Mercurial > repos > iuc > pygenometracks
diff pyGenomeTracks.xml @ 7:326a3db8d9d1 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
| author | iuc |
|---|---|
| date | Fri, 17 Apr 2020 11:57:44 -0400 |
| parents | 5cec5fb749f0 |
| children | 4ac4e7083b7e |
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--- a/pyGenomeTracks.xml Tue Feb 11 10:20:24 2020 -0500 +++ b/pyGenomeTracks.xml Fri Apr 17 11:57:44 2020 -0400 @@ -30,24 +30,20 @@ #if $region and $region is not None: --region '$region' #end if + #if $global_args.title is not None: + --title '$global_args.title' + #end if + --fontSize $global_args.fontsize + --dpi $global_args.dpi + --trackLabelFraction $global_args.trackLabelFraction + --trackLabelHAlign $global_args.trackLabelHAlign --outFileName plot.$image_file_format && mv plot.$image_file_format plot ]]> </command> <configfiles> <configfile name="tracks_config"> -## First the xaxis if where = top -#if $x_axis.x_axis_select == "true": - #if $x_axis.where == 'top': -[x-axis] - #if $x_axis.fontsize: -fontsize = $x_axis.fontsize - #end if -where = top - #end if -#end if - -## Then each track: +## Each track: #for $counter, $track in enumerate($tracks): ## Hi-C Track #if $track.track_file_style_conditional.track_file_style_selector == "hic_matrix_option": @@ -124,8 +120,10 @@ #elif $track.track_file_style_conditional.color_bed.color: color = $track.track_file_style_conditional.color_bed.color #end if - #if $track.track_file_style_conditional.border_color: -border_color = $track.track_file_style_conditional.border_color + #if $track.track_file_style_conditional.border_color_bed.border_color_bed_select == 'manually': +border_color = $track.track_file_style_conditional.border_color_bed.color + #else +border_color = $track.track_file_style_conditional.border_color_bed.border_color_bed_select #end if display = collapsed #if $track.track_file_style_conditional.height_chrom: @@ -148,8 +146,8 @@ #set ext = $data_bed.extension file = ${counter}_${counter_bed}.$ext #if $ext == 'gtf': -prefered_name = $track.track_file_style_conditional.bed_advanced.gtf.prefered_name -merge_transcripts = $track.track_file_style_conditional.bed_advanced.gtf.merge_transcripts +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 #end if #if $track.track_file_style_conditional.title: title = $track.track_file_style_conditional.title @@ -161,33 +159,53 @@ #elif $track.track_file_style_conditional.color_bed.color: color = $track.track_file_style_conditional.color_bed.color #end if - #if $track.track_file_style_conditional.border_color: -border_color = $track.track_file_style_conditional.border_color + #if $track.track_file_style_conditional.border_color_bed.border_color_bed_select == 'manually': +border_color = $track.track_file_style_conditional.border_color_bed.color + #else +border_color = $track.track_file_style_conditional.border_color_bed.border_color_bed_select #end if - #if $track.track_file_style_conditional.flybase: -style = flybase -height_utr = $track.track_file_style_conditional.bed_advanced.flybase.height_utr -color_utr = $track.track_file_style_conditional.bed_advanced.flybase.color_utr - #else -style = UCSC -arrow_interval = $track.track_file_style_conditional.bed_advanced.ucsc.arrow_interval +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 + #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: + #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 + #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 + #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 +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 + #end if file_type = bed #if $track.track_file_style_conditional.fontsize: fontsize = $track.track_file_style_conditional.fontsize #end if - #if $track.track_file_style_conditional.bed_advanced.gene_rows: -gene_rows = $track.track_file_style_conditional.bed_advanced.gene_rows + #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_advanced.global_max_row -max_labels = $track.track_file_style_conditional.bed_advanced.max_labels -line_width = $track.track_file_style_conditional.bed_advanced.line_width -arrowhead_included = $track.track_file_style_conditional.arrowhead_included +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 +line_width = $track.track_file_style_conditional.bed_style.bed_advanced.line_width #if $track.track_file_style_conditional.invert_orientation: orientation = inverted #end if @@ -223,6 +241,10 @@ 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 + #end if #if $track.track_file_style_conditional.invert_orientation: orientation = inverted #end if @@ -263,6 +285,7 @@ #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: @@ -404,13 +427,15 @@ #if $track.track_file_style_conditional.max_value != "": max_value = $track.track_file_style_conditional.max_value #end if - #if $track.track_file_style_conditional.type_lines: -type = $track.track_file_style_conditional.type_lines - #end if +type = $track.track_file_style_conditional.type.type_selector file_type = bedgraph_matrix -show_data_range = $track.track_file_style_conditional.show_data -plot_horizontal_lines = $track.track_file_style_conditional.plot_horizontal_lines -pos_score_in_bin = $track.track_file_style_conditional.pos_score_in_bin + #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 + #else +colormap = $track.track_file_style_conditional.type.colormap + #end if #if $track.track_file_style_conditional.invert_orientation: orientation = inverted #end if @@ -465,28 +490,83 @@ ## Spacer #if $track.track_file_style_conditional.track_file_style_selector == "spacer_option": [spacer] + #if $track.track_file_style_conditional.title: +title = $track.track_file_style_conditional.title + #end if #if $track.track_file_style_conditional.spacer_height != "": height = $track.track_file_style_conditional.spacer_height #end if #end if + + ## Xaxis: + #if $track.track_file_style_conditional.track_file_style_selector == "xaxis_option": +[x-axis] + #if $track.track_file_style_conditional.title: +title = $track.track_file_style_conditional.title + #end if + #if $track.track_file_style_conditional.fontsize != "": +fontsize = $track.track_file_style_conditional.fontsize + #end if +where = $track.track_file_style_conditional.xaxis_where + ## 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 + + ## Scale bar: + #if $track.track_file_style_conditional.track_file_style_selector == "scale_bar_option": +[scale_bar] + #if $track.track_file_style_conditional.title: +title = $track.track_file_style_conditional.title + #end if + #if $track.track_file_style_conditional.color != "": +color = $track.track_file_style_conditional.color + #end if +alpha = $track.track_file_style_conditional.alpha +line_width = $track.track_file_style_conditional.line_width + #if $track.track_file_style_conditional.x_center != "": +x_center = $track.track_file_style_conditional.x_center + #end if + #if $track.track_file_style_conditional.size != "": +size = $track.track_file_style_conditional.size + #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 +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 #end for - -#if $x_axis.x_axis_select == "true": - #if $x_axis.where == 'bottom': -[x-axis] - #if $x_axis.fontsize: -fontsize = $x_axis.fontsize - #end if -where = bottom - #end if -#end if </configfile> </configfiles> <inputs> - <expand macro="region" /> - + <!--Arguments for pgt--> + <param argument="--region" type="text" label="Region of the genome to limit the operation" optional="false" + help="The format is chr:start-end. Also valid is just to specify a chromosome, for example chr10:10-500" /> + <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"/> + <param argument="--fontsize" type="integer" label="Font size for the labels of the plot" value="12"/> + <param argument="--dpi" type="integer" label="Resolution (dpi)" value="72" + help="Resolution for the image in case the ouput is a raster graphics image (e.g png, jpg)"/> + <param argument="--trackLabelFraction" type="float" label="Proportion of space dedicated to track labels" value="0.05" + min="0" max="1"/> + <param argument="--trackLabelHAlign" type="select" label="Horizontal alignment of track labels"> + <option value="left" selected="True">left</option> + <option value="right">right</option> + <option value="center">center</option> + </param> + </section> + <!--Info to build the config file--> <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"> + 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> @@ -501,12 +581,17 @@ <option value="vlines_track_option">Vlines 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> </param> <when value="hic_matrix_option"> <expand macro="plot_title" /> <expand macro="matrix_h5_cooler_multiple_macro" /> - <expand macro="colormap" /> + <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> + <expand macro="colormap_macro"/> + </param> <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"> @@ -530,7 +615,23 @@ <when value="chrom_states_option"> <expand macro="plot_title" /> <expand macro="track_input_bed_macro" /> - <expand macro="color_bed_macro" /> + <conditional name="color_bed"> + <param name="color_bed_select" type="select" label="Define color:"> + <option value="manually" selected="True">manually</option> + <option value="bed_rgb">From the 9th field</option> + <option value="colormap">From the 5th field (score)</option> + </param> + <when value="manually"> + <param name="color" type="color" value="#000000" label="Color of track" optional="True" /> + </when> + <when value="bed_rgb" /> + <when value="colormap"> + <param name="color" type="select" label="Color map to use for the scores" help=" Available color map names can be found here: https://matplotlib.org/examples/color/colormaps_reference.html"> + <expand macro="colormap_macro" /> + </param> + </when> + </conditional> + <expand macro="border_color_bed_macro" /> <param name="line_width" type="float" value="0.5" label="width of lines" /> <param name="height_chrom" type="float" value="1.5" optional="True" label="height"/> <param name="labels" type="boolean" truevalue="true" falsevalue="false" checked="true" @@ -542,22 +643,75 @@ <expand macro="plot_title" /> <expand macro="track_input_bed_gtf_macro" /> - <expand macro="color_bed_macro" /> + <conditional name="color_bed"> + <param name="color_bed_select" type="select" label="Define color:"> + <option value="manually" selected="True">manually</option> + <option value="bed_rgb">From the 9th field</option> + <option value="colormap">From the 5th field (score)</option> + </param> + <when value="manually"> + <param name="color" type="color" value="#000000" label="Color of track" optional="True" /> + </when> + <when value="bed_rgb" /> + <when value="colormap"> + <param name="color" type="select" label="Color map to use for the scores" help=" Available color map names can be found here: https://matplotlib.org/examples/color/colormaps_reference.html"> + <expand macro="colormap_macro" /> + </param> + </when> + </conditional> + <expand macro="border_color_bed_macro" /> <param name="height_bed" type="float" value="1.5" optional="True" label="height"/> - <param name="labels" type="boolean" truevalue="true" falsevalue="false" checked="true" - label="Plot labels" /> - <param name="flybase" type="boolean" checked="true" label="Use flybase style" help="This will be only used for bed with 12 columns"/> + <conditional name="labels"> + <param name="plot_labels" type="select" label="Plot labels"> + <option value="true" selected="True">yes</option> + <option value="false">no</option> + </param> + <when value="true"> + <param name="all_labels_inside" type="boolean" truevalue="true" falsevalue="false" checked="false" + 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."/> + </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> </param> - <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="fontsize" type="integer" value="" optional="True" label="Fontsize" /> - <expand macro="bed_advanced_macro" /> + <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."/> + <section name="bed_advanced" title="Configure other bed parameters" expanded="False"> + <expand macro="utr_macro" /> + <expand macro="bed_advanced_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" /> + </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="utr_macro" /> + <expand macro="bed_advanced_macro" /> + </section> + </when> + </conditional> <expand macro="overlay_macro" /> <expand macro="inverted_macro" /> <expand macro="spacer_macro" /> @@ -566,13 +720,32 @@ <when value="link_track_option"> <expand macro="plot_title" /> <expand macro="track_input_link_macro" /> - <expand macro="links_color_macro" /> + <conditional name="color_link"> + <param name="color_link_select" type="select" label="Define color:"> + <option value="manually" selected="True">manually</option> + <option value="colormap">From the 7th field (score)</option> + </param> + <when value="manually"> + <param name="color" type="color" value="#000000" label="Color of track" optional="True" /> + </when> + <when value="colormap"> + <param name="color" type="select" label="Color map to use for the scores" help=" Available color map names can be found here: https://matplotlib.org/examples/color/colormaps_reference.html"> + <expand macro="colormap_macro" /> + </param> + </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="height" type="float" value="1.5" optional="True" label="height"/> <expand macro="minmax_macro" /> <expand macro="overlay_macro" /> @@ -603,6 +776,7 @@ 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" label="Plot labels (name, p-val, q-val)" /> <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" /> @@ -636,8 +810,18 @@ <expand macro="minmax_macro" /> <param name="height_bigwig" type="float" value="1.5" optional="True" label="height"/> - <expand macro="reading_bw_macro" /> - <expand macro="type_coverage_macro" /> + <section name="reading_bw_conditional" title="Configure bigwig parameters" expanded="False"> + <param name="summary" type="select" label="Summary method"> + <option value="mean" selected="True">mean=mean value</option> + <option value="min">min=minimum value</option> + <option value="max">max=maximum value</option> + <option value="coverage">coverage=number of covered bases</option> + <option value="std">std=standard deviation</option> + </param> + <param name="number_of_bins" type="integer" value="" optional="True" label="Number of bins" /> + <param name="nans_to_zeros" type="boolean" truevalue="true" falsevalue="false" checked="false" + label="NAN's to zeros" /> + </section> <expand macro="type_coverage_macro" /> <param name="show_data" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Show visualization of data range"/> <expand macro="inverted_macro" /> @@ -654,15 +838,30 @@ <param name="height_bedgraph" type="float" value="1.5" optional="True" label="height"/> - <param name="type_lines" type="boolean" truevalue="lines" falsevalue="" checked="false" - label="Set 'type' to 'lines'" help="if type is set as lines, then the TAD score lines are drawn instead - of the matrix."/> - <param name="pos_score_in_bin" type="select" label="Position of the score with respect to bin start and end" help="Only used when type is lines"> - <option value="center" selected="True">Center</option> - <option value="block">Block (draw a horizontal line between start and end)</option> - </param> - <param name="plot_horizontal_lines" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Plot an horizontal line at 0 when type is lines" /> - <param name="show_data" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Show visualization of data range" /> + <conditional name="type"> + <param name="type_selector" type="select" label="type of plotting"> + <option value="lines" selected="True">lines: each column in the bedgraph will be a line and a mean line will be added</option> + <option value="matrix">matrix: each column in the bedgraph will be a raw in the matrix</option> + </param> + <when value="lines"> + <param name="plot_horizontal_lines" type="boolean" truevalue="true" falsevalue="false" checked="false" + label="Plot an horizontal line at 0 when type is lines" /> + <param name="show_data" type="boolean" truevalue="true" falsevalue="false" checked="false" + 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> + </when> + <when value="matrix"> + <param name="colormap" type="select" label="colormap"> + <option value="viridis">Viridis</option> + <expand macro="colormap_macro" /> + </param> + </when> + </conditional> + + <expand macro="inverted_macro" /> <expand macro="spacer_macro" /> @@ -683,28 +882,41 @@ <expand macro="spacer_macro" /> </when> <when value="spacer_option"> + <expand macro="plot_title" /> <param name="spacer_height" type="float" value="" optional="True" label="Height of the spacer."/> </when> + <when value="xaxis_option"> + <expand macro="plot_title" /> + <param name="fontsize" type="float" optional="True" + label="Fontsize of the x-axis."/> + <param name="xaxis_where" type="select" label="chromosome name and coordinates position relative to the axis"> + <option value="bottom" selected="True">below</option> + <option value="top">above</option> + </param> + <expand macro="spacer_macro" /> + </when> + <when value="scale_bar_option"> + <expand macro="plot_title" /> + <param name="color" type="color" label="Color of the scale bar" optional="True" /> + <param name="alpha" type="float" value="1" min="0" max="1" label="level of transparency (alpha)" help="1 is opaque and 0 is totally transparent"/> + <param name="line_width" type="float" value="0.5" label="width of lines"/> + <param name="x_center" type="integer" label="coordinate where the scale bar should be plotted (center)" optional="True" + help="If not set it will be in the middle of the plotted area."/> + <param name="size" type="integer" label="size of the scale bar" optional="True" + help="If not set it will be the higher number that begins with 1, 2 or 5 followed by 0s that is less than half the plotted area."/> + <param name="sb_where" type="select" label="where the size of the scale bar should appear relative to the bar"> + <option value="left" selected="True">left</option> + <option value="right">right</option> + <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."/> + <expand macro="spacer_macro" /> + </when> </conditional> - </repeat> - - - <conditional name="x_axis"> - <param name="x_axis_select" type="select" label="Configure x-axis"> - <option value="false" selected="True">No</option> - <option value="true">Yes</option> - </param> - <when value="true"> - <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" /> - <param name="where" type="select" label="Where to place the x-axis"> - <option value="top" selected="True">Top</option> - <option value="bottom">Bottom</option> - </param> - </when> - <when value="false" /> - </conditional> <param name="image_file_format" type="select" label="Image output format"> <option value="png">png</option> <option value="svg">svg</option> @@ -719,17 +931,21 @@ </data> </outputs> <tests> + <!--test 1--> <test> <param name="region" value="chrX:3000000-3500000"/> - <conditional name="x_axis"> - <param name="x_axis_select" value="true" /> - </conditional> + <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="hic_matrix_option" /> <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.h5"/> <param name="title" value="Kc DpnII (Li et al. 2015)" /> - <param name="colormap" value="RdYlBu_r" /> + <!--<param name="colormap" value="RdYlBu_r" />--> <param name="depth" value="200000" /> <param name="transform" value="log1p" /> <param name="boundaries_file" value="domains.bed" /> @@ -758,6 +974,10 @@ <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.)" /> + <conditional name="type"> + <param name="type_selector" value="matrix" /> + <!--<param name="colormap" value="viridis" />--> + </conditional> <param name="height_bedgraph" value="10" /> </conditional> </repeat> @@ -857,9 +1077,11 @@ <param name="title" value="max num rows 3" /> <param name="height_bed" value="3" /> <param name="fontsize" value="8" /> - <section name="bed_advanced"> - <param name="gene_rows" value="3" /> - </section> + <conditional name="bed_style"> + <section name="bed_advanced"> + <param name="gene_rows" value="3" /> + </section> + </conditional> </conditional> </repeat> <repeat name="tracks"> @@ -875,9 +1097,11 @@ <param name="title" value="bed6 global max row" /> <param name="height_bed" value="20" /> <param name="fontsize" value="10" /> - <section name="bed_advanced"> - <param name="global_max_row" value="true" /> - </section> + <conditional name="bed_style"> + <section name="bed_advanced"> + <param name="global_max_row" value="true" /> + </section> + </conditional> </conditional> </repeat> <repeat name="tracks"> @@ -889,11 +1113,15 @@ <param name="image_file_format" value="png" /> <output name="outFileName" file="master_TADs_plot.png" ftype="png" compare="sim_size" delta="35000" /> </test> + <!--test 2--> <test> <param name="region" value="chrX:3000000-3500000"/> - <conditional name="x_axis"> - <param name="x_axis_select" value="true" /> - </conditional> + <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="bigwig_track_option" /> @@ -949,11 +1177,15 @@ <param name="image_file_format" value="png" /> <output name="outFileName" file="bigwig_multiple.png" ftype="png" compare="sim_size" delta="35000" /> </test> + <!--test 3--> <test> <param name="region" value="chrX:3000000-3500000"/> - <conditional name="x_axis"> - <param name="x_axis_select" value="true" /> - </conditional> + <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="hic_matrix_option" /> @@ -1092,7 +1324,9 @@ <param name="title" value="genes in ucsc" /> <param name="height_bed" value="5" /> <param name="fontsize" value="10" /> - <param name="flybase" value="false"/> + <conditional name="bed_style"> + <param name="bed_style_select" value="UCSC"/> + </conditional> </conditional> </repeat> <repeat name="tracks"> @@ -1102,9 +1336,11 @@ <param name="title" value="bed6 global max row color from score" /> <param name="height_bed" value="20" /> <param name="fontsize" value="10" /> - <section name="bed_advanced"> - <param name="global_max_row" value="true" /> - </section> + <conditional name="bed_style"> + <section name="bed_advanced"> + <param name="global_max_row" value="true" /> + </section> + </conditional> <conditional name="color_bed"> <param name="color_bed_select" value="colormap" /> <param name="color" value="RdYlBu_r" /> @@ -1115,26 +1351,66 @@ <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" /> + <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" /> + <param name="color" value="red" /> + </conditional> + <conditional name="labels"> + <param name="plot_labels" value="false" /> + </conditional> + <param name="display" value="interleaved" /> + </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="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> - <param name="border_color" value="red" /> - <param name="labels" value="false" /> + <conditional name="border_color_bed"> + <param name="border_color_bed_select" value="bed_rgb" /> + </conditional> + <conditional name="labels"> + <param name="plot_labels" value="false" /> + </conditional> + <param name="display" value="interleaved" /> + </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="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" /> + </conditional> + <conditional name="labels"> + <param name="plot_labels" value="false" /> + </conditional> <param name="display" value="interleaved" /> </conditional> </repeat> <param name="image_file_format" value="png" /> <output name="outFileName" file="master_TADs_BW_plot.png" ftype="png" compare="sim_size" delta="35000" /> </test> + <!--test 4--> <test> <param name="region" value="X:2700000-3100000"/> - <conditional name="x_axis"> - <param name="x_axis_select" value="true" /> - <param name="where" value="bottom" /> - </conditional> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="bigwig_track_option" /> @@ -1161,14 +1437,24 @@ <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="xaxis_option" /> + <param name="xaxis_where" value="bottom" /> + </conditional> + </repeat> <param name="image_file_format" value="png" /> <output name="outFileName" file="test_alpha.png" ftype="png" compare="sim_size" delta="35000" /> </test> + <!--test 5--> <test> <param name="region" value="X:3000000-3300000"/> - <conditional name="x_axis"> - <param name="x_axis_select" value="true" /> - </conditional> + <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="gene_track_option" /> @@ -1176,7 +1462,9 @@ <param name="title" value="test" /> <param name="height_bed" value="10" /> <param name="color" value="#000000" /> - <param name="flybase" value="false" /> + <conditional name="bed_style"> + <param name="bed_style_select" value="UCSC"/> + </conditional> <param name="spacer_height" value="1"/> </conditional> </repeat> @@ -1187,19 +1475,18 @@ <param name="title" value="test" /> <param name="height_bed" value="10" /> <param name="color" value="#000000" /> - <param name="flybase" value="false" /> + <conditional name="bed_style"> + <param name="bed_style_select" value="UCSC"/> + </conditional> <param name="spacer_height" value="1"/> </conditional> </repeat> <param name="image_file_format" value="png" /> <output name="outFileName" file="test_gtf_bed4.png" ftype="png" compare="sim_size" delta="35000" /> </test> + <!--test 6--> <test> <param name="region" value="X:2760000-2802000"/> - <conditional name="x_axis"> - <param name="x_axis_select" value="true" /> - <param name="where" value="bottom" /> - </conditional> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="narrow_peak_track_option" /> @@ -1217,6 +1504,21 @@ <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="narrow_peak_track_option" /> + <param name="title" value="box line_width = 2" /> + <param name="track_input_narrow_peak" value="test2.narrowPeak" ftype="encodepeak" /> + <param name="color" value="#9bbb59" /> + <param name="height_narrow_peak" value="4" /> + <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="title" value="peak width 3" /> <param name="track_input_narrow_peak" value="test2.narrowPeak" ftype="encodepeak" /> <param name="color" value="#c0504d" /> @@ -1247,14 +1549,24 @@ <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" /> + <param name="xaxis_where" value="bottom" /> + </conditional> + </repeat> <param name="image_file_format" value="png" /> <output name="outFileName" file="test_narrowPeak.png" ftype="png" compare="sim_size" delta="35000" /> </test> + <!--test 7--> <test> <param name="region" value="chrX:3300000-3500000"/> - <conditional name="x_axis"> - <param name="x_axis_select" value="true" /> - </conditional> + <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="gene_track_option" /> @@ -1269,37 +1581,110 @@ <param name="track_input_bed" value="dm3_subset_BDGP5.78.gtf.gz" ftype="gtf" /> <param name="title" value="gtf" /> <param name="height_bed" value="10" /> - <section name="bed_advanced"> - <section name ="flybase"> + <conditional name="bed_style"> + <section name="bed_advanced"> <param name="height_utr" value="0.75"/> - <param name="color_utr" value="#ff0000"/> + <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"/> + </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_genes_withrgbandscore.bed.gz" ftype="bed" /> + <param name="title" value="genes with scores" /> + <param name="height_bed" value="10" /> + <conditional name="color_bed"> + <param name="color_bed_select" value="colormap" /> + <param name="color" value="cool_r" /> + </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_withrgbandscore.bed.gz" ftype="bed" /> + <param name="title" value="genes with utr as bed_rgb" /> + <param name="height_bed" value="10" /> + <conditional name="bed_style"> + <section name="bed_advanced"> + <conditional name="color_utr"> + <param name="color_utr_select" value="bed_rgb"/> + </conditional> </section> - <section name ="gtf"> - <param name="prefered_name" value="gene_name"/> - <param name="merge_transcripts" value="true"/> + </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_withrgbandscore.bed.gz" ftype="bed" /> + <param name="title" value="genes with coding as bed_rgb - labels_in_margin" /> + <param name="height_bed" value="10" /> + <conditional name="color_bed"> + <param name="color_bed_select" value="bed_rgb" /> + </conditional> + <conditional name="labels"> + <param name="plot_labels" value="true" /> + <param name="labels_in_margin" value="true" /> + </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_withrgbandscore.bed.gz" ftype="bed" /> + <param name="title" value="genes bed_rgb like - all_labels_inside" /> + <param name="height_bed" value="10" /> + <conditional name="color_bed"> + <param name="color_bed_select" value="bed_rgb" /> + </conditional> + <conditional name="bed_style"> + <section name="bed_advanced"> + <conditional name="color_utr"> + <param name="color_utr_select" value="like"/> + </conditional> </section> - </section> + </conditional> + <conditional name="labels"> + <param name="plot_labels" value="true" /> + <param name="all_labels_inside" value="true" /> + </conditional> </conditional> </repeat> <param name="image_file_format" value="png" /> <output name="outFileName" file="test_gtf_flybase_param.png" ftype="png" compare="sim_size" delta="35000" /> </test> + <!--test 8--> <test> <param name="region" value="chrX:3300000-3500000"/> - <conditional name="x_axis"> - <param name="x_axis_select" value="true" /> - </conditional> + <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="gene_track_option" /> <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" /> <param name="title" value="dm3_genes.bed" /> <param name="height_bed" value="10" /> - <param name="flybase" value="false" /> - <section name="bed_advanced"> - <param name="global_max_row" value="true" /> - <param name="max_labels" value="15" /> - </section> + <conditional name="bed_style"> + <param name="bed_style_select" value="UCSC"/> + <section name="bed_advanced"> + <param name="global_max_row" value="true" /> + <param name="max_labels" value="15" /> + </section> + </conditional> </conditional> </repeat> <repeat name="tracks"> @@ -1308,30 +1693,33 @@ <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" /> <param name="title" value="genes.bed.gz" /> <param name="height_bed" value="10" /> - <param name="flybase" value="false" /> - <section name="bed_advanced"> - <param name="line_width" value="2"/> - <section name ="ucsc"> + <conditional name="bed_style"> + <param name="bed_style_select" value="UCSC"/> + <section name="bed_advanced"> <param name="arrow_interval" value="10"/> + <param name="line_width" value="2"/> </section> - </section> + </conditional> </conditional> </repeat> <param name="image_file_format" value="png" /> <output name="outFileName" file="test_ucsc_param.png" ftype="png" compare="sim_size" delta="35000" /> </test> + <!--test 9--> <test> <param name="region" value="X:3133000-3138000"/> - <conditional name="x_axis"> - <param name="x_axis_select" value="true" /> - </conditional> + <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="gene_track_option" /> <param name="track_input_bed" value="dm3_subset_BDGP5.78.gtf.gz" ftype="gtf" /> <param name="title" value="test" /> <param name="height_bed" value="10" /> - <param name="flybase" value="true" /> <param name="spacer_height" value="1"/> </conditional> </repeat> @@ -1345,7 +1733,9 @@ <param name="color_bed_select" value="manually" /> <param name="color" value="red" /> </conditional> - <param name="flybase" value="false" /> + <conditional name="bed_style"> + <param name="bed_style_select" value="UCSC"/> + </conditional> <param name="spacer_height" value="1"/> </conditional> </repeat> @@ -1359,9 +1749,10 @@ <param name="color_bed_select" value="manually" /> <param name="color" value="red" /> </conditional> - <param name="flybase" value="true" /> <param name="spacer_height" value="1"/> - <param name="arrowhead_included" value="true"/> + <conditional name="bed_style"> + <param name="arrowhead_included" value="true"/> + </conditional> </conditional> </repeat> <repeat name="tracks"> @@ -1373,11 +1764,15 @@ <param name="image_file_format" value="png" /> <output name="outFileName" file="test_arrowhead_zoom.png" ftype="png" compare="sim_size" delta="35000" /> </test> + <!--test 10--> <test> <param name="region" value="X:3340000-3380000"/> - <conditional name="x_axis"> - <param name="x_axis_select" value="true" /> - </conditional> + <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="gene_track_option" /> @@ -1419,17 +1814,21 @@ <param name="image_file_format" value="png" /> <output name="outFileName" file="test_middle_triangle.png" ftype="png" compare="sim_size" delta="35000" /> </test> + <!--test 11--> <test> <param name="region" value="chrX:3250000-3400000"/> - <conditional name="x_axis"> - <param name="x_axis_select" value="true" /> - </conditional> + <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="hic_matrix_option" /> <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.h5"/> <param name="title" value="Kc DpnII (Li et al. 2015)" /> - <param name="colormap" value="RdYlBu_r" /> + <!--<param name="colormap" value="RdYlBu_r" />--> <param name="depth" value="100000" /> <param name="transform" value="log1p" /> <param name="show_masked_bins" value="true" /> @@ -1448,10 +1847,12 @@ <param name="track_input_bedgraph_matrix" value="tad_score.gz" ftype="bedgraph" /> <param name="title" value="TAD separation score (Ramirez et al.)" /> <param name="height_bedgraph" value="10" /> - <param name="type_lines" value="lines" /> - <param name="pos_score_in_bin" value="block" /> - <param name="plot_horizontal_lines" value="true" /> - <param name="show_data" value="true" /> + <conditional name="type"> + <param name="type_selector" value="lines" /> + <param name="pos_score_in_bin" value="block" /> + <param name="plot_horizontal_lines" value="true" /> + <param name="show_data" value="true" /> + </conditional> </conditional> </repeat> <repeat name="tracks"> @@ -1460,19 +1861,25 @@ <param name="track_input_bedgraph_matrix" value="tad_score.gz" ftype="bedgraph" /> <param name="title" value="TAD separation score (Ramirez et al.)" /> <param name="height_bedgraph" value="10" /> - <param name="type_lines" value="lines" /> - <param name="pos_score_in_bin" value="center" /> - <param name="plot_horizontal_lines" value="false" /> + <conditional name="type"> + <param name="type_selector" value="lines" /> + <param name="pos_score_in_bin" value="center" /> + <param name="plot_horizontal_lines" value="false" /> + </conditional> </conditional> </repeat> <param name="image_file_format" value="png" /> <output name="outFileName" file="test_TADs_bdgm.png" ftype="png" compare="sim_size" delta="35000" /> </test> + <!--test 12--> <test> <param name="region" value="chrX:3000000-3300000"/> - <conditional name="x_axis"> - <param name="x_axis_select" value="true" /> - </conditional> + <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="hic_matrix_option" /> @@ -1514,6 +1921,156 @@ <param name="image_file_format" value="png" /> <output name="outFileName" file="test_link.png" ftype="png" compare="sim_size" delta="35000" /> </test> + <!--test 13--> + <test> + <param name="region" value="chrX:3000000-3300000"/> + <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.arcs" ftype="bed" /> + <param name="title" value="default" /> + <conditional name="color_link"> + <param name="color_link_select" value="manually" /> + <param name="color" value="#000000" /> + </conditional> + </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.arcs" ftype="bed" /> + <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> + </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.arcs" ftype="bed" /> + <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> + </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.arcs" ftype="bed" /> + <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> + </repeat> + <param name="image_file_format" value="png" /> + <output name="outFileName" file="test_link2.png" ftype="png" compare="sim_size" delta="35000" /> + </test> + <!--test 14--> + <test> + <param name="region" value="chrX:3000000-3300000"/> + <section name="global_args"> + <param name="title" value="Scale bar"/> + <param name="trackLabelFraction" value="0.5"/> + <param name="trackLabelHAlign" value="center"/> + </section> + <repeat name="tracks"> + <conditional name="track_file_style_conditional"> + <param name="track_file_style_selector" value="spacer_option" /> + <param name="spacer_height" value="1.0" /> + </conditional> + </repeat> + <repeat name="tracks"> + <conditional name="track_file_style_conditional"> + <param name="track_file_style_selector" value="scale_bar_option" /> + <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="scale_bar_option" /> + <param name="title" value="scalebar where = right x_center = 3200000 size = 100002 fontsize = 8 line_width =2 color = red alpha = 0.5" /> + <param name="color" value="red"/> + <param name="alpha" value="0.5"/> + <param name="line_width" value="2"/> + <param name="x_center" value="3200000"/> + <param name="size" value="100002"/> + <param name="sb_where" value="right"/> + <param name="fontsize" value="8"/> + <param name="spacer_height" value="4"/> + </conditional> + </repeat> + <param name="image_file_format" value="png" /> + <output name="outFileName" file="test_scale_bar.png" ftype="png" compare="sim_size" delta="35000" /> + </test> + <!--test 15--> + <test> + <param name="region" value="chrX:3300000-3500000"/> + <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> + <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="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_genes.bed.gz" ftype="bed" /> + <param name="title" value="UCSC" /> + <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"/> + </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="tssarrow" /> + <param name="height_bed" value="10" /> + <conditional name="bed_style"> + <param name="bed_style_select" value="tssarrow"/> + </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="tssarrow 5kb" /> + <param name="height_bed" value="10" /> + <conditional name="bed_style"> + <param name="bed_style_select" value="tssarrow"/> + <section name="bed_advanced"> + <param name="arrow_length" value="5000"/> + </section> + </conditional> + </conditional> + </repeat> + <param name="image_file_format" value="png" /> + <output name="outFileName" file="test_tssarrow.png" ftype="png" compare="sim_size" delta="35000" /> + </test> </tests> <help><![CDATA[