# HG changeset patch
# User fabio
# Date 1497463058 14400
# Node ID 39e7294c66e1048da2f423fa74d2efba4aba1689
# Parent  4935e8a8f0b18d9339327138f254b879919f30f6
Uploaded 20170614

diff -r 4935e8a8f0b1 -r 39e7294c66e1 ._loadandplot.R
Binary file ._loadandplot.R has changed
diff -r 4935e8a8f0b1 -r 39e7294c66e1 ._plotwithscale.R
Binary file ._plotwithscale.R has changed
diff -r 4935e8a8f0b1 -r 39e7294c66e1 ._testandplot.R
Binary file ._testandplot.R has changed
diff -r 4935e8a8f0b1 -r 39e7294c66e1 .shed.yml
--- a/.shed.yml	Fri Jun 09 12:27:10 2017 -0400
+++ b/.shed.yml	Wed Jun 14 13:57:38 2017 -0400
@@ -1,5 +1,5 @@
 name: iwtomics
-owner: fabio
+owner: iuc
 categories:
   - Statistics
 description: Interval-Wise Testing for Omics Data
diff -r 4935e8a8f0b1 -r 39e7294c66e1 loadandplot.xml
--- a/loadandplot.xml	Fri Jun 09 12:27:10 2017 -0400
+++ b/loadandplot.xml	Wed Jun 14 13:57:38 2017 -0400
@@ -23,68 +23,68 @@
 
   <command>
 <![CDATA[
-    Rscript $__tool_directory__/loadandplot.R outrdata="${outrdata}" outregions="${outregions}" outfeatures="${outfeatures}" outpdf="${outpdf}"
+    Rscript '$__tool_directory__/loadandplot.R' outrdata='${outrdata}' outregions='${outregions}' outfeatures='${outfeatures}' outpdf='${outpdf}'
 
       #set region_paths = '"\\|"'.join( [ str( $r ) for $r in $regions ] )
-      regionspaths="${region_paths}"
+      regionspaths='${region_paths}'
       #set region_galaxyids = '","'.join( [ str( $r.hid ) for $r in $regions ] )
-      regionsgalaxyids="c(${region_galaxyids})"
+      regionsgalaxyids='c(${region_galaxyids})'
       #set region_names = '"\\|"'.join( [ str( $r.name ) for $r in $regions ] )
-      regionsfilenames="${region_names}"
-      #set region_header = '"\\|"'.join( [ str( $rh.regionsheader ) for $rh in $regionsheaderrepeat ] )
+      regionsfilenames='${region_names}'
+      #set region_header = "${regionsheadersection.regionsheader}"
       #if $region_header != "":
-        regionsheaderfile="${region_header}"
+        regionsheaderfile='${region_header}'
       #end if
-
+      
       #set feature_paths = '"\\|"'.join( [ str( $f ) for $f in $features ] )
-      featurespaths="${feature_paths}"
+      featurespaths='${feature_paths}'
       #set feature_galaxyids = '","'.join( [ str( $f.hid ) for $f in $features ] )
-      featuresgalaxyids="c(${feature_galaxyids})"
+      featuresgalaxyids='c(${feature_galaxyids})'
       #set feature_names = '"\\|"'.join( [ str( $f.name ) for $f in $features ] )
-      featuresfilenames="${feature_names}"
-      #set feature_header = '"\\|"'.join( [ str( $fh.featuresheader ) for $fh in $featuresheaderrepeat ] )
+      featuresfilenames='${feature_names}'
+      #set feature_header = "${featuresheadersection.featuresheader}"
       #if $feature_header != "":
-        featuresheaderfile="${feature_header}"
+        featuresheaderfile='${feature_header}'
       #end if
 
-      smoothing="'${conditionaltype.smoothing}'"
-      start.are.0based="${zerobased}"
+      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}"
+          scale='${conditionaltype.locpolyconditionalscale.scalegrid}'
         #end if
-        bandwidth="${conditionaltype.locpolybandwidth}"
-        degree="${conditionaltype.locpolydegree}"
-        fill_gaps="${conditionaltype.fillgaps}"
+        bandwidth='${conditionaltype.locpolybandwidth}'
+        degree='${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}"
+          scale='${conditionaltype.kernelconditionalscale.scalegrid}'
         #end if
-        bandwidth="${conditionaltype.kernelbandwidth}"
-        fill_gaps="${conditionaltype.fillgaps}"
+        bandwidth='${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}"
+          scale='${conditionaltype.splinesconditionalscale.scalegrid}'
         #end if
-        degree="${conditionaltype.splinesdegree}"
-        dist_knots="${conditionaltype.splinesdistknots}"
-        fill_gaps="${conditionaltype.fillgaps}"
+        degree='${conditionaltype.splinesdegree}'
+        dist_knots='${conditionaltype.splinesdistknots}'
+        fill_gaps='${conditionaltype.fillgaps}'
       #end if
 
-      average="${plotres.average}"
-      size="${plotres.size}"
-      plottype="'${plotres.conditionalplottype.plottype}'"
+      average='${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 ] )
         #if $probs != "":
-          probs="c(${plotres.conditionalplottype.probabilitiessection.prob0},${plotres.conditionalplottype.probabilitiessection.prob1},${plotres.conditionalplottype.probabilitiessection.prob2},${probs})"
+          probs='c(${plotres.conditionalplottype.probabilitiessection.prob0},${plotres.conditionalplottype.probabilitiessection.prob1},${plotres.conditionalplottype.probabilitiessection.prob2},${probs})'
         #else:
-          probs="c(${plotres.conditionalplottype.probabilitiessection.prob0},${plotres.conditionalplottype.probabilitiessection.prob1},${plotres.conditionalplottype.probabilitiessection.prob2})"
+          probs='c(${plotres.conditionalplottype.probabilitiessection.prob0},${plotres.conditionalplottype.probabilitiessection.prob1},${plotres.conditionalplottype.probabilitiessection.prob2})'
         #end if
       #end if
 
@@ -99,15 +99,15 @@
   <inputs>
     <!-- regions -->
     <param format="tabular" name="regions" type="data" label="Select region files" multiple="true" help="" />
-    <repeat name="regionsheaderrepeat" title="Header file for regions (optional)" min="0" max="1" 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" />
-    </repeat>
+    <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>
 
     <!-- features -->
     <param format="tabular" name="features" type="data" label="Select feature files" multiple="true" help="" />
-    <repeat name="featuresheaderrepeat" title="Header file for features (optional)" min="0" max="1" 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" />
-    </repeat>
+    <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>
 
     <!-- zero-base one-base -->
     <param name="zerobased" type="select" label="Start positions are:" multiple="false" help="">
@@ -330,28 +330,6 @@
 .. _ETn_data: https://usegalaxy.org/u/fabio-cumbo/h/iwtomics-etn-example
   ]]></help>
 
-  <citations>
-    <citation type="bibtex">
-      @ARTICLE{
-               iwt-functional-data,
-               author = {Pini, Alessia and Vantini, Simone},
-               title = {Interval-Wise Testing for functional data},
-               journal = {Journal of Nonparametric Statistics},
-               year = {2017},
-               volume = {29},
-               number = {2},
-               pages = {407-424}
-      }
-    </citation>
-    <citation type="bibtex">
-      @MANUAL{
-               iwtomics,
-               author = {Cremona, Marzia A and Pini, Alessia and Chiaromonte, Francesca and Vantini, Simone},
-               title = {IWTomics: Interval-Wise Testing for Omics Data},
-               note = {R package version 1.0.0},
-               year = {2017}
-      }
-    </citation>
-  </citations>
+  <expand macro="citations" />
 
 </tool>
diff -r 4935e8a8f0b1 -r 39e7294c66e1 macros.xml
--- a/macros.xml	Fri Jun 09 12:27:10 2017 -0400
+++ b/macros.xml	Wed Jun 14 13:57:38 2017 -0400
@@ -2,8 +2,33 @@
     <token name="@VERSION@">1.0.0</token>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="3.3.1">R</requirement>
+            <requirement type="package" version="3.3.1">r-base</requirement>
             <requirement type="package" version="@VERSION@">bioconductor-iwtomics</requirement>
         </requirements>
     </xml>
+    <xml name="citations">
+        <citations>
+            <citation type="bibtex">
+                @ARTICLE{
+                        iwt-functional-data,
+                        author = {Pini, Alessia and Vantini, Simone},
+                        title = {Interval-Wise Testing for functional data},
+                        journal = {Journal of Nonparametric Statistics},
+                        year = {2017},
+                        volume = {29},
+                        number = {2},
+                        pages = {407-424}
+                }
+            </citation>
+            <citation type="bibtex">
+                @MANUAL{
+                        iwtomics,
+                        author = {Cremona, Marzia A and Pini, Alessia and Chiaromonte, Francesca and Vantini, Simone},
+                        title = {IWTomics: Interval-Wise Testing for Omics Data},
+                        note = {R package version 1.0.0},
+                        year = {2017}
+                }
+            </citation>
+        </citations>
+    </xml>
 </macros>
\ No newline at end of file
diff -r 4935e8a8f0b1 -r 39e7294c66e1 plotwithscale.xml
--- a/plotwithscale.xml	Fri Jun 09 12:27:10 2017 -0400
+++ b/plotwithscale.xml	Wed Jun 14 13:57:38 2017 -0400
@@ -17,38 +17,38 @@
 
   <command>
 <![CDATA[
-    Rscript $__tool_directory__/plotwithscale.R adjustedpvalue="${adjustedpvalue}" iwtomicsrespdf="${iwtomicsrespdf}" iwtomicssumpdf="${iwtomicssumpdf}"
-      iwtomicsrdata="${rdata}"
-      iwtomicstests="${testids}"
-      iwtomicsselectedfeatures="${featureids}"
+    Rscript '$__tool_directory__/plotwithscale.R' adjustedpvalue='${adjustedpvalue}' iwtomicsrespdf='${iwtomicsrespdf}' iwtomicssumpdf='${iwtomicssumpdf}'
+      iwtomicsrdata='${rdata}'
+      iwtomicstests='${testids}'
+      iwtomicsselectedfeatures='${featureids}'
 
       #set test_subset = '"\\|"'.join( [ str( $e.test ) for $e in $scalesection.thresholdontestscale ] )
-      test_subset="${test_subset}"
+      test_subset='${test_subset}'
       #set feature_subset = '"\\|"'.join( [ str( $e.feature ) for $e in $scalesection.thresholdontestscale ] )
-      feature_subset="${feature_subset}"
+      feature_subset='${feature_subset}'
       #set scale_subset = '","'.join( [ str( $e.scale ) for $e in $scalesection.thresholdontestscale ] )
-      scale_subset="c(${scale_subset})"
+      scale_subset='c(${scale_subset})'
 
-      testalpha="${plotres.alpha}"
-      average="${plotres.average}"
-      size="${plotres.size}"
-      plottype="'${plotres.conditionalplottype.plottype}'"
+      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 ] )
         #if $probs != "":
-          probs="c(${plotres.conditionalplottype.probabilitiessection.prob0},${plotres.conditionalplottype.probabilitiessection.prob1},${plotres.conditionalplottype.probabilitiessection.prob2},${probs})"
+          probs='c(${plotres.conditionalplottype.probabilitiessection.prob0},${plotres.conditionalplottype.probabilitiessection.prob1},${plotres.conditionalplottype.probabilitiessection.prob2},${probs})'
         #else:
-          probs="c(${plotres.conditionalplottype.probabilitiessection.prob0},${plotres.conditionalplottype.probabilitiessection.prob1},${plotres.conditionalplottype.probabilitiessection.prob2})"
+          probs='c(${plotres.conditionalplottype.probabilitiessection.prob0},${plotres.conditionalplottype.probabilitiessection.prob1},${plotres.conditionalplottype.probabilitiessection.prob2})'
         #end if
       #end if
 
-      groupby="'${plotsum.conditionalgroupby.groupby}'"
+      groupby='${plotsum.conditionalgroupby.groupby}'
       #if $plotsum.conditionalgroupby.groupby == "test":
-        summaryalpha="${plotsum.conditionalgroupby.testalphaplot}"
-        only_significant="${plotsum.conditionalgroupby.testonlysig}"
+        summaryalpha='${plotsum.conditionalgroupby.testalphaplot}'
+        only_significant='${plotsum.conditionalgroupby.testonlysig}'
       #elif $plotsum.conditionalgroupby.groupby == "feature":
-        summaryalpha="${plotsum.conditionalgroupby.featurealphaplot}"
-        only_significant="${plotsum.conditionalgroupby.featureonlysig}"
+        summaryalpha='${plotsum.conditionalgroupby.featurealphaplot}'
+        only_significant='${plotsum.conditionalgroupby.featureonlysig}'
       #end if
 
       >& /dev/null
@@ -201,28 +201,6 @@
 .. _vignette: https://bioconductor.org/packages/release/bioc/vignettes/IWTomics/inst/doc/IWTomics.pdf
   ]]></help>
 
-  <citations>
-    <citation type="bibtex">
-      @ARTICLE{
-               iwt-functional-data,
-               author = {A Pini and S. Vantini},
-               title = {Interval-Wise Testing for functional data},
-               journal = {Journal of Nonparametric Statistics},
-               year = {2017},
-               volume = {29},
-               number = {2},
-               pages = {407-424}
-      }
-    </citation>
-    <citation type="bibtex">
-      @MANUAL{
-               iwtomics,
-               author = {Cremona, Marzia A and Pini, Alessia and Chiaromonte, Francesca and Vantini, Simone},
-               title = {IWTomics: Interval-Wise Testing for Omics Data},
-               note = {R package version 1.0.0},
-               year = {2017}
-      }
-    </citation>
-  </citations>
+  <expand macro="citations" />
 
 </tool>
diff -r 4935e8a8f0b1 -r 39e7294c66e1 test-data/._.DS_Store
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diff -r 4935e8a8f0b1 -r 39e7294c66e1 test-data/input/._Controls_regions.bed
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diff -r 4935e8a8f0b1 -r 39e7294c66e1 test-data/input/._Elements1_regions.bed
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diff -r 4935e8a8f0b1 -r 39e7294c66e1 test-data/input/._Elements2_regions.bed
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diff -r 4935e8a8f0b1 -r 39e7294c66e1 test-data/input/._Elements3_regions.bed
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diff -r 4935e8a8f0b1 -r 39e7294c66e1 test-data/input/._Feature1.bed
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diff -r 4935e8a8f0b1 -r 39e7294c66e1 test-data/input/._Feature2.bed
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diff -r 4935e8a8f0b1 -r 39e7294c66e1 test-data/input/._features.header.bed.txt
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diff -r 4935e8a8f0b1 -r 39e7294c66e1 test-data/input/._regions.header.txt
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diff -r 4935e8a8f0b1 -r 39e7294c66e1 test-data/output_loadandplot/._iwtomics.loadandplot.RData
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diff -r 4935e8a8f0b1 -r 39e7294c66e1 test-data/output_loadandplot/._iwtomics.loadandplot.features.txt
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diff -r 4935e8a8f0b1 -r 39e7294c66e1 test-data/output_loadandplot/._iwtomics.loadandplot.pdf
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diff -r 4935e8a8f0b1 -r 39e7294c66e1 test-data/output_loadandplot/._iwtomics.loadandplot.regions.txt
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diff -r 4935e8a8f0b1 -r 39e7294c66e1 test-data/output_plotwithscale/._iwtomics.plotwithscale.adjustedpvalue.txt
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diff -r 4935e8a8f0b1 -r 39e7294c66e1 test-data/output_plotwithscale/._iwtomics.plotwithscale.iwtomicstestresults.pdf
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diff -r 4935e8a8f0b1 -r 39e7294c66e1 test-data/output_plotwithscale/._iwtomics.plotwithscale.summaryplot.pdf
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diff -r 4935e8a8f0b1 -r 39e7294c66e1 test-data/output_testandplot/._iwtomics.testandplot.RData
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diff -r 4935e8a8f0b1 -r 39e7294c66e1 test-data/output_testandplot/._iwtomics.testandplot.adjustedpvalue.matrix.txt
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diff -r 4935e8a8f0b1 -r 39e7294c66e1 test-data/output_testandplot/._iwtomics.testandplot.iwtomicstestresults.pdf
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diff -r 4935e8a8f0b1 -r 39e7294c66e1 test-data/output_testandplot/._iwtomics.testandplot.selectedfeatures.txt
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diff -r 4935e8a8f0b1 -r 39e7294c66e1 test-data/output_testandplot/._iwtomics.testandplot.summaryplot.pdf
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diff -r 4935e8a8f0b1 -r 39e7294c66e1 test-data/output_testandplot/._iwtomics.testandplot.tests.txt
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diff -r 4935e8a8f0b1 -r 39e7294c66e1 testandplot.xml
--- a/testandplot.xml	Fri Jun 09 12:27:10 2017 -0400
+++ b/testandplot.xml	Wed Jun 14 13:57:38 2017 -0400
@@ -15,46 +15,46 @@
 
   <command>
 <![CDATA[
-    Rscript $__tool_directory__/testandplot.R adjustedpvaluematrix="${adjustedpvaluematrix}" iwtomicsrespdf="${iwtomicsrespdf}" iwtomicssumpdf="${iwtomicssumpdf}" iwtomicsrdata="${iwtomicsrdata}" iwtomicstests="${iwtomicstests}" iwtomicsselectedfeatures="${iwtomicsselectedfeatures}"
-      regionids="${regionids}"
-      featureids="${featureids}"
-      rdatafile="${rdata}"
+    Rscript '$__tool_directory__/testandplot.R' adjustedpvaluematrix='${adjustedpvaluematrix}' iwtomicsrespdf='${iwtomicsrespdf}' iwtomicssumpdf='${iwtomicssumpdf}' iwtomicsrdata='${iwtomicsrdata}' iwtomicstests='${iwtomicstests}' iwtomicsselectedfeatures='${iwtomicsselectedfeatures}'
+      regionids='${regionids}'
+      featureids='${featureids}'
+      rdatafile='${rdata}'
 
       #set region1 = '","'.join( [ str( $r.region0 ) for $r in $regionssection.regions ] )
       #set region2 = '","'.join( [ str( $r.region1 ) for $r in $regionssection.regions ] )
-      region1="c(${region1})"
-      region2="c(${region2})"
+      region1='c(${region1})'
+      region2='c(${region2})'
 
-      features_subset="c(${featureslist})"
+      features_subset='c(${featureslist})'
 
-      statistics="'${conditionalstatistics.statistics}'"
+      statistics='${conditionalstatistics.statistics}'
       #if $conditionalstatistics.statistics == "quantile":
         #set probabilities = '","'.join( [ str( $p.qprob ) for $p in $conditionalstatistics.quantilesection.qprobabilities ] )
-        testprobs="c(${probabilities})"
+        testprobs='c(${probabilities})'
       #end if
 
-      B="${permutations}"
+      B='${permutations}'
 
-      testalpha="${plotres.alpha}"
-      average="${plotres.average}"
-      size="${plotres.size}"
-      plottype="'${plotres.conditionalplottype.plottype}'"
+      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 ] )
         #if $probs != "":
-          probs="c(${plotres.conditionalplottype.probabilitiessection.prob0},${plotres.conditionalplottype.probabilitiessection.prob1},${plotres.conditionalplottype.probabilitiessection.prob2},${probs})"
+          probs='c(${plotres.conditionalplottype.probabilitiessection.prob0},${plotres.conditionalplottype.probabilitiessection.prob1},${plotres.conditionalplottype.probabilitiessection.prob2},${probs})'
         #else:
-          probs="c(${plotres.conditionalplottype.probabilitiessection.prob0},${plotres.conditionalplottype.probabilitiessection.prob1},${plotres.conditionalplottype.probabilitiessection.prob2})"
+          probs='c(${plotres.conditionalplottype.probabilitiessection.prob0},${plotres.conditionalplottype.probabilitiessection.prob1},${plotres.conditionalplottype.probabilitiessection.prob2})'
         #end if
       #end if
 
-      groupby="'${plotsum.conditionalgroupby.groupby}'"
+      groupby='${plotsum.conditionalgroupby.groupby}'
       #if $plotsum.conditionalgroupby.groupby == "test":
-        summaryalpha="${plotsum.conditionalgroupby.testalphaplot}"
-        only_significant="${plotsum.conditionalgroupby.testonlysig}"
+        summaryalpha='${plotsum.conditionalgroupby.testalphaplot}'
+        only_significant='${plotsum.conditionalgroupby.testonlysig}'
       #elif $plotsum.conditionalgroupby.groupby == "feature":
-        summaryalpha="${plotsum.conditionalgroupby.featurealphaplot}"
-        only_significant="${plotsum.conditionalgroupby.featureonlysig}"
+        summaryalpha='${plotsum.conditionalgroupby.featurealphaplot}'
+        only_significant='${plotsum.conditionalgroupby.featureonlysig}'
       #end if
 
      >& /dev/null
@@ -251,28 +251,6 @@
 .. _vignette: https://bioconductor.org/packages/release/bioc/vignettes/IWTomics/inst/doc/IWTomics.pdf
   ]]></help>
 
-  <citations>
-    <citation type="bibtex">
-      @ARTICLE{
-               iwt-functional-data,
-               author = {A Pini and S. Vantini},
-               title = {Interval-Wise Testing for functional data},
-               journal = {Journal of Nonparametric Statistics},
-               year = {2017},
-               volume = {29},
-               number = {2},
-               pages = {407-424}
-      }
-    </citation>
-    <citation type="bibtex">
-      @MANUAL{
-               iwtomics,
-               author = {Cremona, Marzia A and Pini, Alessia and Chiaromonte, Francesca and Vantini, Simone},
-               title = {IWTomics: Interval-Wise Testing for Omics Data},
-               note = {R package version 1.0.0},
-               year = {2017}
-      }
-    </citation>
-  </citations>
+  <expand macro="citations" />
 
 </tool>