Mercurial > repos > iuc > pygenometracks
diff pyGenomeTracks.xml @ 11:7dd841a32245 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
| author | iuc |
|---|---|
| date | Sat, 01 Oct 2022 08:43:22 +0000 |
| parents | a1abfa420d9d |
| children | 14e7c35f3d00 |
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--- a/pyGenomeTracks.xml Sun Feb 13 22:43:45 2022 +0000 +++ b/pyGenomeTracks.xml Sat Oct 01 08:43:22 2022 +0000 @@ -7,14 +7,21 @@ <expand macro="requirements" /> <command detect_errors="exit_code"> <![CDATA[ - ## First symlink data of hic to have the good extension + ## First symlink data + ## of hic to have the good extension + ## of fasta to have the index written in the working directory #for $counter, $track in enumerate($tracks): - #if $track.track_file_style_conditional.track_file_style_selector == "hic_matrix_option": + #if $track.track_file_style_conditional.track_file_style_selector in ["hic_matrix_option", "hic_matrix_square_option"]: #for $counter_matrix, $data_matrix in enumerate($track.track_file_style_conditional.matrix_h5_cooler_multiple): #set ext = $data_matrix.extension ln -s $data_matrix ${counter}_${counter_matrix}.$ext && #end for #end if + #if $track.track_file_style_conditional.track_file_style_selector == "fasta_option": + #if $track.track_file_style_conditional.fasta_source.fasta_source_selector == "history": + ln -s $track.track_file_style_conditional.fasta_source.fasta_local fasta_${counter}.fa && + #end if + #end if #end for @@ -46,7 +53,7 @@ <configfile name="tracks_config"> ## Each track: #for $counter, $track in enumerate($tracks): - ## Hi-C Track + ## Hi-C Track triangle #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_${counter}_${counter_matrix}] @@ -106,6 +113,67 @@ #end for #end if + ## Hi-C Track square + #if $track.track_file_style_conditional.track_file_style_selector == "hic_matrix_square_option": + #for $counter_matrix, $data_matrix in enumerate($track.track_file_style_conditional.matrix_h5_cooler_multiple): +[hic_section_${counter}_${counter_matrix}] + #set ext = $data_matrix.extension +file = ${counter}_${counter_matrix}.$ext +file_type = hic_matrix_square + #if $track.track_file_style_conditional.title: +title = $track.track_file_style_conditional.title + #else: +title = $data_matrix.element_identifier + #end if + #if $track.track_file_style_conditional.region2: +region2 = $track.track_file_style_conditional.region2 + #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 + #if $track.track_file_style_conditional.height_matrix != "": +height = $track.track_file_style_conditional.height_matrix + #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.invert_orientation: +orientation = inverted + #end if + #if $track.track_file_style_conditional.scale_factor: +scale_factor = $track.track_file_style_conditional.scale_factor + #end if +rasterize = $track.track_file_style_conditional.rasterize + ## If a boundary file is given a new section needs to be written: + #if str($track.track_file_style_conditional.boundaries_file) != "None": + #if len($track.track_file_style_conditional.boundaries_file)>$counter_matrix: + #set boundary_file = $track.track_file_style_conditional.boundaries_file[$counter_matrix] + #else: + #set boundary_file = $track.track_file_style_conditional.boundaries_file[0] + #end if +[tads_${counter}_${counter_matrix}] +file = $boundary_file +file_type = bed +display = squares +border_color = black +color = none +overlay_previous = share-y + #end if + ## If spacer is asked a new section is created: + #if $track.track_file_style_conditional.spacer_height != "": +[spacer] +height = $track.track_file_style_conditional.spacer_height + #end if + #end for + #end if + ## Chrom_state track #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: @@ -148,7 +216,10 @@ file = $data_bed #if $ext == 'gtf': prefered_name = $track.track_file_style_conditional.bed_style.bed_advanced.gtf.prefered_name -merge_transcripts = $track.track_file_style_conditional.bed_style.bed_advanced.gtf.merge_transcripts + #if $track.track_file_style_conditional.bed_style.bed_advanced.gtf.merge_transcripts.merge_transcripts_select == 'true': +merge_transcripts = true +merge_overlapping_exons = $track.track_file_style_conditional.bed_style.bed_advanced.gtf.merge_transcripts.merge_overlapping_exons + #end if #end if #if $track.track_file_style_conditional.title: title = $track.track_file_style_conditional.title @@ -168,6 +239,11 @@ style = $track.track_file_style_conditional.bed_style.bed_style_select #if $track.track_file_style_conditional.bed_style.bed_style_select == 'UCSC': arrow_interval = $track.track_file_style_conditional.bed_style.bed_advanced.arrow_interval + #if $track.track_file_style_conditional.bed_style.bed_advanced.backbone_color_bed.backbone_color_bed_select == 'manually': +color_backbone = $track.track_file_style_conditional.bed_style.bed_advanced.backbone_color_bed.color + #else +color_backbone = $track.track_file_style_conditional.bed_style.bed_advanced.backbone_color_bed.backbone_color_bed_select + #end if #else: height_utr = $track.track_file_style_conditional.bed_style.bed_advanced.height_utr #if $track.track_file_style_conditional.bed_style.bed_advanced.color_utr.color_utr_select == 'manually': @@ -175,6 +251,7 @@ #elif $track.track_file_style_conditional.bed_style.bed_advanced.color_utr.color_utr_select == 'bed_rgb': color_utr = bed_rgb #else: + ## This is 'like' #if $track.track_file_style_conditional.color_bed.color_bed_select == "bed_rgb": color_utr = bed_rgb #else: @@ -186,6 +263,12 @@ #end if #if $track.track_file_style_conditional.bed_style.bed_style_select == 'flybase': arrowhead_included = $track.track_file_style_conditional.bed_style.arrowhead_included +arrowhead_fraction = $track.track_file_style_conditional.bed_style.arrowhead_fraction + #if $track.track_file_style_conditional.bed_style.bed_advanced.backbone_color_bed.backbone_color_bed_select == 'manually': +color_backbone = $track.track_file_style_conditional.bed_style.bed_advanced.backbone_color_bed.color + #else +color_backbone = $track.track_file_style_conditional.bed_style.bed_advanced.backbone_color_bed.backbone_color_bed_select + #end if #end if #end if display = $track.track_file_style_conditional.display @@ -196,11 +279,12 @@ #if $track.track_file_style_conditional.labels.plot_labels == 'true': all_labels_inside = $track.track_file_style_conditional.labels.all_labels_inside labels_in_margin = $track.track_file_style_conditional.labels.labels_in_margin +fontstyle = $track.track_file_style_conditional.labels.fontstyle + #if $track.track_file_style_conditional.labels.fontsize: +fontsize = $track.track_file_style_conditional.labels.fontsize + #end if #end if file_type = $ext - #if $track.track_file_style_conditional.fontsize: -fontsize = $track.track_file_style_conditional.fontsize - #end if #if $track.track_file_style_conditional.bed_style.bed_advanced.gene_rows: gene_rows = $track.track_file_style_conditional.bed_style.bed_advanced.gene_rows #end if @@ -241,12 +325,17 @@ alpha = $track.track_file_style_conditional.alpha line_width = $track.track_file_style_conditional.line_width line_style = $track.track_file_style_conditional.line_style -links_type = $track.track_file_style_conditional.links_type -compact_arcs_level = $track.track_file_style_conditional.compact_arcs_level - #if $track.track_file_style_conditional.ylim != "": -ylim = $track.track_file_style_conditional.ylim +links_type = $track.track_file_style_conditional.display.links_type + #if $track.track_file_style_conditional.display.links_type in ['arcs', 'triangles']: +compact_arcs_level = $track.track_file_style_conditional.display.compact_arcs_level +use_middle = $track.track_file_style_conditional.display.use_middle #end if -use_middle = $track.track_file_style_conditional.use_middle + #if $track.track_file_style_conditional.display.links_type != 'squares' and $track.track_file_style_conditional.display.ylim != "": +ylim = $track.track_file_style_conditional.display.ylim + #end if + #if $track.track_file_style_conditional.display.links_type == 'squares' and $track.track_file_style_conditional.display.region2 != "": +region2 = $track.track_file_style_conditional.display.region2 + #end if #if $track.track_file_style_conditional.invert_orientation: orientation = inverted #end if @@ -288,10 +377,12 @@ height = $track.track_file_style_conditional.height_narrow_peak #end if line_width = $track.track_file_style_conditional.line_width -show_labels = $track.track_file_style_conditional.show_labels file_type = narrow_peak - #if $track.track_file_style_conditional.fontsize: -fontsize = $track.track_file_style_conditional.fontsize +show_labels = $track.track_file_style_conditional.labels.show_labels + #if $track.track_file_style_conditional.labels.show_labels == 'true': + #if $track.track_file_style_conditional.labels.fontsize: +fontsize = $track.track_file_style_conditional.labels.fontsize + #end if #end if #if $track.track_file_style_conditional.invert_orientation: orientation = inverted @@ -469,6 +560,8 @@ show_data_range = $track.track_file_style_conditional.type.show_data plot_horizontal_lines = $track.track_file_style_conditional.type.plot_horizontal_lines pos_score_in_bin = $track.track_file_style_conditional.type.pos_score_in_bin +individual_color = $track.track_file_style_conditional.type.individual_color +summary_color = $track.track_file_style_conditional.type.summary_color #else colormap = $track.track_file_style_conditional.type.colormap #end if @@ -491,6 +584,15 @@ type = vlines #end if + ## Vhighlight: + #if $track.track_file_style_conditional.track_file_style_selector == "vhighlight_track_option": +[vhighlight_$counter] +file = $track.track_file_style_conditional.track_input_bed_single +color = $track.track_file_style_conditional.color +alpha = $track.track_file_style_conditional.alpha +type = vhighlight + #end if + ## Hlines: #if $track.track_file_style_conditional.track_file_style_selector == "hlines_track_option": [hlines_$counter] @@ -579,6 +681,9 @@ #if $track.track_file_style_conditional.fontsize != "": fontsize = $track.track_file_style_conditional.fontsize #end if + #if $track.track_file_style_conditional.height != "": +height = $track.track_file_style_conditional.height + #end if file_type = scalebar ## If spacer is asked a new section is created: #if $track.track_file_style_conditional.spacer_height != "": @@ -586,12 +691,74 @@ height = $track.track_file_style_conditional.spacer_height #end if #end if + + ## Fasta: + #if $track.track_file_style_conditional.track_file_style_selector == "fasta_option": +[Fasta_${counter}] + #if $track.track_file_style_conditional.fasta_source.fasta_source_selector == "history": +file = fasta_${counter}.fa + #else: +file = $track.track_file_style_conditional.fasta_source.fasta_cached.fields.path + #end if + #if $track.track_file_style_conditional.title: +title = $track.track_file_style_conditional.title + #end if + #if $track.track_file_style_conditional.height != "": +height = $track.track_file_style_conditional.height + #end if + #if $track.track_file_style_conditional.invert_orientation: +orientation = inverted + #end if +overlay_previous = $track.track_file_style_conditional.overlay_select +file_type = fasta + ## If spacer is asked a new section is created: + #if $track.track_file_style_conditional.spacer_height != "": +[spacer] +height = $track.track_file_style_conditional.spacer_height + #end if + #end if + + ## Maf: + #if $track.track_file_style_conditional.track_file_style_selector == "maf_option": +[Maf_${counter}] +file = $track.track_file_style_conditional.track_input_maf +file_index = $track.track_file_style_conditional.track_input_maf.metadata.maf_index +reference = $track.track_file_style_conditional.reference + #if $track.track_file_style_conditional.title: +title = $track.track_file_style_conditional.title + #end if + #if $track.track_file_style_conditional.height != "": +height = $track.track_file_style_conditional.height + #end if + #if $track.track_file_style_conditional.invert_orientation: +orientation = inverted + #end if +overlay_previous = $track.track_file_style_conditional.overlay_select +line_width = $track.track_file_style_conditional.line_width +color_identical = $track.track_file_style_conditional.color_identical +color_mismatch = $track.track_file_style_conditional.color_mismatch +color_gap = $track.track_file_style_conditional.color_gap + #if $track.track_file_style_conditional.species_order != "": +species_order = $track.track_file_style_conditional.species_order + #if $track.track_file_style_conditional.species_labels != "": +species_labels = $track.track_file_style_conditional.species_labels + #end if +species_order_only = $track.track_file_style_conditional.species_order_only + #end if +display_ref_seq = $track.track_file_style_conditional.display_ref_seq +file_type = maf + ## If spacer is asked a new section is created: + #if $track.track_file_style_conditional.spacer_height != "": +[spacer] +height = $track.track_file_style_conditional.spacer_height + #end if + #end if #end for </configfile> </configfiles> <inputs> <!--Arguments for pgt--> - <param argument="--region" type="text" label="Region of the genome to limit the operation" optional="false" + <param argument="--region" type="text" label="Region of the genome to plot" optional="false" help="The format is chr:start-end, for example chr10:10-500"> <validator type="expression" message="Region should be like chr10:10-500">'^[a-zA-Z0-9_]:\d+-\d+$'</validator> </param> @@ -621,7 +788,8 @@ The order you add them represent the order they will be plotted from top to bottom."> <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="hic_matrix_option">TAD visualization (triangle)</option> + <option value="hic_matrix_square_option">TAD visualization (square)</option> <option value="chrom_states_option">Chromatine states</option> <option value="gene_track_option">Gene track / Bed track</option> <option value="link_track_option">Link track</option> @@ -630,10 +798,13 @@ <option value="bedgraph_track_option">Bedgraph track </option> <option value="bedgraph_matrix_track_option">Bedgraph matrix track/TAD score</option> <option value="vlines_track_option">Vlines track</option> + <option value="vhighlight_track_option">Vhighlight track</option> <option value="hlines_track_option">Hlines track</option> <option value="spacer_option">Spacer</option> <option value="xaxis_option">X-axis</option> <option value="scale_bar_option">Scale bar track</option> + <option value="fasta_option">Fasta track</option> + <option value="maf_option">Maf track</option> </param> <when value="hic_matrix_option"> <expand macro="plot_title" /> @@ -644,8 +815,8 @@ <option value="viridis">viridis</option> <expand macro="colormap_macro_noRdYlBu_r_noViridis"/> </param> + <expand macro="minmax_macro" /> <param name="depth" type="integer" value="8000000" optional="True" label="Depth" /> - <expand macro="minmax_macro" /> <param name="transform" type="select" label="Plot the transformed value"> <option value="log1p" selected="True" >log1p</option> <option value="log">log</option> @@ -653,10 +824,40 @@ <option value="no">no transformation</option> </param> - <param name="height_matrix" type="float" value="" optional="True" label="height"/> + <param name="height_matrix" type="float" value="" optional="True" label="height of the heatmap" help="If you leave it empty the height is calculated to have perfect squares rotated 45 degrees."/> <param name="show_masked_bins" type="boolean" truevalue="true" falsevalue="false" checked="false" - label="Show masked bins" /> - <param name="boundaries_file" type="data" optional="True" format="bed" label="Boundaries file" multiple="True"/> + label="Show masked bins" help="If false, neighbour bins will be increase in size to hide the mask bins." /> + <param name="boundaries_file" type="data" optional="True" format="bed" label="Boundaries file" multiple="True" help="Will display triangles on top of the heatmap"/> + <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="rasterize" type="boolean" truevalue="true" falsevalue="false" checked="true" + label="Rasterize the heatmap" /> + <expand macro="inverted_macro" /> + <expand macro="spacer_macro" /> + + </when> + + <when value="hic_matrix_square_option"> + <expand macro="plot_title" /> + <expand macro="matrix_h5_cooler_multiple_macro" /> + + <param name="colormap" type="select" label="Color map to use for the heatmap" help="Available color map names can be found here: https://matplotlib.org/examples/color/colormaps_reference.html"> + <option value="RdYlBu_r">RdYlBu reversed</option> + <option value="viridis">viridis</option> + <expand macro="colormap_macro_noRdYlBu_r_noViridis"/> + </param> + <expand macro="minmax_macro" /> + <expand macro="region2_option" /> + <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> + <option value="no">no transformation</option> + + </param> + <param name="height_matrix" type="float" value="" optional="True" label="height of the heatmap" help="If you leave it empty the height is calculated to have perfect squares."/> + <param name="show_masked_bins" type="boolean" truevalue="true" falsevalue="false" checked="false" + label="Show masked bins" help="If false, neighbour bins will be increase in size to hide the mask bins." /> + <param name="boundaries_file" type="data" optional="True" format="bed" label="Boundaries file" multiple="True" help="Will display squares on top of the heatmap"/> <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="rasterize" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Rasterize the heatmap" /> @@ -729,6 +930,12 @@ <param name="labels_in_margin" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Allow to put labels in the right margin" help="Put labels in the margin if the region ends after the plotted region."/> + <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" /> + <param name="fontstyle" type="select" label="Fontstyle"> + <option value="normal" selected="True">normal</option> + <option value="italic">italic</option> + <option value="oblique">oblique</option> + </param> </when> <when value="false"/> </conditional> @@ -737,8 +944,8 @@ <option value="interleaved">interleaved (everything on 2 lines)</option> <option value="collapsed">collapsed (everything on 1 line)</option> <option value="triangles">triangles (plot triangles between start and end)</option> + <option value="squares">squares (plot squares on the diagonal)</option> </param> - <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" /> <conditional name="bed_style"> <param name="bed_style_select" type="select" label="Bed style"> <option value="flybase" selected="True">flybase (blocks with arrow at extremities)</option> @@ -749,15 +956,20 @@ <param name="arrowhead_included" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Include the arrowhead in the bed interval:" help="When set to False, the arrow indicating the orientation of the interval is plotted outside of the interval."/> + <param name="arrowhead_fraction" type="float" value="0.004" min="0" max="1" + label="Size of arrowhead relative to the plotted region" + help="This size is also used to put space between the bed regions and their labels."/> <section name="bed_advanced" title="Configure other bed parameters" expanded="False"> <expand macro="utr_macro" /> <expand macro="bed_advanced_macro" /> + <expand macro="backbone_color_bed_macro" /> </section> </when> <when value="UCSC"> <section name="bed_advanced" title="Configure other bed parameters" expanded="False"> <param name="arrow_interval" type="integer" value="2" min="0" label="interval between 2 arrows on introns in UCSC style"/> <expand macro="bed_advanced_macro" /> + <expand macro="backbone_color_bed_macro" /> </section> </when> <when value="tssarrow"> @@ -793,21 +1005,28 @@ </when> </conditional> <expand macro="lines_macro" /> - <param name="links_type" type="select" label="Representation of the link:"> - <option value="arcs" selected="True">arcs (a line between the centers of the 2 regions)</option> - <option value="triangles">triangles</option> - <option value="loops">loops (a rectangle highlighting the intersection)</option> - </param> - <param name="compact_arcs_level" type="select" label="Height of arcs and triangles:"> - <option value="0" selected="True">default (proportional to distance)</option> - <option value="1">compacted (the height is proportional to the square root of the distance)</option> - <option value="2">highly compacted (the height is the same for all distances)</option> - </param> - <param name="ylim" type="float" optional="True" label="ylim" help="To be able to see small arcs when big arcs exists, you can set the upper y limit. The unit is bp. This corresponds to the longest arc you will see not truncated."/> - <param name="use_middle" type="select" label="Coordinates to use" help="Not useful with loops"> - <option value="false" selected="True">Extremities (start of first and end of second)</option> - <option value="true">Center (mean of start and end for each)</option> - </param> + <conditional name="display"> + <param name="links_type" type="select" label="Representation of the link:"> + <option value="arcs" selected="True">arcs (a line between the centers of the 2 regions)</option> + <option value="triangles">triangles</option> + <option value="loops">loops (a diamond highlighting the intersection)</option> + <option value="squares">squares (a square highlighting the intersection symetrically to the diagonal)</option> + </param> + <when value="arcs"> + <expand macro="links_arcs_triangles_options" /> + <param name="ylim" type="float" optional="True" label="ylim" help="To be able to see small arcs when big arcs exists, you can set the upper y limit. The unit is bp. This corresponds to the longest arc you will see not truncated."/> + </when> + <when value="triangles"> + <expand macro="links_arcs_triangles_options" /> + <param name="ylim" type="float" optional="True" label="ylim" help="To be able to see small arcs when big arcs exists, you can set the upper y limit. The unit is bp. This corresponds to the longest arc you will see not truncated."/> + </when> + <when value="loops"> + <param name="ylim" type="float" optional="True" label="ylim" help="To be able to see small arcs when big arcs exists, you can set the upper y limit. The unit is bp. This corresponds to the longest arc you will see not truncated."/> + </when> + <when value="squares"> + <expand macro="region2_option" /> + </when> + </conditional> <param name="height" type="float" value="1.5" optional="True" label="height"/> <expand macro="minmax_macro" /> <expand macro="overlay_macro" /> @@ -839,9 +1058,16 @@ </when> </conditional> <param name="line_width" type="float" value="1" label="width of lines" /> - <param name="show_labels" type="boolean" truevalue="true" falsevalue="false" checked="true" - label="Plot labels (name, p-val, q-val)" /> - <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" /> + <conditional name="labels"> + <param name="show_labels" type="select" label="Plot labels (name, p-val, q-val)"> + <option value="true" selected="True">yes</option> + <option value="false">no</option> + </param> + <when value="true"> + <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" /> + </when> + <when value="false"/> + </conditional> <expand macro="overlay_macro" /> <expand macro="inverted_macro" /> <expand macro="spacer_macro" /> @@ -939,6 +1165,8 @@ <option value="center" selected="True">Center</option> <option value="block">Block (draw a horizontal line between start and end)</option> </param> + <param name="individual_color" type="color" value="grey" label="Color of the individual lines" /> + <param name="summary_color" type="color" value="#1f77b4" label="Color of the summary line" /> </when> <when value="matrix"> <param name="colormap" type="select" label="colormap"> @@ -958,12 +1186,17 @@ <expand macro="track_input_bed_single_macro" /> <param name="line_width" type="float" value="0.5" label="width of lines"/> </when> + <when value="vhighlight_track_option"> + <expand macro="track_input_bed_single_macro" /> + <param name="color" type="color" value="yellow" label="color of the highlight"/> + <param name="alpha" type="float" value="0.5" min="0" max="1" label="transparency (alpha) of the highlight"/> + </when> <when value="hlines_track_option"> <expand macro="plot_title" /> <param name="y_values" type="text" value="10, 200" label="Values where horizontal lines should be plotted separated by comma"/> <param name="color" type="color" value="#000000" label="Color of line(s)" optional="True" /> <expand macro="lines_macro" /> - <param name="height" type="float" value="1.5" optional="True" label="height"/> + <param name="height" type="float" value="1.5" optional="True" label="height of the Hlines track"/> <expand macro="minmax_macro" /> <param name="show_data" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Show visualization of data range"/> <expand macro="inverted_macro" /> @@ -1006,6 +1239,39 @@ </param> <param name="fontsize" type="float" optional="True" label="Fontsize of the size of the scale bar."/> + <param name="height" type="float" value="0.5" optional="True" label="height of the Scale bar track"/> + <expand macro="spacer_macro" /> + </when> + <when value="fasta_option"> + <expand macro="track_input_fasta_macro" /> + <expand macro="plot_title" /> + <param name="height" type="float" value="0.5" optional="True" label="height of the Fasta track"/> + <expand macro="inverted_macro" /> + <expand macro="overlay_macro" /> + <expand macro="spacer_macro" /> + </when> + <when value="maf_option"> + <expand macro="track_input_maf_macro" /> + <expand macro="plot_title" /> + <param name="height" type="float" value="0.5" optional="True" label="height of the Fasta track"/> + <param name="reference" type="select" label="Reference"> + <options> + <filter type="data_meta" ref="track_input_maf" key="species" /> + </options> + </param> + <param name="line_width" type="float" value="0.5" label="width of lines"/> + <param name="color_identical" type="color" label="Color when bases are identical" value="black" /> + <param name="color_mismatch" type="color" label="Color when bases are different" value="grey" /> + <param name="color_gap" type="color" label="Color when bases corresponds to gap" value="lightgrey" /> + <param name="species_order" type="text" value="" label="[Optional] The order you want your species (space separated)" + help="checkout the choices for reference to see available species"/> + <param name="species_labels" type="text" value="" label="[Optional] The label you want for the above species (space separated)"/> + <param name="species_order_only" type="boolean" truevalue="true" falsevalue="false" checked="false" + label="Display only the species specified above"/> + <param name="display_ref_seq" type="boolean" truevalue="true" falsevalue="false" checked="false" + label="Display the sequence of the reference"/> + <expand macro="inverted_macro" /> + <expand macro="overlay_macro" /> <expand macro="spacer_macro" /> </when> </conditional> @@ -1154,7 +1420,9 @@ <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 name="labels"> + <param name="fontsize" value="10" /> + </conditional> </conditional> </repeat> <repeat name="tracks"> @@ -1169,7 +1437,9 @@ <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" /> + <conditional name="labels"> + <param name="fontsize" value="8" /> + </conditional> <conditional name="bed_style"> <section name="bed_advanced"> <param name="gene_rows" value="3" /> @@ -1189,7 +1459,9 @@ <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" /> + <conditional name="labels"> + <param name="fontsize" value="10" /> + </conditional> <conditional name="bed_style"> <section name="bed_advanced"> <param name="global_max_row" value="true" /> @@ -1416,7 +1688,9 @@ <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" /> <param name="title" value="genes in ucsc" /> <param name="height_bed" value="5" /> - <param name="fontsize" value="10" /> + <conditional name="labels"> + <param name="fontsize" value="10" /> + </conditional> <conditional name="bed_style"> <param name="bed_style_select" value="UCSC"/> </conditional> @@ -1428,7 +1702,9 @@ <param name="track_input_bed" value="dm3_genes.bed6.gz" ftype="bed" /> <param name="title" value="bed6 global max row color from score" /> <param name="height_bed" value="20" /> - <param name="fontsize" value="10" /> + <conditional name="labels"> + <param name="fontsize" value="10" /> + </conditional> <conditional name="bed_style"> <section name="bed_advanced"> <param name="global_max_row" value="true" /> @@ -1446,7 +1722,6 @@ <param name="track_input_bed" value="domains.bed" ftype="bed" /> <param name="title" value="domains.bed using the 9th field for colors interleaved border=red" /> <param name="height_bed" value="2" /> - <param name="fontsize" value="10" /> <conditional name="color_bed"> <param name="color_bed_select" value="bed_rgb" /> </conditional> @@ -1466,7 +1741,6 @@ <param name="track_input_bed" value="domains.bed" ftype="bed" /> <param name="title" value="domains.bed using the 9th field for colors interleaved border=bed_rgb" /> <param name="height_bed" value="2" /> - <param name="fontsize" value="10" /> <conditional name="color_bed"> <param name="color_bed_select" value="bed_rgb" /> </conditional> @@ -1485,7 +1759,6 @@ <param name="track_input_bed" value="domains.bed" ftype="bed" /> <param name="title" value="domains.bed using the 9th field for colors interleaved border=none" /> <param name="height_bed" value="2" /> - <param name="fontsize" value="10" /> <conditional name="color_bed"> <param name="color_bed_select" value="bed_rgb" /> </conditional> @@ -1591,7 +1864,6 @@ <param name="display_selector" value="box" /> <param name="use_summit" value="true" /> </conditional> - <param name="show_labels" value="true" /> </conditional> </repeat> <repeat name="tracks"> @@ -1606,7 +1878,6 @@ <param name="display_selector" value="box" /> <param name="use_summit" value="true" /> </conditional> - <param name="show_labels" value="true" /> </conditional> </repeat> <repeat name="tracks"> @@ -1623,7 +1894,9 @@ <param name="width_adjust" value="3" /> <param name="max_value" value="50" /> </conditional> - <param name="show_labels" value="false" /> + <conditional name="labels"> + <param name="show_labels" value="false" /> + </conditional> <param name="spacer_height" value="0.5"/> </conditional> </repeat> @@ -1639,7 +1912,6 @@ <param name="use_summit" value="false" /> <param name="show_data" value="false" /> </conditional> - <param name="show_labels" value="true" /> </conditional> </repeat> <repeat name="tracks"> @@ -1663,8 +1935,8 @@ <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="track_input_bed" value="dm3_subset_BDGP5.78.gtf.gz" ftype="gtf" /> + <param name="title" value="gtf default" /> <param name="height_bed" value="10" /> </conditional> </repeat> @@ -1672,7 +1944,7 @@ <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="gene_track_option" /> <param name="track_input_bed" value="dm3_subset_BDGP5.78.gtf.gz" ftype="gtf" /> - <param name="title" value="gtf" /> + <param name="title" value="gtf merge transcripts, use gene_name, red 0.75 UTR" /> <param name="height_bed" value="10" /> <conditional name="bed_style"> <section name="bed_advanced"> @@ -1683,7 +1955,34 @@ </conditional> <section name ="gtf"> <param name="prefered_name" value="gene_name"/> - <param name="merge_transcripts" value="true"/> + <conditional name="merge_transcripts"> + <param name="merge_transcripts_select" value="true"/> + <param name="merge_overlapping_exons" value="false"/> + </conditional> + </section> + </section> + </conditional> + </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_subset_BDGP5.78.gtf.gz" ftype="gtf" /> + <param name="title" value="same but merge overlapping exons" /> + <param name="height_bed" value="10" /> + <conditional name="bed_style"> + <section name="bed_advanced"> + <param name="height_utr" value="0.75"/> + <conditional name="color_utr"> + <param name="color_utr_select" value="manually"/> + <param name="color" value="#ff0000"/> + </conditional> + <section name ="gtf"> + <param name="prefered_name" value="gene_name"/> + <conditional name="merge_transcripts"> + <param name="merge_transcripts_select" value="true"/> + <param name="merge_overlapping_exons" value="true"/> + </conditional> </section> </section> </conditional> @@ -1811,16 +2110,34 @@ <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="gene_track_option" /> <param name="track_input_bed" value="dm3_subset_BDGP5.78.gtf.gz" ftype="gtf" /> - <param name="title" value="test" /> + <param name="title" value="defaut arrowhead fontstyle italic" /> <param name="height_bed" value="10" /> <param name="spacer_height" value="1"/> + <conditional name="labels"> + <param name="fontstyle" value="italic"/> + </conditional> + </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_subset_BDGP5.78.gtf.gz" ftype="gtf" /> + <param name="title" value="arrowhead_fraction 0.1 fontstyle oblique" /> + <param name="height_bed" value="10" /> + <param name="spacer_height" value="1"/> + <conditional name="labels"> + <param name="fontstyle" value="oblique"/> + </conditional> + <conditional name="bed_style"> + <param name="arrowhead_fraction" value="0.1"/> + </conditional> </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_subset_BDGP5.78_asbed4.bed.gz" ftype="bed" /> - <param name="title" value="test" /> + <param name="title" value="genes without orientation" /> <param name="height_bed" value="10" /> <conditional name="color_bed"> <param name="color_bed_select" value="manually" /> @@ -1836,7 +2153,7 @@ <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="gene_track_option" /> <param name="track_input_bed" value="dm3_subset_BDGP5.78.gtf.gz" ftype="gtf" /> - <param name="title" value="test" /> + <param name="title" value="arrowhead included" /> <param name="height_bed" value="10" /> <conditional name="color_bed"> <param name="color_bed_select" value="manually" /> @@ -1938,7 +2255,7 @@ <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="bedgraph_matrix_track_option" /> <param name="track_input_bedgraph_matrix" value="tad_score.gz" ftype="bedgraph" /> - <param name="title" value="TAD separation score (Ramirez et al.)" /> + <param name="title" value="TAD separation score (Ramirez et al.) as block with horizontal lines and data range" /> <param name="height_bedgraph" value="10" /> <conditional name="type"> <param name="type_selector" value="lines" /> @@ -1952,12 +2269,14 @@ <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="bedgraph_matrix_track_option" /> <param name="track_input_bedgraph_matrix" value="tad_score.gz" ftype="bedgraph" /> - <param name="title" value="TAD separation score (Ramirez et al.)" /> + <param name="title" value="TAD separation score (Ramirez et al.) as center without horizontal lines, summary in red and individual in blue" /> <param name="height_bedgraph" value="10" /> <conditional name="type"> <param name="type_selector" value="lines" /> <param name="pos_score_in_bin" value="center" /> <param name="plot_horizontal_lines" value="false" /> + <param name="individual_color" value="blue"/> + <param name="summary_color" value="red"/> </conditional> </conditional> </repeat> @@ -1989,7 +2308,9 @@ <param name="track_input_link" value="test.arcs" ftype="bed" /> <param name="title" value="" /> <param name="line_width" value="10" /> - <param name="links_type" value="loops" /> + <conditional name="display"> + <param name="links_type" value="loops" /> + </conditional> <conditional name="color_link"> <param name="color_link_select" value="manually" /> <param name="color" value="red" /> @@ -2037,7 +2358,9 @@ <param name="color_link_select" value="manually" /> <param name="color" value="#000000" /> </conditional> - <param name="ylim" value="20000" /> + <conditional name="display"> + <param name="ylim" value="20000" /> + </conditional> </conditional> </repeat> <repeat name="tracks"> @@ -2049,7 +2372,9 @@ <param name="color_link_select" value="manually" /> <param name="color" value="#000000" /> </conditional> - <param name="compact_arcs_level" value="1" /> + <conditional name="display"> + <param name="compact_arcs_level" value="1" /> + </conditional> </conditional> </repeat> <repeat name="tracks"> @@ -2061,7 +2386,9 @@ <param name="color_link_select" value="manually" /> <param name="color" value="#000000" /> </conditional> - <param name="compact_arcs_level" value="2" /> + <conditional name="display"> + <param name="compact_arcs_level" value="2" /> + </conditional> </conditional> </repeat> <param name="image_file_format" value="png" /> @@ -2120,20 +2447,33 @@ <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="flybase" /> + <param name="title" value="flybase backbone blue" /> <param name="height_bed" value="10" /> + <conditional name="bed_style"> + <param name="bed_style_select" value="flybase"/> + <section name="bed_advanced"> + <conditional name="backbone_color_bed"> + <param name="backbone_color_bed_select" value="manually" /> + <param name="color" value="blue" /> + </conditional> + </section> + </conditional> </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="UCSC" /> + <param name="title" value="UCSC backbone blue" /> <param name="height_bed" value="10" /> <conditional name="bed_style"> <param name="bed_style_select" value="UCSC"/> <section name="bed_advanced"> <param name="arrow_interval" value="10"/> + <conditional name="backbone_color_bed"> + <param name="backbone_color_bed_select" value="manually" /> + <param name="color" value="blue" /> + </conditional> </section> </conditional> </conditional> @@ -2573,7 +2913,9 @@ <param name="color" value="red" /> </conditional> <param name="line_width" value="5" /> - <param name="links_type" value="loops" /> + <conditional name="display"> + <param name="links_type" value="loops" /> + </conditional> <param name="overlay_select" value="share-y" /> </conditional> </repeat> @@ -2615,7 +2957,9 @@ <param name="color" value="red" /> </conditional> <param name="line_width" value="5" /> - <param name="links_type" value="loops" /> + <conditional name="display"> + <param name="links_type" value="loops" /> + </conditional> <param name="overlay_select" value="share-y" /> </conditional> </repeat> @@ -2628,7 +2972,9 @@ </conditional> <param name="line_width" value="3" /> <param name="invert_orientation" value="true" /> - <param name="use_middle" value="true" /> + <conditional name="display"> + <param name="use_middle" value="true" /> + </conditional> <param name="title" value="links line_width = 3 color RdYlGn use_middle = true" /> <param name="height" value="3" /> </conditional> @@ -2655,7 +3001,7 @@ <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="scale_bar_option" /> <param name="title" value="scalebar where = right" /> - <param name="where" value="right" /> + <param name="sb_where" value="right"/> <param name="spacer_height" value="0.5"/> </conditional> </repeat> @@ -2675,7 +3021,7 @@ <param name="title" value="scalebar scalebar_start_position = 3200000 scalebar_end_position = 3250000" /> <section name="scalebar_pos"> <param name="scalebar_start_position" value="3200000"/> - <param name="scalebar_start_position" value="3250000"/> + <param name="scalebar_end_position" value="3250000"/> </section> <param name="spacer_height" value="0.5"/> </conditional> @@ -2710,7 +3056,6 @@ <param name="scalebar_end_position" value="3200000"/> <param name="size" value="50000"/> </section> - <param name="spacer_height" value="0.5"/> </conditional> </repeat> <repeat name="tracks"> @@ -2722,6 +3067,223 @@ <param name="image_file_format" value="png" /> <output name="outFileName" file="master_scale_bar_startend.png" ftype="png" compare="sim_size" delta="100" /> </test> + <!--test 22--> + <test> + <param name="region" value="chrM:10-30"/> + <repeat name="tracks"> + <conditional name="track_file_style_conditional"> + <param name="track_file_style_selector" value="scale_bar_option" /> + <param name="title" value="scalebar height = 5" /> + <param name="sb_where" value="right"/> + <param name="height" value="5"/> + <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="fasta_option" /> + <param name="title" value="fasta from cached" /> + <conditional name="fasta_source"> + <param name="fasta_source_selector" value="cached"/> + <param name="fasta_cached" value="chrM"/> + </conditional> + <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="fasta_option" /> + <param name="title" value="fasta from history height = 5" /> + <conditional name="fasta_source"> + <param name="fasta_source_selector" value="history"/> + <param name="fasta_local" value="chrM.fa" ftype="fasta" /> + </conditional> + <param name="height" value="5"/> + </conditional> + </repeat> + <param name="image_file_format" value="png" /> + <output name="outFileName" file="master_fasta.png" ftype="png" compare="sim_size" delta="100" /> + </test> + <!--test 23--> + <test> + <param name="region" value="chrX:3000000-3300000"/> + <repeat name="tracks"> + <conditional name="track_file_style_conditional"> + <param name="track_file_style_selector" value="xaxis_option" /> + <param name="xaxis_where" value="top" /> + </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="hic_matrix_option" /> + <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.h5"/> + <param name="title" value="classical depth=300000 with arcs" /> + <param name="depth" value="300000" /> + </conditional> + </repeat> + <repeat name="tracks"> + <conditional name="track_file_style_conditional"> + <param name="track_file_style_selector" value="link_track_option" /> + <param name="track_input_link" value="test_wide.arcs" ftype="bed" /> + <conditional name="color_link"> + <param name="color" value="red" /> + </conditional> + <param name="line_width" value="5" /> + <conditional name="display"> + <param name="links_type" value="loops" /> + </conditional> + <param name="overlay_select" value="share-y" /> + </conditional> + </repeat> + <repeat name="tracks"> + <conditional name="track_file_style_conditional"> + <param name="track_file_style_selector" value="hic_matrix_square_option" /> + <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.h5"/> + <param name="title" value="square with arcs" /> + </conditional> + </repeat> + <repeat name="tracks"> + <conditional name="track_file_style_conditional"> + <param name="track_file_style_selector" value="link_track_option" /> + <param name="track_input_link" value="test_wide.arcs" ftype="bed" /> + <conditional name="color_link"> + <param name="color" value="red" /> + </conditional> + <param name="line_width" value="5" /> + <conditional name="display"> + <param name="links_type" value="squares" /> + </conditional> + <param name="overlay_select" value="share-y" /> + </conditional> + </repeat> + <repeat name="tracks"> + <conditional name="track_file_style_conditional"> + <param name="track_file_style_selector" value="hic_matrix_square_option" /> + <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.h5"/> + <param name="title" value="square with arcs region2=chrX:3000000-3100000" /> + <param name="region2" value="chrX:3000000-3100000"/> + </conditional> + </repeat> + <repeat name="tracks"> + <conditional name="track_file_style_conditional"> + <param name="track_file_style_selector" value="link_track_option" /> + <param name="track_input_link" value="test_wide.arcs" ftype="bed" /> + <conditional name="color_link"> + <param name="color" value="red" /> + </conditional> + <param name="line_width" value="5" /> + <conditional name="display"> + <param name="links_type" value="squares" /> + </conditional> + <param name="overlay_select" value="share-y" /> + </conditional> + </repeat> + <repeat name="tracks"> + <conditional name="track_file_style_conditional"> + <param name="track_file_style_selector" value="hic_matrix_square_option" /> + <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.h5"/> + <param name="title" value="square with domains, colormap = Blues, tranform = no, region2=chrX:3000000-3100000" /> + <param name="region2" value="chrX:3000000-3100000"/> + <param name="colormap" value="Blues"/> + <param name="transform" value="no" /> + <param name="boundaries_file" value="tad_classification.bed" /> + </conditional> + </repeat> + <param name="image_file_format" value="png" /> + <output name="outFileName" file="test_matrix_square.png" ftype="png" compare="sim_size" delta="1200" /> + </test> + <!--test 24--> + <test> + <param name="region" value="2:34704975-34705208"/> + <repeat name="tracks"> + <conditional name="track_file_style_conditional"> + <param name="track_file_style_selector" value="maf_option" /> + <param name="track_input_maf" value="first.maf" ftype="maf"/> + <param name="reference" value="mm10"/> + <param name="title" value="default" /> + <param name="spacer_height" value="1"/> + </conditional> + </repeat> + <repeat name="tracks"> + <conditional name="track_file_style_conditional"> + <param name="track_file_style_selector" value="maf_option" /> + <param name="track_input_maf" value="first.maf" ftype="maf"/> + <param name="reference" value="mm10"/> + <param name="title" value="height = 3 show sequence" /> + <param name="height" value="3"/> + <param name="display_ref_seq" value="true"/> + <param name="spacer_height" value="1"/> + </conditional> + </repeat> + <repeat name="tracks"> + <conditional name="track_file_style_conditional"> + <param name="track_file_style_selector" value="maf_option" /> + <param name="track_input_maf" value="first.maf" ftype="maf"/> + <param name="reference" value="mm10"/> + <param name="title" value="species_order = hg19 rn5, species_labels = Human Rat" /> + <param name="height" value="3"/> + <param name="species_order" value="hg19 rn5"/> + <param name="species_labels" value="Human Rat"/> + <param name="spacer_height" value="1"/> + </conditional> + </repeat> + <repeat name="tracks"> + <conditional name="track_file_style_conditional"> + <param name="track_file_style_selector" value="maf_option" /> + <param name="track_input_maf" value="first.maf" ftype="maf"/> + <param name="reference" value="mm10"/> + <param name="title" value="species_order = hg19, species_labels = Human, species_order_only = true" /> + <param name="height" value="3"/> + <param name="species_order" value="hg19"/> + <param name="species_labels" value="Human"/> + <param name="species_order_only" value="true"/> + <param name="spacer_height" value="1"/> + </conditional> + </repeat> + <repeat name="tracks"> + <conditional name="track_file_style_conditional"> + <param name="track_file_style_selector" value="xaxis_option" /> + <param name="xaxis_where" value="bottom" /> + </conditional> + </repeat> + <param name="image_file_format" value="png" /> + <output name="outFileName" file="test_maf.png" ftype="png" compare="sim_size" delta="1200" /> + </test> + <!--test 25--> + <test> + <param name="region" value="chr2:73,800,000-75,744,000"/> + <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="GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz" ftype="bedgraph" /> + <param name="title" value="bedgraph color = blue" /> + <param name="height_bedgraph" value="5" /> + <param name="color" value="blue" /> + <param name="show_data" value="true" /> + <param name="max_value" value="5" /> + </conditional> + </repeat> + <repeat name="tracks"> + <conditional name="track_file_style_conditional"> + <param name="track_file_style_selector" value="vhighlight_track_option" /> + <param name="track_input_bed_single" value="islands.bed" ftype="bed"/> + </conditional> + </repeat> + <repeat name="tracks"> + <conditional name="track_file_style_conditional"> + <param name="track_file_style_selector" value="xaxis_option" /> + <param name="xaxis_where" value="bottom" /> + </conditional> + </repeat> + <param name="image_file_format" value="png" /> + <output name="outFileName" file="test_vhighlight.png" ftype="png" compare="sim_size" delta="1200" /> + </test> </tests> <help><![CDATA[ @@ -2738,6 +3300,8 @@ - narrow peaks - links - Hi-C matrices (cool or HiCExplorer h5) + - Fasta + - MAF (multiple alignment format) _________________ @@ -2757,10 +3321,13 @@ - **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``. + - **Vhighlight:** vertical rectangles drawn on top of all tracks following a bed file. It is used as a visual support to highlight some regions. - **Hlines:** horizontal lines drawn either by themselves or on top of other tracks. - **Spacer:** Add some space between two tracks. - **X-axis:** Plot x-axis scale wherever you want. - **Scale bar track:** Plot scale bar. + - **Fasta track:** Display sequences from fasta. + - **Maf track:** Display alignments from maf. For each track, parameters for the color, the width or the font size can be defined.