--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/loadandplot.xml	Wed May 31 11:07:22 2017 -0400
@@ -0,0 +1,325 @@
+<tool id="loadandplot" name="IWTomics Load" version="@VERSION@.0">
+  <description>Smooth and Plot</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements" />
+  <stdio>
+    <exit_code range="255" source="both" level="fatal" description="Missing IWTomics package. Please be sure to have it installed before using this tool." />
+    <exit_code range="10" source="both" level="fatal" description="An error has occurred reading the header file for regions. Please try again." />
+    <exit_code range="11" source="both" level="fatal" description="Not all region files are present in the first column of header file for regions." />
+    <exit_code range="20" source="both" level="fatal" description="An error has occurred reading the header file for features. Please try again." />
+    <exit_code range="21" source="both" level="fatal" description="Not all feature files are present in the first column of header file for features." />
+    <exit_code range="30" source="both" level="fatal" description="An error has occurred reading the data. Please try again." />
+    <exit_code range="31" source="both" level="fatal" description="Not enough columns in input file." />
+    <exit_code range="32" source="both" level="fatal" description="Duplicated regions in region file." />
+    <exit_code range="33" source="both" level="fatal" description="Duplicated windows in feature file." />
+    <exit_code range="34" source="both" level="fatal" description="Overlapping windows in feature file." />
+    <exit_code range="35" source="both" level="fatal" description="Windows in feature files do not cover all regions in region files." />
+    <exit_code range="36" source="both" level="fatal" description="All windows in a feature file must have the same size." />
+    <exit_code range="40" source="both" level="fatal" description="An error has occurred smoothing the data. Please try again." />
+    <regex match="Error" source="both" level="fatal" description="An error has occurred. Please try again." />
+  </stdio>
+
+  <command>
+<![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 = '"\\|"'.join( [ str( $rh.regionsheader ) for $rh in $regionsheaderrepeat ] )
+      #if $region_header != "":
+        regionsheaderfile="${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 = '"\\|"'.join( [ str( $fh.featuresheader ) for $fh in $featuresheaderrepeat ] )
+      #if $feature_header != "":
+        featuresheaderfile="${feature_header}"
+      #end if
+
+      smoothing="'${conditionaltype.smoothing}'"
+      start.are.0based="${zerobased}"
+      #if $conditionaltype.smoothing == 'no':
+        alignment="'${conditionaltype.alignment}'"
+      #elif $conditionaltype.smoothing == 'locpoly':
+        alignment="'${conditionaltype.locpolyconditionalscale.alignment}'"
+        #if $conditionaltype.locpolyconditionalscale.alignment == 'scale':
+          scale="${conditionaltype.locpolyconditionalscale.scalegrid}"
+        #end if
+        bandwidth="${conditionaltype.locpolybandwidth}"
+        degree="${conditionaltype.locpolydegree}"
+        fill_gaps="${conditionaltype.fillgaps}"
+      #elif $conditionaltype.smoothing == 'kernel':
+        alignment="'${conditionaltype.kernelconditionalscale.alignment}'"
+        #if $conditionaltype.kernelconditionalscale.alignment == 'scale':
+          scale="${conditionaltype.kernelconditionalscale.scalegrid}"
+        #end if
+        bandwidth="${conditionaltype.kernelbandwidth}"
+        fill_gaps="${conditionaltype.fillgaps}"
+      #elif $conditionaltype.smoothing == 'splines':
+        alignment="'${conditionaltype.splinesconditionalscale.alignment}'"
+        #if $conditionaltype.splinesconditionalscale.alignment == 'scale':
+          scale="${conditionaltype.splinesconditionalscale.scalegrid}"
+        #end if
+        degree="${conditionaltype.splinesdegree}"
+        dist_knots="${conditionaltype.splinesdistknots}"
+        fill_gaps="${conditionaltype.fillgaps}"
+      #end if
+
+      average="${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
+
+      >& /dev/null
+]]>
+    <!--
+    to print the stack add the following line at the end of the command and enable the corresponding entry in output
+    2> "${stackerr}"
+    -->
+  </command>
+
+  <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>
+
+    <!-- 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>
+
+    <!-- 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">
+        <param name="alignment" type="select" label="Region alignment" help="">
+          <option value="center">Center - Alignment on the central position</option>
+          <option value="left">Left - Alignment on the starting position</option>
+          <option value="right">Right - Alignment on the ending position</option>
+        </param>
+      </when>
+      <!-- conditional choice: smoothing=locpoly -->
+      <when value="locpoly">
+        <!-- conditional region alignment -->
+        <conditional name="locpolyconditionalscale">
+          <param name="alignment" type="select" label="Region alignment" help="">
+            <option value="center">Center - Alignment on the central position</option>
+            <option value="left">Left - Alignment on the starting position</option>
+            <option value="right">Right - Alignment on the ending position</option>
+            <option value="scale">Scale - Scaling all regions to the same length</option>
+          </param>
+          <when value="scale">
+            <param name="scalegrid" type="integer" value="0" min="0" label="Number of grid points" help="Number of equally-spaced grid points over which the smoothed curves are evaluated." />
+          </when>
+        </conditional>
+
+        <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="" />
+
+        <!-- fill gaps -->
+        <param name="fillgaps" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Use smoothing to fill gaps (NA measurements)" help="" />
+      </when>
+      <!-- conditional choice: smoothing=kernel -->
+      <when value="kernel">
+        <!-- conditional region alignment -->
+        <conditional name="kernelconditionalscale">
+          <param name="alignment" type="select" label="Region alignment" help="">
+            <option value="center">Center - Alignment on the central position</option>
+            <option value="left">Left - Alignment on the starting position</option>
+            <option value="right">Right - Alignment on the ending position</option>
+            <option value="scale">Scale - Scaling all regions to the same length</option>
+          </param>
+          <when value="scale">
+            <param name="scalegrid" type="integer" value="0" min="0" label="Number of grid points" help="Number of equally-spaced grid points over which the smoothed curves are evaluated." />
+          </when>
+        </conditional>
+
+        <param name="kernelbandwidth" type="integer" value="5" min="2" label="Bandwidth for smoothing" help="" />
+
+        <!-- fill gaps -->
+        <param name="fillgaps" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Use smoothing to fill gaps (NA measurements)" help="" />
+      </when>
+      <!-- conditional choice: smoothing=splines -->
+      <when value="splines">
+        <!-- conditional region alignment -->
+        <conditional name="splinesconditionalscale">
+          <param name="alignment" type="select" label="Region alignment" help="">
+            <option value="center">Center - Alignment on the central position</option>
+            <option value="left">Left - Alignment on the starting position</option>
+            <option value="right">Right - Alignment on the ending position</option>
+            <option value="scale">Scale - Scaling all regions to the same length</option>
+          </param>
+          <when value="scale">
+            <param name="scalegrid" type="integer" value="0" min="0" label="Number of grid points" help="Number of equally-spaced grid points over which the smoothed curves are evaluated." />
+          </when>
+        </conditional>
+
+        <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="" />
+
+        <!-- fill gaps -->
+        <param name="fillgaps" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Use smoothing to fill gaps (NA measurements)" help="" />
+      </when>
+    </conditional>
+
+    <!-- plot IWTomics results -->
+    <section name="plotres" title="Plot data" expanded="True">
+      <!-- average -->
+      <param name="average" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Plot the mean curves" help="" />
+      <!-- sample size in each position -->
+      <param name="size" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Plot sample size in each position" help="" />
+      <!-- conditional plot type -->
+      <conditional name="conditionalplottype">
+        <!-- plot type -->
+        <param name="plottype" type="select" label="Plot type" help="">
+          <option value="boxplot">Pointwise quantile curves (boxplot)</option>
+          <option value="curves">Curves (aligned)</option>
+        </param>
+        <!-- conditional choice: plottype=boxplot -->
+        <when value="boxplot">
+          <section name="probabilitiessection" title="Probabilities" expanded="True" help="Probabilities corresponding to the quantile curves to be drawn.">
+            <param name="prob0" size="3" type="float" value="0.25" min="0.0" max="1.0" label="Probability" />
+            <param name="prob1" size="3" type="float" value="0.5" min="0.0" max="1.0" label="Probability" />
+            <param name="prob2" size="3" type="float" value="0.75" min="0.0" max="1.0" label="Probability" />
+            <repeat name="probabilities" title="Probabilities">
+              <param name="prob" size="3" type="float" value="0.5" min="0.0" max="1.0" label="Probability" />
+            </repeat>
+          </section>
+        </when>
+      </conditional>
+    </section>
+  </inputs>
+
+  <outputs>
+    <!--<data format="txt" name="stackerr" label="iwtomics.loadandplot.stackerr.txt" from_work_dir="iwtomics.loadandplot.stackerr.txt" />-->
+    <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>
+
+  <help>
+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) and Marzia A. Cremona (The Pennsylvania State University, USA).
+
+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
+  </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 0.99.12},
+               year = {2017}
+      }
+    </citation>
+  </citations>
+
+</tool>