# HG changeset patch
# User fabio
# Date 1497023853 14400
# Node ID 0b07bbe59b143ca21d05be93707d78fe3750a129
# Parent  ba2b17e5792ba00ce25664e316855a9bd612f1de
Uploaded 20170609

diff -r ba2b17e5792b -r 0b07bbe59b14 ._loadandplot.R
Binary file ._loadandplot.R has changed
diff -r ba2b17e5792b -r 0b07bbe59b14 ._plotwithscale.R
Binary file ._plotwithscale.R has changed
diff -r ba2b17e5792b -r 0b07bbe59b14 ._testandplot.R
Binary file ._testandplot.R has changed
diff -r ba2b17e5792b -r 0b07bbe59b14 loadandplot.xml
--- a/loadandplot.xml	Thu Jun 08 17:40:15 2017 -0400
+++ b/loadandplot.xml	Fri Jun 09 11:57:33 2017 -0400
@@ -18,7 +18,7 @@
     <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." />
+    <regex match="Error" source="both" level="fatal" description="An error has occurred. Please try again." />
   </stdio>
 
   <command>
diff -r ba2b17e5792b -r 0b07bbe59b14 plotwithscale.xml
--- a/plotwithscale.xml	Thu Jun 08 17:40:15 2017 -0400
+++ b/plotwithscale.xml	Fri Jun 09 11:57:33 2017 -0400
@@ -12,7 +12,7 @@
     <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." />
+    <regex match="Error" source="both" level="fatal" description="An error has occurred. Please try again." />
   </stdio>
 
   <command>
diff -r ba2b17e5792b -r 0b07bbe59b14 test-data/._.DS_Store
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diff -r ba2b17e5792b -r 0b07bbe59b14 test-data/input/._Controls_regions.bed
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diff -r ba2b17e5792b -r 0b07bbe59b14 test-data/input/._Elements1_regions.bed
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diff -r ba2b17e5792b -r 0b07bbe59b14 test-data/input/._Elements2_regions.bed
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diff -r ba2b17e5792b -r 0b07bbe59b14 test-data/input/._Elements3_regions.bed
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diff -r ba2b17e5792b -r 0b07bbe59b14 test-data/input/._Feature1.bed
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diff -r ba2b17e5792b -r 0b07bbe59b14 test-data/input/._Feature2.bed
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diff -r ba2b17e5792b -r 0b07bbe59b14 test-data/input/._features.header.bed.txt
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diff -r ba2b17e5792b -r 0b07bbe59b14 test-data/input/._regions.header.txt
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diff -r ba2b17e5792b -r 0b07bbe59b14 test-data/output_loadandplot/._iwtomics.loadandplot.RData
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diff -r ba2b17e5792b -r 0b07bbe59b14 test-data/output_loadandplot/._iwtomics.loadandplot.features.txt
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diff -r ba2b17e5792b -r 0b07bbe59b14 test-data/output_loadandplot/._iwtomics.loadandplot.pdf
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diff -r ba2b17e5792b -r 0b07bbe59b14 test-data/output_loadandplot/._iwtomics.loadandplot.regions.txt
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diff -r ba2b17e5792b -r 0b07bbe59b14 test-data/output_plotwithscale/._iwtomics.plotwithscale.adjustedpvalue.txt
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diff -r ba2b17e5792b -r 0b07bbe59b14 test-data/output_plotwithscale/._iwtomics.plotwithscale.iwtomicstestresults.pdf
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diff -r ba2b17e5792b -r 0b07bbe59b14 test-data/output_plotwithscale/._iwtomics.plotwithscale.summaryplot.pdf
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diff -r ba2b17e5792b -r 0b07bbe59b14 test-data/output_testandplot/._iwtomics.testandplot.RData
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diff -r ba2b17e5792b -r 0b07bbe59b14 test-data/output_testandplot/._iwtomics.testandplot.adjustedpvalue.matrix.txt
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diff -r ba2b17e5792b -r 0b07bbe59b14 test-data/output_testandplot/._iwtomics.testandplot.iwtomicstestresults.pdf
Binary file test-data/output_testandplot/._iwtomics.testandplot.iwtomicstestresults.pdf has changed
diff -r ba2b17e5792b -r 0b07bbe59b14 test-data/output_testandplot/._iwtomics.testandplot.selectedfeatures.txt
Binary file test-data/output_testandplot/._iwtomics.testandplot.selectedfeatures.txt has changed
diff -r ba2b17e5792b -r 0b07bbe59b14 test-data/output_testandplot/._iwtomics.testandplot.summaryplot.pdf
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diff -r ba2b17e5792b -r 0b07bbe59b14 test-data/output_testandplot/._iwtomics.testandplot.tests.txt
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diff -r ba2b17e5792b -r 0b07bbe59b14 testandplot.xml
--- a/testandplot.xml	Thu Jun 08 17:40:15 2017 -0400
+++ b/testandplot.xml	Fri Jun 09 11:57:33 2017 -0400
@@ -10,7 +10,7 @@
     <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." />
+    <regex match="Error" source="both" level="fatal" description="An error has occurred. Please try again." />
   </stdio>
 
   <command>