local changes

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:

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() )

tool_conf.xml.sample

@@ -1,6 +1,7 @@
 <?xml version="1.0"?>
 <toolbox>
   <section name="Get Data" id="getext">
+    <tool file="rlGAT/rlGAT.xml"/>
     <tool file="data_source/upload.xml"/>
     <tool file="data_source/ucsc_tablebrowser.xml" />
     <tool file="data_source/ucsc_tablebrowser_test.xml" />

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)

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)

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" />
     <param name="firstbamf" type="data" label="BAM file from your history to count reads overlapping BED regions" format="bam" />
     <repeat name="bamfiles" title="Additional BAM files from your history to count reads overlapping BED regions" min="10">
-        <param name="bamf" type="data" label="Additional BAM file from your history" format="bam" size="100"/>
+        <param name="bamf" type="data" label="Additional BAM file from your history" format="bam" size="100" optional="true"/>
     </repeat>
   </inputs>
   <outputs>