFastQC.py

Updates to FastQC wrapper

2012-02-10 10:40:00 +11:00

rgFastQC.xml

Updates to FastQC wrapper

2012-02-10 10:40:00 +11:00

rgGLM_code.py

Revised rgenetics tools to remove post job hooks

2011-03-25 13:12:21 -04:00

rgGLM.py

Revised rgenetics tools to remove post job hooks

2011-03-25 13:12:21 -04:00

rgGLM.xml

Revised rgenetics tools to remove post job hooks

2011-03-25 13:12:21 -04:00

rgGRR.py

Fixes to some rgenetics tests and test outputs

2010-08-31 02:27:33 -04:00

rgGRR.xml

Revised rgenetics tools to remove post job hooks

2011-03-25 13:12:21 -04:00

rgGTOOL.py

Adding rg test outputs and updated tools

2010-03-26 14:42:15 -04:00

rgGTOOL.xml

Revised rgenetics tools to remove post job hooks

2011-03-25 13:12:21 -04:00

rgHaploView.py

title not alt for popups on thumbnails for Haploview outputs

2011-04-15 09:35:41 -04:00

rgHaploView.xml

rgHaploView tool version upgrade - now shows thumbnail of ld plots

2010-11-09 12:12:32 -05:00

rgLDIndep_code.py

Revised rgenetics tools to remove post job hooks

2011-03-25 13:12:21 -04:00

rgLDIndep.py

Adding rg test outputs and updated tools

2010-03-26 14:42:15 -04:00

rgLDIndep.xml

More tweaks to some snp/wga composite output test comparisons - all png/pdf should be sim_size rather than lines_diff

2010-05-20 12:38:35 -04:00

rgManQQ_code.py

Adding rg test outputs and updated tools

2010-03-26 14:42:15 -04:00

rgManQQ.py

fixes for rgManQQ plots to create a compressed PDF using GS as the downloadable artifact - much more useful for publication

2011-08-04 10:57:03 +10:00

rgManQQ.xml

fixes for rgManQQ plots to create a compressed PDF using GS as the downloadable artifact - much more useful for publication

2011-08-04 10:57:03 +10:00

rgPedSub.py

Adding rg test outputs and updated tools

2010-03-26 14:42:15 -04:00

rgPedSub.xml

Revised rgenetics tools to remove post job hooks

2011-03-25 13:12:21 -04:00

rgQC.py

Fix for pdfnup blathering to stdout causing buildbot to barf

2010-08-31 08:25:44 -04:00

rgQC.xml

Changes to allow all test outputs generated by twill to be saved to a folder pointed to by

2011-04-14 08:09:48 -04:00

rgQQ_code.py

Revised rgenetics tools to remove post job hooks

2011-03-25 13:12:21 -04:00

rgQQ.py

Adding rg test outputs and updated tools

2010-03-26 14:42:15 -04:00

rgQQ.xml

Revised rgenetics tools to remove post job hooks

2011-03-25 13:12:21 -04:00

rgRegion.py

Adding rg test outputs and updated tools

2010-03-26 14:42:15 -04:00

rgRegion.xml

fixed some configuration files

2011-04-13 21:02:06 +02:00

rgTDT.py

Revised rgenetics tools to remove post job hooks

2011-03-25 13:12:21 -04:00

rgTDT.xml

Revised rgenetics tools to remove post job hooks

2011-03-25 13:12:21 -04:00

rgtest_one_tool.sh

rg LD tool fixes

2010-09-06 17:00:16 -04:00

rgtest.sh

rg LD tool fixes

2010-09-06 17:00:16 -04:00

rgutils.py

Remove bogus makeGFF from rgutils

2011-03-25 13:26:40 -04:00

rgWebLogo3.py

WebLogo3 wrapper repair to a string format edge case. Reports are good for finding these - user hadn't reported...

2011-08-20 14:27:30 +10:00

rgWebLogo3.xml

More comprehensive error detection for weblogo installation or execution errors

2011-07-07 10:04:20 +10:00