Binary file ._loadandplot.R has changed

Binary file ._plotwithscale.R has changed

Binary file ._testandplot.R has changed

--- a/loadandplot.xml	Wed Jun 14 13:58:04 2017 -0400
+++ b/loadandplot.xml	Wed Jun 14 15:20:32 2017 -0400
@@ -25,34 +25,34 @@
 <![CDATA[
     Rscript '$__tool_directory__/loadandplot.R' outrdata='${outrdata}' outregions='${outregions}' outfeatures='${outfeatures}' outpdf='${outpdf}'
 
-      #set region_paths = '"\\|"'.join( [ str( $r ) for $r in $regions ] )
+      #set region_paths = '|'.join( [ str( $r ) for $r in $regions ] )
       regionspaths='${region_paths}'
-      #set region_galaxyids = '","'.join( [ str( $r.hid ) for $r in $regions ] )
+      #set region_galaxyids = ','.join( [ str( $r.hid ) for $r in $regions ] )
       regionsgalaxyids='c(${region_galaxyids})'
-      #set region_names = '"\\|"'.join( [ str( $r.name ) for $r in $regions ] )
+      #set region_names = '|'.join( [ str( $r.name ) for $r in $regions ] )
       regionsfilenames='${region_names}'
-      #set region_header = "${regionsheadersection.regionsheader}"
+      #set region_header = $regionsheadersection.regionsheader
       #if $region_header != "":
         regionsheaderfile='${region_header}'
       #end if
       
-      #set feature_paths = '"\\|"'.join( [ str( $f ) for $f in $features ] )
+      #set feature_paths = '|'.join( [ str( $f ) for $f in $features ] )
       featurespaths='${feature_paths}'
-      #set feature_galaxyids = '","'.join( [ str( $f.hid ) for $f in $features ] )
+      #set feature_galaxyids = ','.join( [ str( $f.hid ) for $f in $features ] )
       featuresgalaxyids='c(${feature_galaxyids})'
-      #set feature_names = '"\\|"'.join( [ str( $f.name ) for $f in $features ] )
+      #set feature_names = '|'.join( [ str( $f.name ) for $f in $features ] )
       featuresfilenames='${feature_names}'
-      #set feature_header = "${featuresheadersection.featuresheader}"
+      #set feature_header = $featuresheadersection.featuresheader
       #if $feature_header != "":
         featuresheaderfile='${feature_header}'
       #end if
 
-      smoothing='${conditionaltype.smoothing}'
+      smoothing="'${conditionaltype.smoothing}'"
       start.are.0based='${zerobased}'
       #if $conditionaltype.smoothing == 'no':
-        alignment='${conditionaltype.alignment}'
+        alignment="'${conditionaltype.alignment}'"
       #elif $conditionaltype.smoothing == 'locpoly':
-        alignment='${conditionaltype.locpolyconditionalscale.alignment}'
+        alignment="'${conditionaltype.locpolyconditionalscale.alignment}'"
         #if $conditionaltype.locpolyconditionalscale.alignment == 'scale':
           scale='${conditionaltype.locpolyconditionalscale.scalegrid}'
         #end if
@@ -60,14 +60,14 @@
         degree='${conditionaltype.locpolydegree}'
         fill_gaps='${conditionaltype.fillgaps}'
       #elif $conditionaltype.smoothing == 'kernel':
-        alignment='${conditionaltype.kernelconditionalscale.alignment}'
+        alignment="'${conditionaltype.kernelconditionalscale.alignment}'"
         #if $conditionaltype.kernelconditionalscale.alignment == 'scale':
           scale='${conditionaltype.kernelconditionalscale.scalegrid}'
         #end if
         bandwidth='${conditionaltype.kernelbandwidth}'
         fill_gaps='${conditionaltype.fillgaps}'
       #elif $conditionaltype.smoothing == 'splines':
-        alignment='${conditionaltype.splinesconditionalscale.alignment}'
+        alignment="'${conditionaltype.splinesconditionalscale.alignment}'"
         #if $conditionaltype.splinesconditionalscale.alignment == 'scale':
           scale='${conditionaltype.splinesconditionalscale.scalegrid}'
         #end if
@@ -78,9 +78,9 @@
 
       average='${plotres.average}'
       size='${plotres.size}'
-      plottype='${plotres.conditionalplottype.plottype}'
+      plottype="'${plotres.conditionalplottype.plottype}'"
       #if $plotres.conditionalplottype.plottype == 'boxplot':
-        #set probs = '","'.join( [ str( $p.prob ) for $p in $plotres.conditionalplottype.probabilitiessection.probabilities ] )
+        #set probs = ','.join( [ str( $p.prob ) for $p in $plotres.conditionalplottype.probabilitiessection.probabilities ] )
         #if $probs != "":
           probs='c(${plotres.conditionalplottype.probabilitiessection.prob0},${plotres.conditionalplottype.probabilitiessection.prob1},${plotres.conditionalplottype.probabilitiessection.prob2},${probs})'
         #else:

--- a/plotwithscale.xml	Wed Jun 14 13:58:04 2017 -0400
+++ b/plotwithscale.xml	Wed Jun 14 15:20:32 2017 -0400
@@ -22,19 +22,19 @@
       iwtomicstests='${testids}'
       iwtomicsselectedfeatures='${featureids}'
 
-      #set test_subset = '"\\|"'.join( [ str( $e.test ) for $e in $scalesection.thresholdontestscale ] )
+      #set test_subset = '|'.join( [ str( $e.test ) for $e in $scalesection.thresholdontestscale ] )
       test_subset='${test_subset}'
-      #set feature_subset = '"\\|"'.join( [ str( $e.feature ) for $e in $scalesection.thresholdontestscale ] )
+      #set feature_subset = '|'.join( [ str( $e.feature ) for $e in $scalesection.thresholdontestscale ] )
       feature_subset='${feature_subset}'
-      #set scale_subset = '","'.join( [ str( $e.scale ) for $e in $scalesection.thresholdontestscale ] )
+      #set scale_subset = ','.join( [ str( $e.scale ) for $e in $scalesection.thresholdontestscale ] )
       scale_subset='c(${scale_subset})'
 
       testalpha='${plotres.alpha}'
       average='${plotres.average}'
       size='${plotres.size}'
-      plottype='${plotres.conditionalplottype.plottype}'
+      plottype="'${plotres.conditionalplottype.plottype}'"
       #if $plotres.conditionalplottype.plottype == 'boxplot':
-        #set probs = '","'.join( [ str( $p.prob ) for $p in $plotres.conditionalplottype.probabilitiessection.probabilities ] )
+        #set probs = ','.join( [ str( $p.prob ) for $p in $plotres.conditionalplottype.probabilitiessection.probabilities ] )
         #if $probs != "":
           probs='c(${plotres.conditionalplottype.probabilitiessection.prob0},${plotres.conditionalplottype.probabilitiessection.prob1},${plotres.conditionalplottype.probabilitiessection.prob2},${probs})'
         #else:
@@ -42,7 +42,7 @@
         #end if
       #end if
 
-      groupby='${plotsum.conditionalgroupby.groupby}'
+      groupby="'${plotsum.conditionalgroupby.groupby}'"
       #if $plotsum.conditionalgroupby.groupby == "test":
         summaryalpha='${plotsum.conditionalgroupby.testalphaplot}'
         only_significant='${plotsum.conditionalgroupby.testonlysig}'

Binary file test-data/._.DS_Store has changed

Binary file test-data/input/._Controls_regions.bed has changed

Binary file test-data/input/._Elements1_regions.bed has changed

Binary file test-data/input/._Elements2_regions.bed has changed

Binary file test-data/input/._Elements3_regions.bed has changed

Binary file test-data/input/._Feature1.bed has changed

Binary file test-data/input/._Feature2.bed has changed

Binary file test-data/input/._features.header.bed.txt has changed

Binary file test-data/input/._regions.header.txt has changed

Binary file test-data/output_loadandplot/._iwtomics.loadandplot.RData has changed

Binary file test-data/output_loadandplot/._iwtomics.loadandplot.features.txt has changed

Binary file test-data/output_loadandplot/._iwtomics.loadandplot.pdf has changed

Binary file test-data/output_loadandplot/._iwtomics.loadandplot.regions.txt has changed

Binary file test-data/output_plotwithscale/._iwtomics.plotwithscale.adjustedpvalue.txt has changed

Binary file test-data/output_plotwithscale/._iwtomics.plotwithscale.iwtomicstestresults.pdf has changed

Binary file test-data/output_plotwithscale/._iwtomics.plotwithscale.summaryplot.pdf has changed

Binary file test-data/output_testandplot/._iwtomics.testandplot.RData has changed

Binary file test-data/output_testandplot/._iwtomics.testandplot.adjustedpvalue.matrix.txt has changed

Binary file test-data/output_testandplot/._iwtomics.testandplot.iwtomicstestresults.pdf has changed

Binary file test-data/output_testandplot/._iwtomics.testandplot.selectedfeatures.txt has changed

Binary file test-data/output_testandplot/._iwtomics.testandplot.summaryplot.pdf has changed

Binary file test-data/output_testandplot/._iwtomics.testandplot.tests.txt has changed

--- a/testandplot.xml	Wed Jun 14 13:58:04 2017 -0400
+++ b/testandplot.xml	Wed Jun 14 15:20:32 2017 -0400
@@ -20,16 +20,16 @@
       featureids='${featureids}'
       rdatafile='${rdata}'
 
-      #set region1 = '","'.join( [ str( $r.region0 ) for $r in $regionssection.regions ] )
-      #set region2 = '","'.join( [ str( $r.region1 ) for $r in $regionssection.regions ] )
+      #set region1 = ','.join( [ str( $r.region0 ) for $r in $regionssection.regions ] )
+      #set region2 = ','.join( [ str( $r.region1 ) for $r in $regionssection.regions ] )
       region1='c(${region1})'
       region2='c(${region2})'
 
       features_subset='c(${featureslist})'
 
-      statistics='${conditionalstatistics.statistics}'
+      statistics="'${conditionalstatistics.statistics}'"
       #if $conditionalstatistics.statistics == "quantile":
-        #set probabilities = '","'.join( [ str( $p.qprob ) for $p in $conditionalstatistics.quantilesection.qprobabilities ] )
+        #set probabilities = ','.join( [ str( $p.qprob ) for $p in $conditionalstatistics.quantilesection.qprobabilities ] )
         testprobs='c(${probabilities})'
       #end if
 
@@ -38,9 +38,9 @@
       testalpha='${plotres.alpha}'
       average='${plotres.average}'
       size='${plotres.size}'
-      plottype='${plotres.conditionalplottype.plottype}'
-      #if $plotres.conditionalplottype.plottype == 'boxplot':
-        #set probs = '","'.join( [ str( $p.prob ) for $p in $plotres.conditionalplottype.probabilitiessection.probabilities ] )
+      plottype="'${plotres.conditionalplottype.plottype}'"
+      #if $plotres.conditionalplottype.plottype == "boxplot":
+        #set probs = ','.join( [ str( $p.prob ) for $p in $plotres.conditionalplottype.probabilitiessection.probabilities ] )
         #if $probs != "":
           probs='c(${plotres.conditionalplottype.probabilitiessection.prob0},${plotres.conditionalplottype.probabilitiessection.prob1},${plotres.conditionalplottype.probabilitiessection.prob2},${probs})'
         #else:
@@ -48,7 +48,7 @@
         #end if
       #end if
 
-      groupby='${plotsum.conditionalgroupby.groupby}'
+      groupby="'${plotsum.conditionalgroupby.groupby}'"
       #if $plotsum.conditionalgroupby.groupby == "test":
         summaryalpha='${plotsum.conditionalgroupby.testalphaplot}'
         only_significant='${plotsum.conditionalgroupby.testonlysig}'