--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/chicPlotViewpoint.xml	Mon Dec 16 15:40:31 2019 -0500
@@ -0,0 +1,220 @@
+<tool id="hicexplorer_chicplotviewpoint" name="@BINARY@" version="@WRAPPER_VERSION@.0">
+    <description>creates plots for viewpoints</description>
+    <macros>
+        <token name="@BINARY@">chicPlotViewpoint</token>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+        #import re
+
+        mkdir interactionFiles &&
+        mkdir differentialFolder &&
+        mkdir significantFolder &&
+        mkdir plots &&
+
+        
+        #for $file in $interactionFiles:
+            #set identifier = @ESCAPE_IDENTIFIER_FILE@
+            ln -s '$file' 'interactionFiles/$identifier' &&
+        #end for
+
+        #if $differentialFiles:
+            #for $file in $differentialFiles:
+                #set identifier = @ESCAPE_IDENTIFIER_FILE@
+                ln -s '$file' 'differentialFolder/$identifier' &&
+            #end for
+        #end if
+
+        #if $significantFiles:
+            #for $file in $significantFiles:
+                #set identifier = @ESCAPE_IDENTIFIER_FILE@
+                ln -s '$file' 'significantFolder/$identifier' &&
+            #end for
+        #end if
+
+        #if $batchmode_conditional.batchmode_selector == 'optionSinglemode':
+            #set $interactonfileslist = ' '.join([ '\'interactionFiles/%s\'' % @ESCAPE_IDENTIFIER_FILE@ for $file in $interactionFiles ])
+            #set $differentialfileslist = ' '.join([ '\'differentialFolder/%s\'' % @ESCAPE_IDENTIFIER_FILE@ for $file in $differentialFiles ])
+            #set $significantfileslist = ' '.join([ '\'significantFolder/%s\'' % @ESCAPE_IDENTIFIER_FILE@ for $file in $significantFiles ])
+        
+        #end if
+
+        @BINARY@
+            #if $batchmode_conditional.batchmode_selector == 'optionSinglemode':
+                --interactionFile $interactonfileslist
+                #if $differentialFiles:
+                    --differentialTestResult $differentialfileslist
+                #end if
+
+                #if $significantFiles:
+                    --significantInteractions $significantfileslist 
+                #end if
+
+                -o out_plot.$image_file_format
+            #else:
+                --interactionFile $batchmode_conditional.interactionFilesOrderFile
+                --interactionFileFolder interactionFiles
+                #if $batchmode_conditional.differentialFilesOrderFile:
+                    --differentialTestResult $batchmode_conditional.differentialFilesOrderFile
+                    --differentialTestResultsFolder differentialFolder
+                #end if
+                #if $batchmode_conditional.significantInteractionFilesOrderFile:
+                    --significantInteractions $batchmode_conditional.significantInteractionFilesOrderFile
+                    --significantInteractionFileFolder significantFolder
+                #end if
+                --plotSampleNumber $batchmode_conditional.computeSampleNumber
+
+                --batchMode
+                --outputFolder plots
+                --outputFormat $image_file_format
+
+
+            #end if
+
+            --range $rangeUpstream $rangeDownstream
+            #if $backgroundModelFile:
+                --backgroundModelFile $backgroundModelFile
+            #end if
+
+            #if $dpi:
+                --dpi $dpi
+            #end if 
+
+            #if $maxPValue:
+                --maxPValue $maxPValue
+            #end if
+
+            #if $minPValue:
+                --minPValue $minPValue
+            #end if
+
+            --binResolution $resolution
+            #if $colormap:
+                --colorMapPvalue $colormap
+            #end if
+
+            $pvalue
+            #if $xFold:
+                --xFold $xFold
+            #end if
+            --colorList $colorList
+            --threads @THREADS@
+
+            #if $batchmode_conditional.batchmode_selector == 'optionSinglemode':
+                && mv out_plot.$image_file_format plots/out_plot.$image_file_format
+            #end if
+    ]]></command>
+    <inputs>
+        <param name='interactionFiles' type="data" format="interval" label="Interaction files" multiple="true"/>
+        <param name='differentialFiles' type="data" format="interval" label="Rejected H0 files" multiple="true" optional='true'/>
+        <param name='significantFiles' type="data" format="interval" label="Significant interaction files" multiple="true" optional='true'/>
+        
+        <param name="rangeUpstream" type="integer" value="500000"  label="Upstream range" help='Defines the region upstream of a reference point which should be considered in the analysis.' />
+        <param name="rangeDownstream" type="integer" value="500000"  label="Downstream range" help='Defines the region upstream of a reference point which should be considered in the analysis.' />   
+        <param argument="--backgroundModelFile" type="data" format='tabular'
+                        label="Background model"
+                        help="The background file computed by chicViewpointBackgroundModel" optional='true'/>
+     
+        <conditional name="batchmode_conditional">
+            <param name="batchmode_selector" type="select" label="Compute files individually or in batch mode">
+                <option value="optionBatchmode">Batch processing</option>
+                <option value="optionSinglemode" selected="True">Single file processing</option>
+            </param>
+            <when value="optionBatchmode">
+                <param name='interactionFilesOrderFile' type="data" format="txt" label="Interaction file order"/> 
+                <param name='differentialFilesOrderFile' type="data" format="txt" label="Rejected H0 file order" optional='true'/>
+                <param name='significantInteractionFilesOrderFile' type="data" format="txt" label="Significant file order" optional='true'/>
+                <param name='computeSampleNumber' type="integer" value='2' label="Plot n sample in one plot"/> 
+
+            </when>
+            <when value="optionSinglemode">              
+            </when>
+        </conditional>
+
+
+        <param argument="--maxPValue" type="float" optional="true" label="Max p-value" help="Maximum value of the plotted p-value."/>
+        <param argument="--minPValue" type="float" optional="true" label="Min p-value" help="Minimum value of the plotted p-value."/>
+        <param name='resolution' type='integer' value='1000' label='Resolution of cHi-C data' help='Resolution of the bin in genomic units. Values are usually e.g. 1000 for a 1kb, 5000 for a 5kb or 10000 for a 10kb resolution.' optional='true'/>
+        <param name='pvalue' type='boolean' truevalue='--pValue'  falsevalue="" checked="false" label="Plot p-values as a colorbar"/>
+        <expand macro="colormap" />
+
+        <param name='xFold' type='float' value='' label='X-fold mean background' help='Plot x-fold region for the mean background.' optional='true'/>
+
+        <param name="image_file_format" type="select" label="Image output format">
+            <option value="png" selected="True">png</option>
+            <option value="svg">svg</option>
+            <option value="pdf">pdf</option>
+        </param>
+        <param name='dpi' type='integer' label='DPI for image' help='Change the default resolution of the plot.' optional='true'/>
+        <param name='colorList' type='text' value='g b c m y k' label='Color list' help='Colorlist for the viewpoint lines. For all available colors please check matplotlib documentation: https://matplotlib.org/3.1.0/gallery/color/named_colors.html' optional='true'/>
+
+    
+    </inputs>
+    <outputs>
+        <collection name="plotsCollection" type="list" label="cHi-C viewpoint plots">
+            <discover_datasets pattern="__name_and_ext__" directory="plots" />
+        </collection>
+      
+    </outputs>
+    <tests>
+        <test>
+            <param name="interactionFiles" value="cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.bed,cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_4487435_4487435_Sox17.bed,cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.bed,cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_4487435_4487435_Sox17.bed,cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.bed,cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.bed"/>
+            <param name="differentialFiles" value="cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_rejected.bed,cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_rejected.bed,cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_rejected.bed"/>
+            <param name="significantFiles" value="cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_output_significant.bed,cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.bed,cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_output_significant.bed,cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_4487435_4487435_Sox17_output_significant.bed,cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_output_significant.bed,cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_output_significant.bed"/>
+
+            
+            <conditional name="batchmode_conditional">
+                <param name="batchmode_selector" value='optionBatchmode'/>
+                <param name="interactionFilesOrderFile" value='cHi-C/chicViewpoint/fileNames_two_matrices.txt'/>
+                <param name="differentialFilesOrderFile" value='cHi-C/chicDifferentialTest/rejectedFilesList.txt'/>
+                <param name="significantInteractionFilesOrderFile" value='cHi-C/chicSignificantInteractions/output_5_significant_files.txt'/>
+                <param name='computeSampleNumber' value='2'/>
+            </conditional>
+            <param name="pvalue" value='True'/>
+            <param name="alpha" value='0.5'/>
+            <param name='backgroundModelFile' value='cHi-C/background.bed'/>
+            <param name='xFold' value='1.5'/>
+            <output_collection name="plotsCollection" type="list" count="3">
+                <element name="Eya1_FL-E13-5_MB-E10-5_chr1_chr1_14300280" file="cHi-C/chicPlotViewpoint/batchMode/two/Eya1_FL-E13-5_MB-E10-5_chr1_chr1_14300280.png" ftype="png" compare='sim_size' delta='40000'/>
+                <element name="Sox17_FL-E13-5_MB-E10-5_chr1_chr1_4487435" file="cHi-C/chicPlotViewpoint/batchMode/two/Sox17_FL-E13-5_MB-E10-5_chr1_chr1_4487435.png" ftype="png" compare='sim_size' delta='40000'/>
+                <element name="Tfap2d_FL-E13-5_MB-E10-5_chr1_chr1_19093103" file="cHi-C/chicPlotViewpoint/batchMode/two/Tfap2d_FL-E13-5_MB-E10-5_chr1_chr1_19093103.png" ftype="png" compare='sim_size' delta='40000'/>
+            </output_collection>
+
+        </test>
+        <test>
+            <param name="interactionFiles" value="cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.bed"/>
+            
+            <conditional name="batchmode_conditional">
+                <param name="batchmode_selector" value='optionSinglemode'/>
+            </conditional>
+
+            <output_collection name="plotsCollection" type="list" count="1">
+                <element name="out_plot" file="cHi-C/chicPlotViewpoint/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.png" ftype="png" compare='sim_size' delta='40000'/>
+
+            </output_collection>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+Plot of viewpoints
+==================
+
+chicPlotViewpoint plots one or many viewpoints with the average background model and the computed p-value per sample. Moreover it can highlight differential interactions of two samples and or significant regions.
+
+An example usage is:
+
+`$ chicPlotViewpoint --interactionFile viewpoint1.bed viewpoint2.bed --range 500000 500000  --backgroundModelFile background_model.bed --pValue --outFileName viewpoint1_2.png --dpi 300`
+
+
+In batch mode the list of file names and the folders containing the files need to be given:
+
+`$ chicPlotViewpoint --interactionFile viewpoint_names.txt -interactionFileFolder viewpointFilesFolder --differentialTestResult rejected_H0.txt --differentialTestResultsFolder differentialFolder --range 500000 500000 --backgroundModelFile background_model.bed --pValue --outputFolder plotsFOlder --dpi 300 --threads 20`
+
+
+For more information about HiCExplorer please consider our documentation on readthedocs.io_
+
+.. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
+]]></help>
+    <expand macro="citations" />
+</tool>