changeset 78:dc2707da8ba4 draft

Uploaded 20170620
author fabio
date Tue, 20 Jun 2017 13:07:55 -0400
parents 7bd04a4f29df
children acf45085f9d4
files ._loadandplot.R ._plotwithscale.R ._testandplot.R loadandplot.xml test-data/._.DS_Store test-data/input/._Controls_regions.bed test-data/input/._Elements1_regions.bed test-data/input/._Elements2_regions.bed test-data/input/._Elements3_regions.bed test-data/input/._Feature1.bed test-data/input/._Feature2.bed test-data/input/._features.header.bed.txt test-data/input/._regions.header.txt test-data/output_loadandplot/._iwtomics.loadandplot.RData test-data/output_loadandplot/._iwtomics.loadandplot.features.txt test-data/output_loadandplot/._iwtomics.loadandplot.pdf test-data/output_loadandplot/._iwtomics.loadandplot.regions.txt test-data/output_plotwithscale/._iwtomics.plotwithscale.adjustedpvalue.txt test-data/output_plotwithscale/._iwtomics.plotwithscale.iwtomicstestresults.pdf test-data/output_plotwithscale/._iwtomics.plotwithscale.summaryplot.pdf test-data/output_testandplot/._iwtomics.testandplot.RData test-data/output_testandplot/._iwtomics.testandplot.adjustedpvalue.matrix.txt test-data/output_testandplot/._iwtomics.testandplot.iwtomicstestresults.pdf test-data/output_testandplot/._iwtomics.testandplot.selectedfeatures.txt test-data/output_testandplot/._iwtomics.testandplot.summaryplot.pdf test-data/output_testandplot/._iwtomics.testandplot.tests.txt
diffstat 26 files changed, 4 insertions(+), 8 deletions(-) [+]
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Binary file ._loadandplot.R has changed
Binary file ._plotwithscale.R has changed
Binary file ._testandplot.R has changed
--- a/loadandplot.xml	Tue Jun 20 12:57:30 2017 -0400
+++ b/loadandplot.xml	Tue Jun 20 13:07:55 2017 -0400
@@ -15,7 +15,7 @@
       regionsgalaxyids='c(${region_galaxyids})'
       #set region_names = '|'.join( [ str( $r.name ) for $r in $regions ] )
       regionsfilenames='${region_names}'
-      #set region_header = $regionsheadersection.regionsheader
+      #set region_header = $regionsheader
       #if $region_header != "":
         regionsheaderfile='${region_header}'
       #end if
@@ -26,7 +26,7 @@
       featuresgalaxyids='c(${feature_galaxyids})'
       #set feature_names = '|'.join( [ str( $f.name ) for $f in $features ] )
       featuresfilenames='${feature_names}'
-      #set feature_header = $featuresheadersection.featuresheader
+      #set feature_header = $featuresheader
       #if $feature_header != "":
         featuresheaderfile='${feature_header}'
       #end if
@@ -74,15 +74,11 @@
   <inputs>
     <!-- regions -->
     <param format="tabular" name="regions" type="data" label="Select region files" multiple="true" help="" />
-    <section name="regionsheadersection" title="Insert header file for regions (optional)" expanded="false" help="Tabular file. Column 1: names of the region files; Column 2: unique identifiers of the region datasets (spaces and special characters are not allowed); Column 3: name of the region datasets to be used in the output.">
-      <param format="tabular" name="regionsheader" type="data" label="Select header file" optional="true" />
-    </section>
+    <param format="tabular" name="regionsheader" type="data" label="Insert header file for regions (optional)" optional="true" help="Tabular file. Column 1: names of the region files; Column 2: unique identifiers of the region datasets (spaces and special characters are not allowed); Column 3: name of the region datasets to be used in the output." />
 
     <!-- features -->
     <param format="tabular" name="features" type="data" label="Select feature files" multiple="true" help="" />
-    <section name="featuresheadersection" title="Insert header file for features (optional)" expanded="false" help="Tabular file. Column 1: names of the feature files; Column 2: unique identifiers of the features (spaces and special characters are not allowed); Column 3: name of the features to be used in the output.">
-      <param format="tabular" name="featuresheader" type="data" label="Select header file" optional="true" />
-    </section>
+    <param format="tabular" name="featuresheader" type="data" label="Insert header file for features (optional)" optional="true" help="Tabular file. Column 1: names of the feature files; Column 2: unique identifiers of the features (spaces and special characters are not allowed); Column 3: name of the features to be used in the output." />
 
     <!-- zero-base one-base -->
     <param name="zerobased" type="select" label="Start positions are:" multiple="false" help="">
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