--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pyGenomeTracks.xml	Sat Jun 23 02:28:35 2018 -0400
@@ -0,0 +1,768 @@
+<tool id="pygenomeTracks" name="@BINARY@" version="@WRAPPER_VERSION@.0">
+    <description>plot genomic data tracks</description>
+    <macros>
+        <token name="@BINARY@">pyGenomeTracks</token>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code">
+<![CDATA[
+
+        sed '/^$/d' '$tracks_config' &&
+        @BINARY@
+            --tracks '$tracks_config'
+            #if $region and $region is not None:
+                --region '$region'
+            #end if
+            --outFileName plot.$image_file_format
+        && mv plot.$image_file_format plot
+]]>
+    </command>
+    <configfiles>
+        <configfile name="tracks_config">
+#if $x_axis.x_axis_select == "yes":
+[x-axis]
+#if $x_axis.fontsize:
+fontsize = $x_axis.fontsize
+#end if
+#if $x_axis.where:
+where = $x_axis.where
+#end if
+#end if
+#for $counter, $track in enumerate($tracks):
+#if $track.track_file_style_conditional.track_file_style_selector == "hic_matrix_option":
+
+#for $counter_matrix, $data_matrix in enumerate($track.track_file_style_conditional.matrix_h5_cooler_multiple):
+[hic_section_$counter]
+file = $data_matrix
+file_type = hic_matrix
+#if $track.track_file_style_conditional.title:
+title = $track.track_file_style_conditional.title
+#else:
+title = $data_matrix.name
+#end if
+#if $track.track_file_style_conditional.depth:
+depth = $track.track_file_style_conditional.depth
+#end if
+#if $track.track_file_style_conditional.colormap:
+colormap = $track.track_file_style_conditional.colormap
+#end if
+#if $track.track_file_style_conditional.min_value:
+min_value = $track.track_file_style_conditional.min_value
+#end if
+#if $track.track_file_style_conditional.max_value:
+max_value = $track.track_file_style_conditional.max_value
+#end if
+transform = $track.track_file_style_conditional.transform
+height = $track.track_file_style_conditional.height_matrix
+
+#if $track.track_file_style_conditional.boundaries_file is not None:
+#set boundary_file = $track.track_file_style_conditional.boundaries_file[$counter_matrix]
+boundaries_file = $boundary_file
+#end if
+
+#if $track.track_file_style_conditional.x_labels:
+x labels = $track.track_file_style_conditional.x_labels
+#end if
+#if $track.track_file_style_conditional.type:
+type = $track.track_file_style_conditional.type
+#end if
+#if $track.track_file_style_conditional.show_masked_bins:
+show_masked_bins = $track.track_file_style_conditional.show_masked_bins
+#end if
+#if $track.track_file_style_conditional.scale_factor:
+scale factor = $track.track_file_style_conditional.scale_factor
+#end if
+
+[spacer]
+#if $track.track_file_style_conditional.spacer_height:
+height = $track.track_file_style_conditional.spacer_height
+#end if
+#end for
+
+#end if
+
+
+
+#if $track.track_file_style_conditional.track_file_style_selector == "tad_score_track_option":
+
+#for $data_bedgraph in $track.track_file_style_conditional.track_input_bedgraph:
+[tad_score_$counter]
+file = $data_bedgraph 
+#if $track.track_file_style_conditional.title:
+title = $track.track_file_style_conditional.title
+#else:
+title = $data_bedgraph.name
+#end if
+#if $track.track_file_style_conditional.color:
+color = $track.track_file_style_conditional.color
+#end if
+#if $track.track_file_style_conditional.height_tad:
+height = $track.track_file_style_conditional.height_tad
+#end if
+#if $track.track_file_style_conditional.type_lines:
+type = $track.track_file_style_conditional.type_lines
+#end if
+#if $track.track_file_style_conditional.show_data:
+show data range = $track.track_file_style_conditional.show_data
+#end if
+
+#set $columns = len(open(str($track.track_file_style_conditional.track_input_bedgraph)).readline().split('\t'))
+#if $columns > 5:
+file_type = bedgraph_matrix
+#else:
+file_type = bedgraph
+#end if
+type = lines
+[spacer]
+#if $track.track_file_style_conditional.spacer_height:
+height = $track.track_file_style_conditional.spacer_height
+#end if
+#end for
+#end if
+
+
+
+
+#if $track.track_file_style_conditional.track_file_style_selector == "chrom_states_option":
+#for $data_bed in $track.track_file_style_conditional.track_input_bed:
+
+[chrom states_$counter]
+file = $data_bed
+#if $track.track_file_style_conditional.title:
+title = $track.track_file_style_conditional.title
+#else:
+title = $data_bed.name
+#end if
+#if $track.track_file_style_conditional.color:
+color = $track.track_file_style_conditional.color
+#end if
+display = collapsed
+#if $track.track_file_style_conditional.height_chrom:
+height = $track.track_file_style_conditional.height_chrom
+#end if
+#if $track.track_file_style_conditional.border_color:
+border_color = $track.track_file_style_conditional.border_color
+#end if
+file_type = bed
+[spacer]
+#if $track.track_file_style_conditional.spacer_height:
+height = $track.track_file_style_conditional.spacer_height
+#end if
+#end for
+
+#end if
+
+
+
+
+#if $track.track_file_style_conditional.track_file_style_selector == "gene_track_option":
+#for $data_bed in $track.track_file_style_conditional.track_input_bed:
+
+[genes_$counter]
+file = $data_bed
+#if $track.track_file_style_conditional.title:
+title = $track.track_file_style_conditional.title
+#else:
+title = $data_bed.name
+#end if
+#if $track.track_file_style_conditional.color:
+color = $track.track_file_style_conditional.color
+#end if
+
+#if $track.track_file_style_conditional.height_bed:
+height = $track.track_file_style_conditional.height_bed
+#end if
+
+#if $track.track_file_style_conditional.labels:
+labels = $track.track_file_style_conditional.labels
+#end if
+
+#if $track.track_file_style_conditional.type:
+type = $track.track_file_style_conditional.type
+#end if
+
+file_type = bed
+#if $track.track_file_style_conditional.fontsize:
+fontsize = $track.track_file_style_conditional.fontsize
+#end if
+
+#if $track.track_file_style_conditional.gene_rows:
+gene rows = $track.track_file_style_conditional.gene_rows
+#end if
+
+#if $track.track_file_style_conditional.global_max_row:
+global max row = $track.track_file_style_conditional.global_max_row
+#end if
+[spacer]
+#if $track.track_file_style_conditional.spacer_height:
+height = $track.track_file_style_conditional.spacer_height
+#end if
+#end for
+#end if
+
+
+#if $track.track_file_style_conditional.track_file_style_selector == "bedgraph_track_option":
+#for $data_bedgraph in $track.track_file_style_conditional.track_input_bedgraph:
+
+[bedgraph_$counter]
+file = $data_bedgraph
+#if $track.track_file_style_conditional.title:
+title = $track.track_file_style_conditional.title
+#else:
+title = $data_bedgraph.name
+#end if
+#if $track.track_file_style_conditional.color:
+color = $track.track_file_style_conditional.color
+#end if
+#if $track.track_file_style_conditional.height_bedgraph:
+height = $track.track_file_style_conditional.height_bedgraph
+#end if
+#if $track.track_file_style_conditional.show_data:
+show data range = $track.track_file_style_conditional.show_data
+#end if
+
+#set $columns = len(open(str($track.track_file_style_conditional.track_input_bedgraph)).readline().split('\t'))
+#if $columns > 5:
+file_type = bedgraph_matrix
+#else:
+file_type = bedgraph
+#end if
+type = lines
+[spacer]
+#if $track.track_file_style_conditional.spacer_height:
+height = $track.track_file_style_conditional.spacer_height
+#end if
+#end for
+#end if
+
+#if $track.track_file_style_conditional.track_file_style_selector == "bigwig_track_option":
+#for $data_bigwig in $track.track_file_style_conditional.track_input_bigwig:
+[bigwig_$counter]
+file = $data_bigwig
+#if $track.track_file_style_conditional.title:
+title = $track.track_file_style_conditional.title
+#else:
+title = $data_bigwig.name
+#end if
+color = $track.track_file_style_conditional.color
+#if $track.track_file_style_conditional.min_value:
+min_value = $track.track_file_style_conditional.min_value
+#else:
+min_value = 0
+#end if
+#if $track.track_file_style_conditional.max_value:
+max_value = $track.track_file_style_conditional.max_value
+#else:
+max_value = auto
+#end if
+height = $track.track_file_style_conditional.height_bigwig
+#if $track.track_file_style_conditional.number_of_bins:
+number of bins = $track.track_file_style_conditional.number_of_bins
+#end if
+nans to zeros = $track.track_file_style_conditional.nans_to_zeros
+#if $track.track_file_style_conditional.type_conditional == 'fill_option':
+type = fill
+#elif $track.track_file_style_conditional.type_conditional == 'line_option':
+type = line:$track.track_file_style_conditional.type_conditional.height_line
+#elif $track.track_file_style_conditional.type_conditional == 'point_option':
+type = points:$track.track_file_style_conditional.type_conditional.width_point
+#end if
+#if $track.track_file_style_conditional.data_range:
+show data range = $track.track_file_style_conditional.data_range
+#end if
+file_type = bigwig
+[spacer]
+#if $track.track_file_style_conditional.spacer_height:
+height = $track.track_file_style_conditional.spacer_height
+#end if
+#end for
+#end if
+
+
+#if $track.track_file_style_conditional.track_file_style_selector == "bedgraph_matrix_track_option":
+#for $data_bedgraph_matrix in $track.track_file_style_conditional.track_input_bedgraph_matrix:
+
+[bedgraph_matrix_$counter]
+file = $data_bedgraph_matrix
+#if $track.track_file_style_conditional.title:
+title = $track.track_file_style_conditional.title
+#else:
+title = $data_bedgraph_matrix.name
+#end if
+#if $track.track_file_style_conditional.height_bedgraph:
+height = $track.track_file_style_conditional.height_bedgraph
+#end if
+orientation = inverted
+#if $track.track_file_style_conditional.min_value:
+min_value = $track.track_file_style_conditional.min_value
+#end if
+#if $track.track_file_style_conditional.max_value:
+max_value = $track.track_file_style_conditional.max_value
+#end if
+#if $track.track_file_style_conditional.type_lines:
+type = $track.track_file_style_conditional.type_lines
+#end if
+file_type = bedgraph_matrix
+plot horizontal lines=False
+[spacer]
+#if $track.track_file_style_conditional.spacer_height:
+height = $track.track_file_style_conditional.spacer_height
+#end if
+#end for
+#end if
+
+#if $track.track_file_style_conditional.track_file_style_selector == "vlines_track_option":
+
+[vlines_$counter]
+file = $track.track_file_style_conditional.track_input_bed_single
+type = vlines
+file_type = bed
+#end if
+#if $track.track_file_style_conditional.track_file_style_selector == "spacer_option":
+
+[spacer]
+#if $track.track_file_style_conditional.spacer_height:
+height = $track.track_file_style_conditional.spacer_height
+#end if
+#end if
+#end for</configfile>
+    </configfiles>
+    <inputs>
+        <expand macro="region" />
+
+        <repeat name="tracks" min="1" title="Include tracks in your plot"
+            help="Tracks can be of different filetypes. E.g BED, HiC-Matrix, BigWig or BedGraph">
+            <conditional name="track_file_style_conditional">
+                <param name="track_file_style_selector" type="select" label="Choose style of the track">
+                    <option value="hic_matrix_option">TAD visualization</option>
+                    <option value="chrom_states_option">Chromatine states</option>
+                    <option value="tad_score_track_option">TAD score</option>
+                    <option value="gene_track_option">Gene track / Bed track</option>
+                    <option value="bigwig_track_option">Bigwig track</option>
+                    <option value="bedgraph_track_option">Bedgraph track </option>
+                    <option value="bedgraph_matrix_track_option">Bedgraph matrix track</option>
+                    <option value="vlines_track_option">Vlines track</option>
+                    <option value="spacer_option">Spacer</option>
+                </param>
+                <when value="hic_matrix_option">
+                    <expand macro="plot_title" />
+                    <expand macro="matrix_h5_cooler_multiple_macro" />
+
+                    <expand macro="colormap" />
+                    <param name="depth" type="integer" value="8000000" optional="True" label="Depth" />
+                    <param name="min_value" type="float" value="" optional="True" label="Minimum value"/>
+                    <param name="max_value" type="float" value="" optional="True" label="Maximum value"/>
+                    <param name="transform" type="select" label="Plot the transformed value">
+                        <option value="log1p" selected="True" >log1p</option>
+                        <option value="log">log</option>
+                        <option value="-log">-log</option>
+
+                    </param>
+                    <param name="height_matrix" type="float" value="1.5" optional="True" label="height"/>
+
+                    <param name="type" type="select" optional="True" label="Plotting type">
+                        <option value="arcplot">arcplot</option>
+                        <option value="interaction">interaction</option>
+                    </param>
+                    <param name="show_masked_bins" type="boolean" truevalue="yes" falsevalue="no" checked="false"
+                            label="Show masked bins" />
+                    <param name="boundaries_file" type="data" optional="True" format="bed" label="Boundaries file" multiple='True'/> <!-- multiple='True'-->
+                    <param name="scale_factor" type="float" value="1.0" optional="True" label="Scale factor" help="if the values in the matrix need to be scaled the following parameter can be used" />
+                    <param name="x_labels" type="boolean" truevalue="yes" falsevalue="no" optional="True" label="Show x labels" />
+                    <expand macro="spacer_macro" />
+
+                </when>
+                <when value="tad_score_track_option">
+                    <expand macro="plot_title" />
+                    <expand macro="track_input_bedgraph_macro" />
+                    <param name="color" type="color" value="#000000" label="Color of track" optional="True" />
+                    <param name="type_lines" type="boolean" truevalue="lines" falsevalue="" checked="false"
+                            label="Set 'type' to 'lines'" help="if type is set as lines, then the TAD score lines are drawn instead
+                            of the matrix set to lines if a heatmap representing the matrix is not wanted"/>
+                    <param name="height_tad" type="float" value="0.2" optional="True" label="height"/>
+                    <param name='show_data' type="boolean" truevalue="yes" falsevalue="no" checked="false" optional="True" label="Show visualization of data range" />
+                    <expand macro="spacer_macro" />
+
+                </when>
+                <when value="chrom_states_option">
+                    <expand macro="plot_title" />
+
+                    <expand macro="track_input_bed_macro" />
+                    <param name="color" type="color" value="#000000" label="Color of track" optional="True" />
+
+                    <param name="border_color" type="color" value="#000000" label="Border color" optional="True" />
+                    <param name="height_chrom" type="float" value="1.5" optional="True" label="height"/>
+                    <param name="labels" type="boolean" truevalue="on" falsevalue="off" checked="true"
+                            label="Plot labels" />
+                    <expand macro="spacer_macro" />
+                    
+                </when>
+                <when value="gene_track_option">
+                    <expand macro="plot_title" />
+
+                    <expand macro="track_input_bed_macro" />
+                    <param name="color" type="color" value="#000000" label="Color of track" optional="True" />
+                    <param name="height_bed" type="float" value="1.5" optional="True" label="height"/>
+                    <param name="labels" type="boolean" truevalue="on" falsevalue="off" checked="true"
+                            label="Plot labels" />
+                    <param name="type" type="select" optional="True" label="Type">
+                        <option value="genes">genes</option>
+                        <option value="domains">domains</option>
+                    </param>
+                    <param name="global_max_row" type="boolean" truevalue="yes" falsevalue="no" checked="false"
+                            label="Global max rows" />
+                    <param name="gene_rows" type="integer" value="" optional="True" label="Gene rows" />
+                    <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" />
+                    <expand macro="spacer_macro" />
+
+                </when>
+                <when value="bedgraph_track_option">
+                    <expand macro="plot_title" />
+                    <expand macro="track_input_bedgraph_macro" />
+                    <param name="color" type="color" value="#000000" label="Color of track" optional="True" />
+
+                    <param name="height_bedgraph" type="float" value="0.2" optional="True" label="height"/>
+                    <param name='show_data' type="boolean" truevalue="yes" falsevalue="no" checked="false" optional="True" label="Show visualization of data range" />
+                    <expand macro="spacer_macro" />
+
+                </when>
+                <when value="bigwig_track_option">
+                    <expand macro="plot_title" />
+
+                    <expand macro="track_input_bigwig_macro" />
+                    <param name="color" type="color" value="#000000" label="Color of track" optional="True" />
+
+                    <param name="min_value" type="float" value="" optional="True" label="Minimum value"/>
+                    <param name="max_value" type="float" value="" optional="True" label="Maximum value"/>
+
+                    <param name="height_bigwig" type="float" value="1.5" optional="True" label="height"/>
+                    <param name="number_of_bins" type="integer" value="" optional="True" label="Number of bins" />
+                    <param name="nans_to_zeros" type="boolean" truevalue="True" falsevalue="False" checked="false"
+                            label="NAN's to zeros" />
+                    <conditional name="type_conditional">
+                         <param name="type_selector" type="select" label="Choose style of the plot.">
+                            <option value="fill_option">fill</option>
+                            <option value="line_option">line</option>
+                            <option value="point_option">point</option>
+                        </param>
+                    <when value="line_option">
+                        <param name="width_line" type="float" value="0.5" optional="True" label="Width"/>
+                    </when>
+                    <when value="point_option">
+                        <param name="width_point" type="float" value="0.5" optional="True" label="Width"/>
+                    </when>
+                    <when value="fill_option" />
+                    </conditional>
+                    <param name="data_range" type="boolean" truevalue="yes" falsevalue="no" optional="True" checked="false" />
+                    <expand macro="spacer_macro" />
+
+                </when>
+
+
+                <when value="bedgraph_matrix_track_option">
+                    <expand macro="plot_title" />
+
+                    <expand macro="track_input_bedgraph_matrix_macro" />
+                    <param name="min_value" type="float" value="" optional="True" label="Minimum value"/>
+                    <param name="max_value" type="float" value="" optional="True" label="Maximum value"/>
+
+                    <param name="height_bedgraph" type="float" value="1.5" optional="True" label="height"/>
+
+                     <param name="type_lines" type="boolean" truevalue="lines" falsevalue="" checked="false"
+                            label="Set 'type' to 'lines'" help="if type is set as lines, then the TAD score lines are drawn instead
+                            of the matrix set to lines if a heatmap representing the matrix is not wanted"/>
+                    <expand macro="spacer_macro" />
+
+                </when>
+                <when value="vlines_track_option">
+                    <expand macro="track_input_bed_single_macro" />
+                </when>
+                <when value="spacer_option">
+                    <expand macro="spacer_macro" />
+                </when>
+            </conditional>
+
+        </repeat>
+
+
+        <conditional name="x_axis">
+            <param name="x_axis_select" type="select" label="Configure x-axis">
+                <option value="no" selected="True">No</option>
+                <option value="yes">Yes</option>
+            </param>
+            <when value="yes">
+                <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" />
+                <param name="where" type="select" optional="True" label="Where to place the x-axis">
+                    <option value="top">Top</option>
+                    <option value="bottom">Bottom</option>
+                </param>
+            </when>
+            <when value="no" />
+        </conditional>
+        <param name="image_file_format" type="select" label="Image output format">
+                <option value="png">png</option>
+                <option value="svg">svg</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data format="png" name="outFileName" from_work_dir="plot" label="${tool.name} on [${on_string}]: Plot">
+            <change_format>
+                <when input="image_file_format" value="png" format="png" />
+                <when input="image_file_format" value="svg" format="svg" />
+            </change_format>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="region" value="chrX:3000000-3500000"/>
+            <conditional name="x_axis">
+                <param name="x_axis_select" value="yes" />
+            </conditional>
+            <repeat name="tracks">
+                <conditional name="track_file_style_conditional">
+                    <param name="track_file_style_selector" value="hic_matrix_option" />
+                    <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.h5"/>
+
+                    <param name="title" value="Kc DpnII (Li et al. 2015)" />
+                    <param name="colormap" value="RdYlBu_r" />
+                    <param name="depth" value="200000" />
+                    <param name="transform" value="log1p" />
+                    <param name="boundaries_file" value="domains.bed" />
+                    <param name="x_labels" value="True" />
+                </conditional>
+            </repeat>
+            <repeat name="tracks">
+                <conditional name="track_file_style_conditional">
+                    <param name="track_file_style_selector" value="spacer_option" />
+                    <param name="spacer_height" value="0.05" />
+                </conditional>
+            </repeat>
+            <repeat name="tracks">
+                <conditional name="track_file_style_conditional">
+                    <param name="track_file_style_selector" value="chrom_states_option" />
+                    <param name="track_input_bed" value="tad_classification.bed" ftype="bed" />
+                    <param name="title" value="TAD state" />
+                    <param name="height_chrom" value="0.5" />
+                    <param name="labels" value="off" />
+                </conditional>
+            </repeat>
+            <repeat name="tracks">
+                <conditional name="track_file_style_conditional">
+                    <param name="track_file_style_selector" value="tad_score_track_option" />
+                    <param name="track_input_bedgraph" value="tad_score.gz" ftype="bedgraph" />
+                    <param name="title" value="TAD separation score (Ramirez et al.)" />
+                    <param name="height_tad" value="10" />
+                </conditional>
+            </repeat>
+            <repeat name="tracks">
+                <conditional name="track_file_style_conditional">
+                    <param name="track_file_style_selector" value="spacer_option" />
+                    <param name="spacer_height" value="1" />
+                </conditional>
+            </repeat>
+            <repeat name="tracks">
+                <conditional name="track_file_style_conditional">
+                    <param name="track_file_style_selector" value="bedgraph_track_option" />
+                    <param name="track_input_bedgraph" value="bedgraph_chrx_2e6_5e6.bg" ftype="bedgraph" />
+                    <param name="title" value="bedgraph" />
+                    <param name="height_bedgraph" value="4" />
+                    <param name="color" value="blue" />
+                </conditional>
+            </repeat>
+            <repeat name="tracks">
+                <conditional name="track_file_style_conditional">
+                    <param name="track_file_style_selector" value="bigwig_track_option" />
+                    <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" />
+                    <param name="title" value="rep 1 test fill" />
+                    <param name="height_bigwig" value="4" />
+                    <param name="color" value="blue" />
+                    <conditional name="type_conditional">
+                        <param name="type_selector" value="fill_option" />
+                    </conditional>
+                </conditional>
+            </repeat>
+
+            <repeat name="tracks">
+                <conditional name="track_file_style_conditional">
+                    <param name="track_file_style_selector" value="bigwig_track_option" />
+                    <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" />
+                    <param name="title" value="rep 1 test line" />
+                    <param name="height_bigwig" value="4" />
+                    <param name="color" value="red" />
+                    <conditional name="type_conditional">
+                        <param name="type_selector" value="line_option" />
+                        <param name="width_line" value="1" />
+                    </conditional>
+                </conditional>
+            </repeat>
+
+            <repeat name="tracks">
+                <conditional name="track_file_style_conditional">
+                    <param name="track_file_style_selector" value="bigwig_track_option" />
+                    <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" />
+                    <param name="title" value="rep 1 test lw=0.2" />
+                    <param name="height_bigwig" value="4" />
+                    <param name="color" value="red" />
+                    <conditional name="type_conditional">
+                        <param name="type_selector" value="line_option" />
+                        <param name="width_line" value="0.1" />
+
+                    </conditional>
+                </conditional>
+            </repeat>
+
+            <repeat name="tracks">
+                <conditional name="track_file_style_conditional">
+                    <param name="track_file_style_selector" value="bigwig_track_option" />
+                    <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" />
+                    <param name="title" value="rep 1 test point:0.5" />
+                    <param name="height_bigwig" value="4" />
+                    <param name="color" value="black" />
+                    <conditional name="type_conditional">
+                        <param name="type_selector" value="point_option" />
+                        <param name="width_point" value="0.5" />
+
+                    </conditional>
+                </conditional>
+            </repeat>
+
+            <repeat name="tracks">
+                <conditional name="track_file_style_conditional">
+                    <param name="track_file_style_selector" value="spacer_option" />
+                    <param name="spacer_height" value="0.5" />
+                </conditional>
+            </repeat>
+            <repeat name="tracks">
+                <conditional name="track_file_style_conditional">
+                    <param name="track_file_style_selector" value="gene_track_option" />
+                    <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" />
+                    <param name="title" value="genes" />
+                    <param name="height_bed" value="5" />
+                    <param name="fontsize" value="10" />
+                </conditional>
+            </repeat>
+            <repeat name="tracks">
+                <conditional name="track_file_style_conditional">
+                    <param name="track_file_style_selector" value="spacer_option" />
+                    <param name="spacer_height" value="1" />
+                </conditional>
+            </repeat>
+            <repeat name="tracks">
+                <conditional name="track_file_style_conditional">
+                    <param name="track_file_style_selector" value="gene_track_option" />
+                    <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" />
+                    <param name="title" value="max num rows 3" />
+                    <param name="height_bed" value="3" />
+                    <param name="fontsize" value="8" />
+                    <param name="gene_rows" value="3" />
+                </conditional>
+            </repeat>
+            <repeat name="tracks">
+                <conditional name="track_file_style_conditional">
+                    <param name="track_file_style_selector" value="spacer_option" />
+                    <param name="spacer_height" value="1" />
+                </conditional>
+            </repeat> 
+            <repeat name="tracks">
+                <conditional name="track_file_style_conditional">
+                    <param name="track_file_style_selector" value="gene_track_option" />
+                    <param name="track_input_bed" value="dm3_genes.bed6.gz" ftype="bed" />
+                    <param name="title" value="bed6 global max row" />
+                    <param name="height_bed" value="20" />
+                    <param name="fontsize" value="10" />
+                    <param name="global_max_row" value="True" />
+                </conditional>
+            </repeat>
+            <repeat name="tracks">
+                <conditional name="track_file_style_conditional">
+                    <param name="track_file_style_selector" value="vlines_track_option" />
+                    <param name="track_input_bed_single" value="domains.bed" ftype="bed" />
+                    <param name="type" value="vlines" />
+                </conditional>
+            </repeat>
+            <param name="image_file_format" value="png" />
+            <output name="outFileName" file="master_TADs_plot.png" ftype="png" compare="sim_size" delta="35000" />
+        </test>
+        <test>
+        <param name="region" value="chrX:3000000-3500000"/>
+        <conditional name="x_axis">
+            <param name="x_axis_select" value="yes" />
+        </conditional>
+        <repeat name="tracks">
+            <conditional name="track_file_style_conditional">
+                <param name="track_file_style_selector" value="bigwig_track_option" />
+                <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw,bigwig_chrx_2e6_5e6.bw" ftype="bigwig" />
+                <param name="title" value="rep 1 test line" />
+                <param name="height_bigwig" value="4" />
+                <param name="color" value="red" />
+                <conditional name="type_conditional">
+                    <param name="type_selector" value="line_option" />
+                    <param name="width_line" value="1" />
+                </conditional>
+            </conditional>
+            </repeat>
+            <param name="image_file_format" value="png" />
+            <output name="outFileName" file="bigwig_multiple.png" ftype="png" compare="sim_size" delta="35000" />
+        </test>
+    </tests>
+    <help><![CDATA[
+
+pyGenomeTracks
+==============
+
+**pyGenomeTracks** is a visualization tool which aims to produce high-quality genome browser tracks that are highly customizable. 
+    Currently, it is possible to plot: 
+
+    - bigwig
+    - bed (many options)
+    - bedgraph
+    - links (represented as arcs)
+    - Hi-C matrices
+
+_________________
+
+Usage
+-----
+
+This tool takes various types of tracks as input:
+
+    - **Chromatin states:** display blocks of different colors following a bed file.
+    - **Gene track / Bed Track:** display genes or bed files. Labels like gene names can be toggled on or off.
+    - **Bigwig track:** generic bigwig track plotting.
+    - **Bedgraph track:** generic bedgraph track plotting.
+    - **Bedgraph matrix track** is used to specifically plot bm files computed by HiCExplorer's ``hicFindTADs`` (TAD seperation scores).
+    - **Vlines:** vertical lines drawn on top of all tracks following a bed file. It is used as a visual support where regions start / end over all tracks, for example to display TAD boundaries computed by HiCExplorer's ``hicFindTADs``.
+    - **Spacer:** Add some space between two tracks.
+    - **Hi-C tracks:**
+        - **TAD vizualisation:** corrected Hi-C contact matrix to plot a contact heatmap. It is recommended to follow HiCExplorer's ``hicPlotMatrix`` instructions. Boundaries file can used, which is the output of HiCExplorer's ``hicFindTADs`` in bed format. If selected, TADs will be drawn directly on the contact heatmap.
+        - **TAD score:** display TAD seperation score computed by HiCExplorer's ``hicFindTADs``.
+
+
+For each track, parameters for the color, the width or the font size can be defined.
+
+_________________
+
+Output
+------
+
+**pyGenomeTracks** output is similar to a genome browser screen-shot that besides the usual genes, and score data (like bigwig or bedgraph files) 
+also contains Hi-C data. The plot is composed of tracks that need to be specified.
+Below is represented the 85 Mb to 110 Mb region from human chromosome 2 visualized using **pyGenomeTracks**.
+TADs were computed by HiCExplorer's ``hicFindTADs``. The additional tracks added correspond to: 
+TAD-separation score (as reported by HiCExplorer's ``hicFindTADs``), chromatin states, 
+principal component 1 (A/B compartment) computed using HiCExplorer's ``hicPCA``, ChIP-seq coverage for the H3K27ac mark, DNA methylation, and a gene track. 
+Data are from mouse cardiac myocytes, published by `Nothjunge et al. (2017)`_.
+
+.. image:: $PATH_TO_IMAGES/pyGenomeTracks.png
+   :width: 70 %
+
+_________________
+
+| For more information about pyGenomeTracks please consider our documentation on github_
+
+.. _github: https://github.com/deeptools/pyGenomeTracks
+.. _`Nothjunge et al. (2017)`: https://www.nature.com/articles/s41467-017-01724-9
+]]></help>
+    <expand macro="citations" />
+</tool>