Binary file ._loadandplot.R has changed

Binary file ._plotwithscale.R has changed

Binary file ._testandplot.R has changed

--- a/loadandplot.xml	Thu Jun 08 17:12:15 2017 -0400
+++ b/loadandplot.xml	Thu Jun 08 17:39:47 2017 -0400
@@ -5,20 +5,20 @@
   </macros>
   <expand macro="requirements" />
   <stdio>
-    <exit_code range="255" source="both" level="fatal" description="Missing IWTomics package. Please be sure to have it installed before using this tool." />
-    <exit_code range="10" source="both" level="fatal" description="An error has occurred reading the header file for regions. Please try again." />
-    <exit_code range="11" source="both" level="fatal" description="Not all region files are present in the first column of header file for regions." />
-    <exit_code range="20" source="both" level="fatal" description="An error has occurred reading the header file for features. Please try again." />
-    <exit_code range="21" source="both" level="fatal" description="Not all feature files are present in the first column of header file for features." />
-    <exit_code range="30" source="both" level="fatal" description="An error has occurred reading the data. Please try again." />
-    <exit_code range="31" source="both" level="fatal" description="Not enough columns in input file." />
-    <exit_code range="32" source="both" level="fatal" description="Duplicated regions in region file." />
-    <exit_code range="33" source="both" level="fatal" description="Duplicated windows in feature file." />
-    <exit_code range="34" source="both" level="fatal" description="Overlapping windows in feature file." />
-    <exit_code range="35" source="both" level="fatal" description="Windows in feature files do not cover all regions in region files." />
-    <exit_code range="36" source="both" level="fatal" description="All windows in a feature file must have the same size." />
-    <exit_code range="40" source="both" level="fatal" description="An error has occurred smoothing the data. Please try again." />
-    <regex match="Error" source="both" level="fatal" description="An error has occurred. Please try again." />
+    <exit_code range="255" level="fatal" description="Missing IWTomics package. Please be sure to have it installed before using this tool." />
+    <exit_code range="10" level="fatal" description="An error has occurred reading the header file for regions. Please try again." />
+    <exit_code range="11" level="fatal" description="Not all region files are present in the first column of header file for regions." />
+    <exit_code range="20" level="fatal" description="An error has occurred reading the header file for features. Please try again." />
+    <exit_code range="21" level="fatal" description="Not all feature files are present in the first column of header file for features." />
+    <exit_code range="30" level="fatal" description="An error has occurred reading the data. Please try again." />
+    <exit_code range="31" level="fatal" description="Not enough columns in input file." />
+    <exit_code range="32" level="fatal" description="Duplicated regions in region file." />
+    <exit_code range="33" level="fatal" description="Duplicated windows in feature file." />
+    <exit_code range="34" level="fatal" description="Overlapping windows in feature file." />
+    <exit_code range="35" level="fatal" description="Windows in feature files do not cover all regions in region files." />
+    <exit_code range="36" level="fatal" description="All windows in a feature file must have the same size." />
+    <exit_code range="40" level="fatal" description="An error has occurred smoothing the data. Please try again." />
+    <regex match="Error" level="fatal" description="An error has occurred. Please try again." />
   </stdio>
 
   <command>

--- a/plotwithscale.xml	Thu Jun 08 17:12:15 2017 -0400
+++ b/plotwithscale.xml	Thu Jun 08 17:39:47 2017 -0400
@@ -5,14 +5,14 @@
   </macros>
   <expand macro="requirements" />
   <stdio>
-    <exit_code range="-1" source="both" level="fatal" description="Missing IWTomics package. Please be sure to have it installed before using this tool." />
-    <exit_code range="10" source="both" level="fatal" description="Wrong test ids." />
-    <exit_code range="20" source="both" level="fatal" description="Wrong feature ids." />
-    <exit_code range="30" source="both" level="fatal" description="Two scale thresholds selected for the same test and feature." />
-    <exit_code range="40" source="both" level="fatal" description="Scale threshold too high." />
-    <exit_code range="50" source="both" level="fatal" description="Group by 'test' but selected features with different resolution." />
-    <exit_code range="60" source="both" level="fatal" description="Summary plot error. Please try again." />
-    <regex match="Error" source="both" level="fatal" description="An error has occurred. Please try again." />
+    <exit_code range="-1" level="fatal" description="Missing IWTomics package. Please be sure to have it installed before using this tool." />
+    <exit_code range="10" level="fatal" description="Wrong test ids." />
+    <exit_code range="20" level="fatal" description="Wrong feature ids." />
+    <exit_code range="30" level="fatal" description="Two scale thresholds selected for the same test and feature." />
+    <exit_code range="40" level="fatal" description="Scale threshold too high." />
+    <exit_code range="50" level="fatal" description="Group by 'test' but selected features with different resolution." />
+    <exit_code range="60" level="fatal" description="Summary plot error. Please try again." />
+    <regex match="Error" level="fatal" description="An error has occurred. Please try again." />
   </stdio>
 
   <command>

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	Thu Jun 08 17:12:15 2017 -0400
+++ b/testandplot.xml	Thu Jun 08 17:39:47 2017 -0400
@@ -5,12 +5,12 @@
   </macros>
   <expand macro="requirements" />
   <stdio>
-    <exit_code range="-1" source="both" level="fatal" description="Missing IWTomics package. Please be sure to have it installed before using this tool." />
-    <exit_code range="10" source="both" level="fatal" description="Wrong region ids." />
-    <exit_code range="20" source="both" level="fatal" description="Wrong feature ids." />
-    <exit_code range="30" source="both" level="fatal" description="Same test repeated multiple times." />
-    <exit_code range="40" source="both" level="fatal" description="Testing error." />
-    <regex match="Error" source="both" level="fatal" description="An error has occurred. Please try again." />
+    <exit_code range="-1" level="fatal" description="Missing IWTomics package. Please be sure to have it installed before using this tool." />
+    <exit_code range="10" level="fatal" description="Wrong region ids." />
+    <exit_code range="20" level="fatal" description="Wrong feature ids." />
+    <exit_code range="30" level="fatal" description="Same test repeated multiple times." />
+    <exit_code range="40" level="fatal" description="Testing error." />
+    <regex match="Error" level="fatal" description="An error has occurred. Please try again." />
   </stdio>
 
   <command>