From 7938d1fc8165ab6f39bfbb6d31f9bf3cfb308ea9 Mon Sep 17 00:00:00 2001 From: Ross Lazarus Date: Sat, 5 Oct 2013 09:51:18 +1000 Subject: [PATCH] local changes --- lib/galaxy/tools/actions/__init__.py | 2 +- scripts/functional_tests.py | 1 + tool_conf.xml.sample | 1 + tools/rgedgeR/rgedgeRpaired.xml | 3 ++- tools/rgenetics/bams2mx.py | 2 ++ tools/rgenetics/bams2mx.xml | 2 +- 6 files changed, 8 insertions(+), 3 deletions(-) diff --git a/lib/galaxy/tools/actions/__init__.py b/lib/galaxy/tools/actions/__init__.py index 42ad0de5e9e..b4b671d2e56 100644 --- a/lib/galaxy/tools/actions/__init__.py +++ b/lib/galaxy/tools/actions/__init__.py @@ -200,7 +200,7 @@ class DefaultToolAction( object ): if data.dbkey not in [None, '?']: input_dbkey = data.dbkey data_name_sane = re.sub('[^a-zA-Z0-9_]+', '', data.name) - if trans.app.config.use_data_id_on_string: + if not trans.app.config.use_data_id_on_string: # we want names in our on_strings not numbers input_names.append(data_name_sane) else: diff --git a/scripts/functional_tests.py b/scripts/functional_tests.py index fa783b50598..9d9c8fbb6bc 100644 --- a/scripts/functional_tests.py +++ b/scripts/functional_tests.py @@ -454,4 +454,5 @@ def main(): return 1 if __name__ == "__main__": + print '\n\n\n\n#### SGE_ROOT=', os.environ.get('SGE_ROOT','##### no SGE_ROOT!'),'\n\n\n' sys.exit( main() ) diff --git a/tool_conf.xml.sample b/tool_conf.xml.sample index 623e71abefd..9b98b1f10db 100644 --- a/tool_conf.xml.sample +++ b/tool_conf.xml.sample @@ -1,6 +1,7 @@
+ diff --git a/tools/rgedgeR/rgedgeRpaired.xml b/tools/rgedgeR/rgedgeRpaired.xml index 88348113ac8..0f1b0fb1a9c 100644 --- a/tools/rgedgeR/rgedgeRpaired.xml +++ b/tools/rgedgeR/rgedgeRpaired.xml @@ -682,11 +682,12 @@ edgeIt = function (Count_Matrix=c(),group=c(),out_edgeR=F,out_VOOM=F,out_DESeq2= # DESeq2 require('DESeq2') library('RColorBrewer') - pdata = data.frame(Name=colnames(workCM),Rx=group,subjects=subjects,row.names=colnames(workCM)) if (length(subjects) == 0) { + pdata = data.frame(Name=colnames(workCM),Rx=group,row.names=colnames(workCM)) deSEQds = DESeqDataSetFromMatrix(countData = workCM, colData = pdata, design = formula(~ Rx)) } else { + pdata = data.frame(Name=colnames(workCM),Rx=group,subjects=subjects,row.names=colnames(workCM)) deSEQds = DESeqDataSetFromMatrix(countData = workCM, colData = pdata, design = formula(~ subjects + Rx)) } #DESeq2 = DESeq(deSEQds,fitType='local',pAdjustMethod=fdrtype) diff --git a/tools/rgenetics/bams2mx.py b/tools/rgenetics/bams2mx.py index 248387c3d53..ab5a88f69ef 100644 --- a/tools/rgenetics/bams2mx.py +++ b/tools/rgenetics/bams2mx.py @@ -296,6 +296,8 @@ if __name__ == "__main__": bcolname = [x.split(',')[2].replace("'",'').replace('"','') for x in bamdat] assert len(bamf) == len(baif) == len(bcolname), '##ERROR bams2mx: Count of bam/bai/cname not consistent - %d/%d/%d' % (len(bamf),len(baif),len(bcolname)) for i,b in enumerate(bamf): + if b.lower() == "none": + continue assert os.path.isfile(b),'## Supplied input bam file "%s" not found' % b bn = os.path.basename(b) tf,tbam = tempfile.mkstemp(suffix='%s.bam' % bn,dir=opts.tmpdir) diff --git a/tools/rgenetics/bams2mx.xml b/tools/rgenetics/bams2mx.xml index 69c1121a79c..994c8b97aaa 100644 --- a/tools/rgenetics/bams2mx.xml +++ b/tools/rgenetics/bams2mx.xml @@ -27,7 +27,7 @@ truevalue="true" falsevalue="false" checked="no" help="Controls counting of optical/pcr duplicates if flagged by upstream processing - leave alone unless you know what you are doing" /> - +