# HG changeset patch
# User fabio
# Date 1497025603 14400
# Node ID 971bb414cc4fbff4799bff814bafcf427fe5831e
# Parent  05b7f688c2470f03db0fa29a0cb83f40aa71a839
Uploaded 20170609

diff -r 05b7f688c247 -r 971bb414cc4f ._loadandplot.R
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diff -r 05b7f688c247 -r 971bb414cc4f ._plotwithscale.R
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diff -r 05b7f688c247 -r 971bb414cc4f ._testandplot.R
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diff -r 05b7f688c247 -r 971bb414cc4f loadandplot.xml
--- a/loadandplot.xml	Fri Jun 09 11:57:59 2017 -0400
+++ b/loadandplot.xml	Fri Jun 09 12:26:43 2017 -0400
@@ -256,7 +256,7 @@
     </test>
   </tests>
 
-  <help>
+  <help><![CDATA[
 This tool imports a collection of genomic region datasets, and associates to each region
 multiple genomic feature measurements. It allows to align the regions in multiple ways
 (center, left, right or scale alignment), to smooth the feature curves (possibly filling gaps in the
@@ -328,7 +328,7 @@
 
 .. _Simulated_data: https://usegalaxy.org/u/fabio-cumbo/h/iwtomics-example
 .. _ETn_data: https://usegalaxy.org/u/fabio-cumbo/h/iwtomics-etn-example
-  </help>
+  ]]></help>
 
   <citations>
     <citation type="bibtex">
diff -r 05b7f688c247 -r 971bb414cc4f plotwithscale.xml
--- a/plotwithscale.xml	Fri Jun 09 11:57:59 2017 -0400
+++ b/plotwithscale.xml	Fri Jun 09 12:26:43 2017 -0400
@@ -60,10 +60,6 @@
   </command>
 
   <inputs>
-    <help>
-    ...
-    </help>
-
     <!-- RData -->
     <param format="rdata" name="rdata" type="data" label="Select IWTomicsData object with test results" help="File created by 'IWTomics Test and Plot'." />
     <!-- test IDs -->
@@ -169,7 +165,7 @@
     </test>
   </tests>
 
-  <help>
+  <help><![CDATA[
 This tool allows to select the scale for the Interval-Wise Testing results. In particular, it returns the p-value curves
 for the different tests performed at the selected scale, and it creates a graphical representation of the
 Interval-Wise Testing results and a summary plot (optional) at the selected scale.
@@ -203,7 +199,7 @@
 The complete version can be found in the *R/Bioconductor* package *IWTomics* (see vignette_).
 
 .. _vignette: https://bioconductor.org/packages/release/bioc/vignettes/IWTomics/inst/doc/IWTomics.pdf
-  </help>
+  ]]></help>
 
   <citations>
     <citation type="bibtex">
diff -r 05b7f688c247 -r 971bb414cc4f test-data/._.DS_Store
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diff -r 05b7f688c247 -r 971bb414cc4f test-data/input/._Controls_regions.bed
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diff -r 05b7f688c247 -r 971bb414cc4f test-data/input/._Elements1_regions.bed
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diff -r 05b7f688c247 -r 971bb414cc4f test-data/input/._Elements2_regions.bed
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diff -r 05b7f688c247 -r 971bb414cc4f test-data/input/._Elements3_regions.bed
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diff -r 05b7f688c247 -r 971bb414cc4f test-data/input/._Feature1.bed
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diff -r 05b7f688c247 -r 971bb414cc4f test-data/input/._Feature2.bed
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diff -r 05b7f688c247 -r 971bb414cc4f test-data/input/._features.header.bed.txt
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diff -r 05b7f688c247 -r 971bb414cc4f test-data/input/._regions.header.txt
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diff -r 05b7f688c247 -r 971bb414cc4f test-data/output_loadandplot/._iwtomics.loadandplot.RData
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diff -r 05b7f688c247 -r 971bb414cc4f test-data/output_loadandplot/._iwtomics.loadandplot.features.txt
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diff -r 05b7f688c247 -r 971bb414cc4f test-data/output_loadandplot/._iwtomics.loadandplot.pdf
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diff -r 05b7f688c247 -r 971bb414cc4f test-data/output_plotwithscale/._iwtomics.plotwithscale.adjustedpvalue.txt
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diff -r 05b7f688c247 -r 971bb414cc4f test-data/output_plotwithscale/._iwtomics.plotwithscale.iwtomicstestresults.pdf
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diff -r 05b7f688c247 -r 971bb414cc4f test-data/output_plotwithscale/._iwtomics.plotwithscale.summaryplot.pdf
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diff -r 05b7f688c247 -r 971bb414cc4f test-data/output_testandplot/._iwtomics.testandplot.RData
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diff -r 05b7f688c247 -r 971bb414cc4f test-data/output_testandplot/._iwtomics.testandplot.iwtomicstestresults.pdf
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diff -r 05b7f688c247 -r 971bb414cc4f test-data/output_testandplot/._iwtomics.testandplot.selectedfeatures.txt
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diff -r 05b7f688c247 -r 971bb414cc4f test-data/output_testandplot/._iwtomics.testandplot.summaryplot.pdf
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diff -r 05b7f688c247 -r 971bb414cc4f test-data/output_testandplot/._iwtomics.testandplot.tests.txt
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diff -r 05b7f688c247 -r 971bb414cc4f testandplot.xml
--- a/testandplot.xml	Fri Jun 09 11:57:59 2017 -0400
+++ b/testandplot.xml	Fri Jun 09 12:26:43 2017 -0400
@@ -206,7 +206,7 @@
     </test>
   </tests>
 
-  <help>
+  <help><![CDATA[
 This tool statistically evaluates differences in genomic features between groups of regions along the genome.
 In particular, it implements the Interval-Wise Testing for omics data, an extended version of the Interval-Wise
 Testing for functional data presented in Pini and Vantini (2017). It allows to perform multiple two sample permutation
@@ -249,7 +249,7 @@
 The complete version can be found in the *R/Bioconductor* package *IWTomics* (see vignette_).
 
 .. _vignette: https://bioconductor.org/packages/release/bioc/vignettes/IWTomics/inst/doc/IWTomics.pdf
-  </help>
+  ]]></help>
 
   <citations>
     <citation type="bibtex">