--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/loadandplot.xml	Fri Oct 06 11:06:44 2017 -0400
@@ -0,0 +1,237 @@
+<tool id="iwtomics_loadandplot" name="IWTomics Load" version="@VERSION@.0">
+  <description>Smooth and Plot</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements" />
+
+  <command detect_errors="exit_code">
+<![CDATA[
+    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}'
+      #set region_galaxyids = ','.join( [ str( $r.hid ) for $r in $regions ] )
+      regionsgalaxyids='c(${region_galaxyids})'
+      #set region_names = '|'.join( [ str( $r.name ) for $r in $regions ] )
+      regionsfilenames='${region_names}'
+      #set region_header = str( $regionsheader )
+      #if $region_header != "None":
+        regionsheaderfile='${region_header}'
+      #end if
+      
+      #set feature_paths = '|'.join( [ str( $f ) for $f in $features ] )
+      featurespaths='${feature_paths}'
+      #set feature_galaxyids = ','.join( [ str( $f.hid ) for $f in $features ] )
+      featuresgalaxyids='c(${feature_galaxyids})'
+      #set feature_names = '|'.join( [ str( $f.name ) for $f in $features ] )
+      featuresfilenames='${feature_names}'
+      #set feature_header = str( $featuresheader )
+      #if $feature_header != "None":
+        featuresheaderfile='${feature_header}'
+      #end if
+
+      smoothing="'${conditionaltype.smoothing}'"
+      start.are.0based='${zerobased}'
+      #if $conditionaltype.smoothing == 'no':
+        alignment="'${conditionaltype.alignment}'"
+      #elif $conditionaltype.smoothing == 'locpoly':
+        bandwidth='${conditionaltype.locpolybandwidth}'
+        degree='${conditionaltype.locpolydegree}'
+        alignment="'${conditionaltype.conditionalscale.alignment}'"
+      #elif $conditionaltype.smoothing == 'kernel':
+        bandwidth='${conditionaltype.kernelbandwidth}'
+        alignment="'${conditionaltype.conditionalscale.alignment}'"
+      #elif $conditionaltype.smoothing == 'splines':
+        degree='${conditionaltype.splinesdegree}'
+        dist_knots='${conditionaltype.splinesdistknots}'
+        alignment="'${conditionaltype.conditionalscale.alignment}'"
+      #end if
+
+      #if $conditionaltype.smoothing != 'no':
+        #if $conditionaltype.conditionalscale.alignment == 'scale':
+          scale='${conditionaltype.conditionalscale.scalegrid}'
+          fill_gaps='TRUE'
+        #else
+          fill_gaps='${conditionaltype.conditionalscale.fillgaps}'
+        #end if
+      #end if
+
+      average='${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},${probs})'
+        #else:
+          probs='c(${plotres.conditionalplottype.probabilitiessection.prob0},${plotres.conditionalplottype.probabilitiessection.prob1},${plotres.conditionalplottype.probabilitiessection.prob2})'
+        #end if
+      #end if      
+]]>
+  </command>
+
+  <inputs>
+    <!-- regions -->
+    <param format="tabular" name="regions" type="data" label="Select region files" multiple="true" help="" />
+    <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="" />
+    <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="">
+      <option value="TRUE">0-based</option>
+      <option value="FALSE">1-based</option>
+    </param>
+
+    <!-- conditional smoothing -->
+    <conditional name="conditionaltype">
+      <!-- smoothing -->
+      <param name="smoothing" type="select" label="Smoothing" help="Type of smoothing to be applied to the feature curves.">
+        <option value="no">No</option>
+        <option value="locpoly">Local Polynomials</option>
+        <option value="kernel">Gaussian Kernel</option>
+        <option value="splines">B-Splines</option>
+      </param>
+      <!-- conditional choice: smoothing=no -->
+      <when value="no">
+        <expand macro="alignment" />
+      </when>
+      <!-- conditional choice: smoothing=locpoly -->
+      <when value="locpoly">
+        <param name="locpolybandwidth" type="integer" value="5" min="2" label="Bandwidth for smoothing" help="" />
+        <param name="locpolydegree" type="integer" value="3" min="0" label="Degree of local polynomial" help="" />
+        <!-- conditional region alignment -->
+        <expand macro="alignment-s" />
+      </when>
+      <!-- conditional choice: smoothing=kernel -->
+      <when value="kernel">
+        <param name="kernelbandwidth" type="integer" value="5" min="2" label="Bandwidth for smoothing" help="" />
+        <!-- conditional region alignment -->
+        <expand macro="alignment-s" />
+      </when>
+      <!-- conditional choice: smoothing=splines -->
+      <when value="splines">
+        <param name="splinesdegree" type="integer" value="3" min="0" label="Degree of B-splines" help="" />
+        <param name="splinesdistknots" type="integer" value="10" min="2" label="Distance between nodes (approximate)" help="" />
+        <!-- conditional region alignment -->
+        <expand macro="alignment-s" />
+      </when>
+    </conditional>
+
+    <!-- plot IWTomics results -->
+    <section name="plotres" title="Plot data" expanded="True">
+      <expand macro="plot-params" />
+    </section>
+  </inputs>
+
+  <outputs>
+    <data format="rdata" name="outrdata" label="${tool.name} on ${on_string}: IWTomicsData Object" from_work_dir="iwtomics.loadandplot.RData" />
+    <data format="tabular" name="outregions" label="${tool.name} on ${on_string}: Region Dataset IDs" from_work_dir="iwtomics.loadandplot.regions.txt" />
+    <data format="tabular" name="outfeatures" label="${tool.name} on ${on_string}: Feature IDs" from_work_dir="iwtomics.loadandplot.features.txt" />
+    <data format="pdf" name="outpdf" label="${tool.name} on ${on_string}: Plotted Data" from_work_dir="iwtomics.loadandplot.pdf" />
+  </outputs>
+
+  <tests>
+    <test>
+      <param name="regions" value="input/Controls_regions.bed,input/Elements1_regions.bed,input/Elements2_regions.bed,input/Elements3_regions.bed" ftype="bed" />
+      <param name="regionsheader" value="input/regions.header.txt" ftype="tabular" />
+      <param name="features" value="input/Feature1.bed,input/Feature2.bed" ftype="bed" />
+      <param name="featuresheader" value="input/features.header.bed.txt" ftype="tabular" />
+      <param name="zerobased" value="TRUE" />
+      <param name="smoothing" value="kernel" />
+      <param name="alignment" value="center" />
+      <param name="kernelbandwidth" value="5" />
+      <param name="fillgaps" value="TRUE" />
+      <param name="average" value="TRUE" />
+      <param name="size" value="TRUE" />
+      <param name="plottype" value="boxplot" />
+      <param name="prob0" value="0.25" />
+      <param name="prob1" value="0.5" />
+      <param name="prob2" value="0.75" />
+      <output name="outrdata" file="output_loadandplot/iwtomics.loadandplot.RData" compare="sim_size" />
+      <output name="outregions" file="output_loadandplot/iwtomics.loadandplot.regions.txt" />
+      <output name="outfeatures" file="output_loadandplot/iwtomics.loadandplot.features.txt" />
+      <output name="outpdf" file="output_loadandplot/iwtomics.loadandplot.pdf" compare="sim_size" />
+    </test>
+  </tests>
+
+  <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
+measurements) and to create a graphical representation of the feature measurements in each
+region datasets (aligned curves or pointwise quantile curves).
+
+-----
+
+**Region datasets**
+
+Each region dataset can be provided as a BED or Tabular file with tab delimited columns chr
+start end (extra columns present in the input file are ignored). Regions can be of different
+length::
+
+    chr2  49960150  50060150
+    chr2  55912445  56012445
+    ...
+
+-----
+
+**Feature measurements**
+
+Feature measurements corresponding to all the regions can be provided as a BED or Tabular
+file with tab delimited columns chr start end value::
+
+    chr2  49960150  49962150  0.9426
+    chr2  49962150  49964150  0.7816
+    ...
+
+Each feature must be measured in windows of a fixed size inside all the regions (missing
+values must be indicated as NA). Another way to import feature measurements is from a
+Tabular file with the first three columns chr start end corresponding to the different genomic
+regions, followed on the same row by all the measurements in fixed-size windows::
+
+    chr2  49960150  50060150  0.9426  0.7816  0.8921  ...  ...  1.2063
+    chr2  55912445  56012445  0.8719  0.9975  1.1619  ...  ...  0.9601
+    ...
+
+-----
+
+**Output**
+
+The tool returns:
+
+1. RData with the IWTomicsData object, that stores the aligned genomic region datasets, and their associated feature measurements;
+2. Region dataset identifiers;
+3. Feature identifiers;
+4. PDF file with the plotted data.
+
+1-3 can be used as input of the tool *IWTomics Test and Plot*
+
+-----
+
+.. class:: infomark
+
+**Notes**
+
+This Galaxy tool has been developed by Fabio Cumbo (Third University of Rome, Italy - fabio.cumbo@iasi.cnr.it) and Marzia A. Cremona (The Pennsylvania State University, USA - mac78@psu.edu).
+
+It implements a simplified version of the methods *smooth* and *plot* for *IWTomicsData* objects.
+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
+
+Example data can be found at:
+
+1. Simulated_data_
+2. ETn_data_
+
+.. _Simulated_data: https://usegalaxy.org/u/fabio-cumbo/h/iwtomics-example
+.. _ETn_data: https://usegalaxy.org/u/fabio-cumbo/h/iwtomics-etn-example
+  ]]></help>
+
+  <expand macro="citations" />
+
+</tool>