pygenometracks: pyGenomeTracks.xml comparison

comparison 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

comparison

equal deleted inserted replaced

-:a1abfa420d9d
+:7dd841a32245
 <import>macros.xml</import>
 </macros>
 <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
 sed '/^$/d' '$tracks_config' &&
 </command>
 <configfiles>
 <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}]
 #set ext = $data_matrix.extension
 file = ${counter}_${counter_matrix}.$ext
 height = $track.track_file_style_conditional.spacer_height
 #end if
 #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 $track.track_file_style_conditional.track_input_bed:
 [chrom states_$counter]
 file = $data_bed
 [genes_${counter}_${counter_bed}]
 #set ext = $data_bed.extension
 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
 #elif $track.track_file_style_conditional.overlay_select == 'no':
 title = $data_bed.element_identifier
 border_color = $track.track_file_style_conditional.border_color_bed.border_color_bed_select
 #end if
 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':
 color_utr = $track.track_file_style_conditional.bed_style.bed_advanced.color_utr.color
 #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:
 color_utr = $track.track_file_style_conditional.color_bed.color
 #end if
 #if $track.track_file_style_conditional.bed_style.bed_style_select == 'tssarrow' and $track.track_file_style_conditional.bed_style.bed_advanced.arrow_length != '':
 arrow_length = $track.track_file_style_conditional.bed_style.bed_advanced.arrow_length
 #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
 #if $track.track_file_style_conditional.height_bed:
 height = $track.track_file_style_conditional.height_bed
 #end if
 labels = $track.track_file_style_conditional.labels.plot_labels
 #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
 global_max_row = $track.track_file_style_conditional.bed_style.bed_advanced.global_max_row
 max_labels = $track.track_file_style_conditional.bed_style.bed_advanced.max_labels
 #end if
 color = $track.track_file_style_conditional.color_link.color
 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
+links_type = $track.track_file_style_conditional.display.links_type
-compact_arcs_level = $track.track_file_style_conditional.compact_arcs_level
+#if $track.track_file_style_conditional.display.links_type in ['arcs', 'triangles']:
-#if $track.track_file_style_conditional.ylim != "":
+compact_arcs_level = $track.track_file_style_conditional.display.compact_arcs_level
-ylim = $track.track_file_style_conditional.ylim
+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
 overlay_previous = $track.track_file_style_conditional.overlay_select
 file_type = links
 #end if
 #if $track.track_file_style_conditional.height_narrow_peak:
 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:
+show_labels = $track.track_file_style_conditional.labels.show_labels
-fontsize = $track.track_file_style_conditional.fontsize
+#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
 #end if
 overlay_previous = $track.track_file_style_conditional.overlay_select
 file_type = bedgraph_matrix
 #if $track.track_file_style_conditional.type.type_selector == 'lines':
 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
 #if $track.track_file_style_conditional.invert_orientation:
 orientation = inverted
 #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
 line_width = $track.track_file_style_conditional.line_width
 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]
 #end if
 where = $track.track_file_style_conditional.sb_where
 #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 != "":
+[spacer]
+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 = $track.track_file_style_conditional.spacer_height
 #end if
 #end for
 </configfile>
 </configfiles>
 <inputs>
 <!--Arguments for pgt-->
-<param argument="--region" type="text" label="Region of the genome to limit the operation" optional="false"
+<param argument="--region" type="text" label="Region of the genome to plot" optional="false"
 help="The format is chr:start-end, for example chr10:10-500">
 <validator type="expression" message="Region should be like chr10:10-500">'^[a-zA-Z0-9_]:\d+-\d+$'</validator>
 </param>
 <section name="global_args" title="Configure figure parameters" expanded="False">
 <param argument="--title" type="text" label="Plot title" help="If set, you may need to start by a spacer track"/>
 <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.
 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>
 <option value="narrow_peak_track_option">NarrowPeak 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/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" />
 <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" />
 <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>
 <option value="-log">-log</option>
 <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" />
+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"/>
+<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" />
 <expand macro="inverted_macro" />
 <expand macro="spacer_macro" />
 label="Put all labels inside the plotted region"
 help="Put labels on the left of the region if the region ends after the plotted region."/>
 <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>
 <param name="display" type="select" label="display to use">
 <option value="stacked" selected="True">stacked (no overlap even with the label)</option>
 <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>
 <option value="UCSC">UCSC (blocks with arrows in introns)</option>
 <option value="tssarrow">tssarrow (blocks with arrow above at beginning)</option>
 </param>
 <when value="flybase">
 <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">
 <section name="bed_advanced" title="Configure other bed parameters" expanded="False">
 <param name="arrow_length" type="integer" optional="true" label="arrow length" help="the length of the arrow in bp (default is 4% of the plotted region)"/>
 <expand macro="colormap_macro_noRdYlBu_r_noViridis" />
 </param>
 </when>
 </conditional>
 <expand macro="lines_macro" />
-<param name="links_type" type="select" label="Representation of the link:">
+<conditional name="display">
-<option value="arcs" selected="True">arcs (a line between the centers of the 2 regions)</option>
+<param name="links_type" type="select" label="Representation of the link:">
-<option value="triangles">triangles</option>
+<option value="arcs" selected="True">arcs (a line between the centers of the 2 regions)</option>
-<option value="loops">loops (a rectangle highlighting the intersection)</option>
+<option value="triangles">triangles</option>
-</param>
+<option value="loops">loops (a diamond highlighting the intersection)</option>
-<param name="compact_arcs_level" type="select" label="Height of arcs and triangles:">
+<option value="squares">squares (a square highlighting the intersection symetrically to the diagonal)</option>
-<option value="0" selected="True">default (proportional to distance)</option>
+</param>
-<option value="1">compacted (the height is proportional to the square root of the distance)</option>
+<when value="arcs">
-<option value="2">highly compacted (the height is the same for all distances)</option>
+<expand macro="links_arcs_triangles_options" />
-</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="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>
-<param name="use_middle" type="select" label="Coordinates to use" help="Not useful with loops">
+<when value="triangles">
-<option value="false" selected="True">Extremities (start of first and end of second)</option>
+<expand macro="links_arcs_triangles_options" />
-<option value="true">Center (mean of start and end for each)</option>
+<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>
+</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" />
 <expand macro="inverted_macro" />
 <expand macro="spacer_macro" />
 <param name="use_summit" type="boolean" truevalue="true" falsevalue="false" checked="true"
 optional="True" label="Plot a vertical bar at the summit position." />
 </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"
+<conditional name="labels">
-label="Plot labels (name, p-val, q-val)" />
+<param name="show_labels" type="select" label="Plot labels (name, p-val, q-val)">
-<param name="fontsize" type="integer" value="" optional="True" label="Fontsize" />
+<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" />
 </when>
 label="Show visualization of data range" />
 <param name="pos_score_in_bin" type="select" label="Position of the score with respect to bin start and end">
 <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">
 <option value="viridis">viridis</option>
 <option value="RdYlBu_r">RdYlBu reversed</option>
 </when>
 <when value="vlines_track_option">
 <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" />
 <expand macro="overlay_macro" />
 <expand macro="spacer_macro" />
 <option value="bottom">below</option>
 <option value="top">above</option>
 </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>
 </repeat>
 <param name="image_file_format" type="select" label="Image output format">
 <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 name="labels">
+<param name="fontsize" value="10" />
+</conditional>
 </conditional>
 </repeat>
 <repeat name="tracks">
 <conditional name="track_file_style_conditional">
 <param name="track_file_style_selector" value="spacer_option" />
 <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" />
+<conditional name="labels">
+<param name="fontsize" value="8" />
+</conditional>
 <conditional name="bed_style">
 <section name="bed_advanced">
 <param name="gene_rows" value="3" />
 </section>
 </conditional>
 <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" />
+<conditional name="labels">
+<param name="fontsize" value="10" />
+</conditional>
 <conditional name="bed_style">
 <section name="bed_advanced">
 <param name="global_max_row" value="true" />
 </section>
 </conditional>
 <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 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>
 </conditional>
 </repeat>
 <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 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" />
 </section>
 </conditional>
 <conditional name="track_file_style_conditional">
 <param name="track_file_style_selector" value="gene_track_option" />
 <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>
 <conditional name="border_color_bed">
 <param name="border_color_bed_select" value="manually" />
 <conditional name="track_file_style_conditional">
 <param name="track_file_style_selector" value="gene_track_option" />
 <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>
 <conditional name="border_color_bed">
 <param name="border_color_bed_select" value="bed_rgb" />
 <conditional name="track_file_style_conditional">
 <param name="track_file_style_selector" value="gene_track_option" />
 <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>
 <conditional name="border_color_bed">
 <param name="border_color_bed_select" value="none" />
 <param name="height_narrow_peak" value="4" />
 <conditional name="display">
 <param name="display_selector" value="box" />
 <param name="use_summit" value="true" />
 </conditional>
-<param name="show_labels" value="true" />
 </conditional>
 </repeat>
 <repeat name="tracks">
 <conditional name="track_file_style_conditional">
 <param name="track_file_style_selector" value="narrow_peak_track_option" />
 <param name="line_width" value="2" />
 <conditional name="display">
 <param name="display_selector" value="box" />
 <param name="use_summit" value="true" />
 </conditional>
-<param name="show_labels" value="true" />
 </conditional>
 </repeat>
 <repeat name="tracks">
 <conditional name="track_file_style_conditional">
 <param name="track_file_style_selector" value="narrow_peak_track_option" />
 <param name="use_summit" value="true" />
 <param name="show_data" value="true" />
 <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>
 <repeat name="tracks">
 <conditional name="track_file_style_conditional">
 <conditional name="display">
 <param name="display_selector" value="peak" />
 <param name="use_summit" value="false" />
 <param name="show_data" value="false" />
 </conditional>
-<param name="show_labels" value="true" />
 </conditional>
 </repeat>
 <repeat name="tracks">
 <conditional name="track_file_style_conditional">
 <param name="track_file_style_selector" value="xaxis_option" />
 </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="track_input_bed" value="dm3_subset_BDGP5.78.gtf.gz" ftype="gtf" />
-<param name="title" value="genes" />
+<param name="title" value="gtf default" />
 <param name="height_bed" value="10" />
 </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="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">
 <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"/>
-<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>
 </conditional>
 </repeat>
 </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="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" />
 <param name="color" value="red" />
 </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="test" />
+<param name="title" value="arrowhead included" />
 <param name="height_bed" value="10" />
 <conditional name="color_bed">
 <param name="color_bed_select" value="manually" />
 <param name="color" value="red" />
 </conditional>
 </repeat>
 <repeat name="tracks">
 <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" />
 <param name="pos_score_in_bin" value="block" />
 <param name="plot_horizontal_lines" value="true" />
 </repeat>
 <repeat name="tracks">
 <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>
 <param name="image_file_format" value="png" />
 <output name="outFileName" file="test_TADs_bdgm.png" ftype="png" compare="sim_size" delta="100" />
 <conditional name="track_file_style_conditional">
 <param name="track_file_style_selector" value="link_track_option" />
 <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" />
 </conditional>
 <param name="overlay_select" value="share-y" />
 <param name="title" value="ylim 20kb" />
 <conditional name="color_link">
 <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">
 <conditional name="track_file_style_conditional">
 <param name="track_file_style_selector" value="link_track_option" />
 <param name="title" value="compacted" />
 <conditional name="color_link">
 <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">
 <conditional name="track_file_style_conditional">
 <param name="track_file_style_selector" value="link_track_option" />
 <param name="title" value="highly compacted" />
 <conditional name="color_link">
 <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" />
 <output name="outFileName" file="test_link2.png" ftype="png" compare="sim_size" delta="100" />
 </test>
 </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="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>
 </repeat>
 <repeat name="tracks">
 <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" />
-<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>
 <repeat name="tracks">
 <conditional name="track_file_style_conditional">
 <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" />
-<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>
 <repeat name="tracks">
 <conditional name="track_file_style_conditional">
 <conditional name="color_link">
 <param name="color" value="RdYlGn" />
 </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>
 </repeat>
 <repeat name="tracks">
 </section>
 <repeat name="tracks">
 <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>
 <repeat name="tracks">
 <conditional name="track_file_style_conditional">
 <conditional name="track_file_style_conditional">
 <param name="track_file_style_selector" value="scale_bar_option" />
 <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>
 </repeat>
 <repeat name="tracks">
 <param name="title" value="scalebar scalebar_end_position = 3200000 size = 50000" />
 <section name="scalebar_pos">
 <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">
 <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="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[
 pyGenomeTracks
 - bedgraph
 - epilogos
 - narrow peaks
 - links
 - Hi-C matrices (cool or HiCExplorer h5)
+- Fasta
+- MAF (multiple alignment format)
 _________________
 Usage
 -----
 - **NarrowPeak track:** display narrowPeak (encode format) as boxes or as curve (reconstructed peak).
 - **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``.
+- **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.
 _________________

Mercurial > repos > iuc > pygenometracks

comparison pyGenomeTracks.xml @ 11:7dd841a32245 draft