Mercurial > repos > iuc > pygenometracks
view pyGenomeTracks.xml @ 1:0ea86f6bf2a1 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit f834c2a294c002123ef0613dc703aca00201b5bf
author | iuc |
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date | Mon, 02 Jul 2018 19:32:13 -0400 |
parents | 2074627b0f83 |
children | c171f2b7d76e |
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<tool id="pygenomeTracks" name="@BINARY@" version="@WRAPPER_VERSION@.1"> <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": #if $x_axis.where == 'top': [x-axis] #if $x_axis.fontsize: fontsize = $x_axis.fontsize #end if #if $x_axis.where: where = $x_axis.where #end if #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 #if $x_axis.x_axis_select == "yes": #if $x_axis.where == 'bottom': [x-axis] #if $x_axis.fontsize: fontsize = $x_axis.fontsize #end if #if $x_axis.where: where = $x_axis.where #end if #end if #end if </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>