Mercurial > repos > iuc > pygenometracks
diff pyGenomeTracks.xml @ 5:eca03db4f612 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
| author | iuc |
|---|---|
| date | Wed, 08 Jan 2020 09:15:19 -0500 |
| parents | c237ba772225 |
| children | 5cec5fb749f0 |
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--- a/pyGenomeTracks.xml Thu Sep 19 17:18:54 2019 -0400 +++ b/pyGenomeTracks.xml Wed Jan 08 09:15:19 2020 -0500 @@ -1,4 +1,4 @@ -<tool id="pygenomeTracks" name="@BINARY@" version="@WRAPPER_VERSION@.1"> +<tool id="pygenomeTracks" name="@BINARY@" version="@WRAPPER_VERSION@"> <description>plot genomic data tracks</description> <macros> <token name="@BINARY@">pyGenomeTracks</token> @@ -7,6 +7,7 @@ <expand macro="requirements" /> <command detect_errors="exit_code"> <![CDATA[ + ## First symlink data of hic or bed/gtf to have the good extension #for $counter, $track in enumerate($tracks): #if $track.track_file_style_conditional.track_file_style_selector == "hic_matrix_option": #for $counter_matrix, $data_matrix in enumerate($track.track_file_style_conditional.matrix_h5_cooler_multiple): @@ -35,426 +36,449 @@ </command> <configfiles> <configfile name="tracks_config"> -#if $x_axis.x_axis_select == "yes": -#if $x_axis.where == 'top': +## First the xaxis if where = top +#if $x_axis.x_axis_select == "true": + #if $x_axis.where == 'top': [x-axis] -#if $x_axis.fontsize: + #if $x_axis.fontsize: fontsize = $x_axis.fontsize -#end if -#if $x_axis.where: -where = $x_axis.where + #end if +where = top + #end if #end if -#end if -#end if + +## Then each track: #for $counter, $track in enumerate($tracks): -#if $track.track_file_style_conditional.track_file_style_selector == "hic_matrix_option": - -#for $counter_matrix, $data_matrix in enumerate($track.track_file_style_conditional.matrix_h5_cooler_multiple): + ## Hi-C Track + #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 + #set ext = $data_matrix.extension file = ${counter}_${counter_matrix}.$ext file_type = hic_matrix -#if $track.track_file_style_conditional.title: + #if $track.track_file_style_conditional.title: title = $track.track_file_style_conditional.title -#else: + #else: title = $data_matrix.name -#end if -#if $track.track_file_style_conditional.depth: + #end if + #if $track.track_file_style_conditional.depth: depth = $track.track_file_style_conditional.depth -#end if -#if $track.track_file_style_conditional.colormap: + #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: + #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: + #end if + #if $track.track_file_style_conditional.max_value: max_value = $track.track_file_style_conditional.max_value -#end if -#if $track.track_file_style_conditional.transform != "": + #end if transform = $track.track_file_style_conditional.transform -#end if -#if $track.track_file_style_conditional.height_matrix != "": + #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: + #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: + #end if + #if $track.track_file_style_conditional.invert_orientation: orientation = inverted -#end if -#if $track.track_file_style_conditional.scale_factor: -scale factor = $track.track_file_style_conditional.scale_factor -#end if - -#if str($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 + #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 = domains -border color = black +border_color = black color = none -overlay previous = share-y -#end if - - -#if $track.track_file_style_conditional.spacer_height != "": +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 - - - -#if $track.track_file_style_conditional.track_file_style_selector == "tad_score_track_option": + #end if + #end for + #end if -#for $data_bedgraph in $track.track_file_style_conditional.track_input_bedgraph: -[tad_score_$counter] -file = $data_bedgraph -#if $track.track_file_style_conditional.title: -title = $track.track_file_style_conditional.title -#else: -title = $data_bedgraph.name -#end if -#if $track.track_file_style_conditional.color: -color = $track.track_file_style_conditional.color -#end if -#if $track.track_file_style_conditional.height_tad: -height = $track.track_file_style_conditional.height_tad -#end if -show data range = $track.track_file_style_conditional.show_data - -#set $columns = len(open(str($track.track_file_style_conditional.track_input_bedgraph)).readline().split('\t')) -#if $columns > 4: -file_type = bedgraph_matrix -#if $track.track_file_style_conditional.type_lines: -type = $track.track_file_style_conditional.type_lines -#end if -#else: -file_type = bedgraph -#end if -#if $track.track_file_style_conditional.spacer_height != "": -[spacer] -height = $track.track_file_style_conditional.spacer_height -#end if -#end for -#end if - - - - -#if $track.track_file_style_conditional.track_file_style_selector == "chrom_states_option": -#for $data_bed in $track.track_file_style_conditional.track_input_bed: - + ## Chrom_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 -#if $track.track_file_style_conditional.title: + #if $track.track_file_style_conditional.title: title = $track.track_file_style_conditional.title -#else: + #else: title = $data_bed.name -#end if -#if $track.track_file_style_conditional.color_bed.color_bed_select == "bed_rgb": + #end if + #if $track.track_file_style_conditional.color_bed.color_bed_select == "bed_rgb": color = bed_rgb -#elif $track.track_file_style_conditional.color_bed.color: + #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 -#end if + #end if + #if $track.track_file_style_conditional.border_color: +border_color = $track.track_file_style_conditional.border_color + #end if display = collapsed -#if $track.track_file_style_conditional.height_chrom: + #if $track.track_file_style_conditional.height_chrom: height = $track.track_file_style_conditional.height_chrom -#end if + #end if +line_width = $track.track_file_style_conditional.line_width file_type = bed -#if $track.track_file_style_conditional.spacer_height != "": + ## 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 - - - - -#if $track.track_file_style_conditional.track_file_style_selector == "gene_track_option": -#for $counter_bed, $data_bed in enumerate($track.track_file_style_conditional.track_input_bed): - -[genes_${counter}_${counter_bed}] -#set ext = $data_bed.extension -file = ${counter}_${counter_bed}.$ext -#if $track.track_file_style_conditional.title: -title = $track.track_file_style_conditional.title -#else: -title = $data_bed.name -#end if -#if $track.track_file_style_conditional.color_bed.color_bed_select == "bed_rgb": -color = bed_rgb -#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 -#end if + #end if + #end for + #end if -#if $track.track_file_style_conditional.flybase: + ## Gene/gtf track + #if $track.track_file_style_conditional.track_file_style_selector == "gene_track_option": + #for $counter_bed, $data_bed in enumerate($track.track_file_style_conditional.track_input_bed): +[genes_${counter}_${counter_bed}] + #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 + #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.name + #end if + #if $track.track_file_style_conditional.color_bed.color_bed_select == "bed_rgb": +color = bed_rgb + #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 + #end if + #if $track.track_file_style_conditional.flybase: style = flybase -#else +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 -#end if - +arrow_interval = $track.track_file_style_conditional.bed_advanced.ucsc.arrow_interval + #end if display = $track.track_file_style_conditional.display - -#if $track.track_file_style_conditional.height_bed: + #if $track.track_file_style_conditional.height_bed: height = $track.track_file_style_conditional.height_bed -#end if - + #end if labels = $track.track_file_style_conditional.labels - file_type = bed -#if $track.track_file_style_conditional.fontsize: + #if $track.track_file_style_conditional.fontsize: fontsize = $track.track_file_style_conditional.fontsize -#end if - -#if $track.track_file_style_conditional.gene_rows: -gene rows = $track.track_file_style_conditional.gene_rows -#end if - -#if $track.track_file_style_conditional.global_max_row: -global max row = $track.track_file_style_conditional.global_max_row -#end if -#if $track.track_file_style_conditional.spacer_height != "": + #end if + #if $track.track_file_style_conditional.bed_advanced.gene_rows: +gene_rows = $track.track_file_style_conditional.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 + #if $track.track_file_style_conditional.invert_orientation: +orientation = inverted + #end if +overlay_previous = $track.track_file_style_conditional.overlay_select + ## 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 + #end if + #end for + #end if -#if $track.track_file_style_conditional.track_file_style_selector == "narrow_peak_track_option": -#for $counter_narrow_peak, $data_narrow_peak in enumerate($track.track_file_style_conditional.track_input_narrow_peak): + ## Link + #if $track.track_file_style_conditional.track_file_style_selector == "link_track_option": +[links_$counter] +file = $track.track_file_style_conditional.track_input_link + #if $track.track_file_style_conditional.title: +title = $track.track_file_style_conditional.title + #elif $track.track_file_style_conditional.overlay_select == 'no': +title = $track.track_file_style_conditional.track_input_link.name + #end if + #if $track.track_file_style_conditional.height: +height = $track.track_file_style_conditional.height + #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 +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 + #if $track.track_file_style_conditional.invert_orientation: +orientation = inverted + #end if +overlay_previous = $track.track_file_style_conditional.overlay_select +file_type = links + ## 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 + ## Narrow peak + #if $track.track_file_style_conditional.track_file_style_selector == "narrow_peak_track_option": + #for $counter_narrow_peak, $data_narrow_peak in enumerate($track.track_file_style_conditional.track_input_narrow_peak): [narrow_peak_${counter}_${counter_narrow_peak}] file = $data_narrow_peak -#if $track.track_file_style_conditional.title: + #if $track.track_file_style_conditional.title: title = $track.track_file_style_conditional.title -#else: + #elif $track.track_file_style_conditional.overlay_select == 'no': title = $data_narrow_peak.name -#end if + #end if color = $track.track_file_style_conditional.color type = $track.track_file_style_conditional.display.display_selector -use summit = $track.track_file_style_conditional.display.use_summit -#if $track.track_file_style_conditional.display.display_selector == "peak": -show data range = $track.track_file_style_conditional.display.show_data -#if $track.track_file_style_conditional.display.width_adjust: -width adjust = $track.track_file_style_conditional.display.width_adjust -#end if -#if $track.track_file_style_conditional.display.min_value: +use_summit = $track.track_file_style_conditional.display.use_summit + #if $track.track_file_style_conditional.display.display_selector == "peak": +show_data_range = $track.track_file_style_conditional.display.show_data + #if $track.track_file_style_conditional.display.width_adjust: +width_adjust = $track.track_file_style_conditional.display.width_adjust + #end if + #if $track.track_file_style_conditional.display.min_value: min_value = $track.track_file_style_conditional.display.min_value -#end if -#if $track.track_file_style_conditional.display.max_value: + #end if + #if $track.track_file_style_conditional.display.max_value: max_value = $track.track_file_style_conditional.display.max_value -#end if -#end if - - -#if $track.track_file_style_conditional.height_narrow_peak: + #end if + #end if + #if $track.track_file_style_conditional.height_narrow_peak: height = $track.track_file_style_conditional.height_narrow_peak -#end if - -show labels = $track.track_file_style_conditional.show_labels - + #end if +show_labels = $track.track_file_style_conditional.show_labels file_type = narrow_peak -#if $track.track_file_style_conditional.fontsize: + #if $track.track_file_style_conditional.fontsize: fontsize = $track.track_file_style_conditional.fontsize -#end if - -#if $track.track_file_style_conditional.spacer_height != "": + #end if + #if $track.track_file_style_conditional.invert_orientation: +orientation = inverted + #end if +overlay_previous = $track.track_file_style_conditional.overlay_select + ## 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 + #end if + #end for + #end if - -#if $track.track_file_style_conditional.track_file_style_selector == "bedgraph_track_option": -#for $data_bedgraph in $track.track_file_style_conditional.track_input_bedgraph: - + ## Bedgraph track + #if $track.track_file_style_conditional.track_file_style_selector == "bedgraph_track_option": + #for $data_bedgraph in $track.track_file_style_conditional.track_input_bedgraph: [bedgraph_$counter] file = $data_bedgraph -#if $track.track_file_style_conditional.title: + #if $track.track_file_style_conditional.title: title = $track.track_file_style_conditional.title -#elif $track.track_file_style_conditional.overlay_select == "no": + #elif $track.track_file_style_conditional.overlay_select == "no": title = $data_bedgraph.name -#end if -#if $track.track_file_style_conditional.color: + #end if + #if $track.track_file_style_conditional.color: color = $track.track_file_style_conditional.color -#end if + #end if alpha = $track.track_file_style_conditional.alpha -#if $track.track_file_style_conditional.color_negative.color_negative_select == "yes": -negative color = $track.track_file_style_conditional.color_negative.color -#end if -#if $track.track_file_style_conditional.height_bedgraph: + #if $track.track_file_style_conditional.color_negative.color_negative_select == "true": +negative_color = $track.track_file_style_conditional.color_negative.color + #end if + #if $track.track_file_style_conditional.height_bedgraph: height = $track.track_file_style_conditional.height_bedgraph -#end if -#if $track.track_file_style_conditional.min_value: + #end if + #if $track.track_file_style_conditional.min_value: min_value = $track.track_file_style_conditional.min_value -#else: -min_value = auto -#end if -#if $track.track_file_style_conditional.max_value: + #end if + #if $track.track_file_style_conditional.max_value: max_value = $track.track_file_style_conditional.max_value -#else: -max_value = auto -#end if - -show data range = $track.track_file_style_conditional.show_data - -#set $columns = len(open(str($track.track_file_style_conditional.track_input_bedgraph)).readline().split('\t')) -#if $columns > 4: + #end if +show_data_range = $track.track_file_style_conditional.show_data +nans_to_zeros = $track.track_file_style_conditional.nans_to_zeros +use_middle = $track.track_file_style_conditional.use_middle + #set $columns = len(open(str($track.track_file_style_conditional.track_input_bedgraph)).readline().split('\t')) + #if $columns > 4: file_type = bedgraph_matrix type = lines -#else: + #else: file_type = bedgraph -#if $track.track_file_style_conditional.type_conditional.type_selector == 'fill_option': + #if $track.track_file_style_conditional.type_conditional.type_selector == 'fill_option': type = fill -#elif $track.track_file_style_conditional.type_conditional.type_selector == 'line_option': + #elif $track.track_file_style_conditional.type_conditional.type_selector == 'line_option': type = line:$track.track_file_style_conditional.type_conditional.width_line -#elif $track.track_file_style_conditional.type_conditional.type_selector == 'point_option': + #elif $track.track_file_style_conditional.type_conditional.type_selector == 'point_option': type = points:$track.track_file_style_conditional.type_conditional.width_point -#end if -#end if -#if $track.track_file_style_conditional.invert_orientation: + #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 -#if $track.track_file_style_conditional.spacer_height != "": + #end if +overlay_previous = $track.track_file_style_conditional.overlay_select + ## 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 + #end if + #end for + #end if -#if $track.track_file_style_conditional.track_file_style_selector == "bigwig_track_option": -#for $data_bigwig in $track.track_file_style_conditional.track_input_bigwig: + ## Bigwig tracks + #if $track.track_file_style_conditional.track_file_style_selector == "bigwig_track_option": + #for $data_bigwig in $track.track_file_style_conditional.track_input_bigwig: [bigwig_$counter] file = $data_bigwig -#if $track.track_file_style_conditional.title: + #if $track.track_file_style_conditional.title: title = $track.track_file_style_conditional.title -#elif $track.track_file_style_conditional.overlay_select == "no": + #elif $track.track_file_style_conditional.overlay_select == "no": title = $data_bigwig.name -#end if -#if $track.track_file_style_conditional.color: + #end if + #if $track.track_file_style_conditional.color: color = $track.track_file_style_conditional.color -#end if + #end if alpha = $track.track_file_style_conditional.alpha -#if $track.track_file_style_conditional.color_negative.color_negative_select == "yes": -negative color = $track.track_file_style_conditional.color_negative.color -#end if -#if $track.track_file_style_conditional.min_value: + #if $track.track_file_style_conditional.color_negative.color_negative_select == "true": +negative_color = $track.track_file_style_conditional.color_negative.color + #end if + #if $track.track_file_style_conditional.min_value: min_value = $track.track_file_style_conditional.min_value -#else: -min_value = 0 -#end if -#if $track.track_file_style_conditional.max_value: + #end if + #if $track.track_file_style_conditional.max_value: max_value = $track.track_file_style_conditional.max_value -#else: -max_value = auto -#end if + #end if height = $track.track_file_style_conditional.height_bigwig -summary method = $track.track_file_style_conditional.reading_bw_conditional.summary -nans to zeros = $track.track_file_style_conditional.reading_bw_conditional.nans_to_zeros -#if $track.track_file_style_conditional.reading_bw_conditional.number_of_bins: -number of bins = $track.track_file_style_conditional.reading_bw_conditional.number_of_bins -#end if -#if $track.track_file_style_conditional.type_conditional.type_selector == 'fill_option': +summary_method = $track.track_file_style_conditional.reading_bw_conditional.summary +nans_to_zeros = $track.track_file_style_conditional.reading_bw_conditional.nans_to_zeros + #if $track.track_file_style_conditional.reading_bw_conditional.number_of_bins: +number_of_bins = $track.track_file_style_conditional.reading_bw_conditional.number_of_bins + #end if + #if $track.track_file_style_conditional.type_conditional.type_selector == 'fill_option': type = fill -#elif $track.track_file_style_conditional.type_conditional.type_selector == 'line_option': + #elif $track.track_file_style_conditional.type_conditional.type_selector == 'line_option': type = line:$track.track_file_style_conditional.type_conditional.width_line -#elif $track.track_file_style_conditional.type_conditional.type_selector == 'point_option': + #elif $track.track_file_style_conditional.type_conditional.type_selector == 'point_option': type = points:$track.track_file_style_conditional.type_conditional.width_point -#end if -show data range = $track.track_file_style_conditional.show_data + #end if +show_data_range = $track.track_file_style_conditional.show_data file_type = bigwig -#if $track.track_file_style_conditional.invert_orientation: + #if $track.track_file_style_conditional.invert_orientation: orientation = inverted -#end if -overlay previous = $track.track_file_style_conditional.overlay_select -#if $track.track_file_style_conditional.spacer_height != "": + #end if +overlay_previous = $track.track_file_style_conditional.overlay_select + ## 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 + #end if + #end for + #end if - -#if $track.track_file_style_conditional.track_file_style_selector == "bedgraph_matrix_track_option": -#for $data_bedgraph_matrix in $track.track_file_style_conditional.track_input_bedgraph_matrix: - + ## bedgraph_matrix + #if $track.track_file_style_conditional.track_file_style_selector == "bedgraph_matrix_track_option": + #for $data_bedgraph_matrix in $track.track_file_style_conditional.track_input_bedgraph_matrix: [bedgraph_matrix_$counter] file = $data_bedgraph_matrix -#if $track.track_file_style_conditional.title: + #if $track.track_file_style_conditional.title: title = $track.track_file_style_conditional.title -#else: + #else: title = $data_bedgraph_matrix.name -#end if -#if $track.track_file_style_conditional.height_bedgraph: + #end if + #if $track.track_file_style_conditional.height_bedgraph: height = $track.track_file_style_conditional.height_bedgraph -#end if -orientation = inverted -#if $track.track_file_style_conditional.min_value: + #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: + #end if + #if $track.track_file_style_conditional.max_value: max_value = $track.track_file_style_conditional.max_value -#end if -#if $track.track_file_style_conditional.type_lines: + #end if + #if $track.track_file_style_conditional.type_lines: type = $track.track_file_style_conditional.type_lines -#end if + #end if file_type = bedgraph_matrix -plot horizontal lines=False -#if $track.track_file_style_conditional.invert_orientation: +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.invert_orientation: orientation = inverted -#end if -#if $track.track_file_style_conditional.spacer_height != "": + #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 + #end if + #end for + #end if -#if $track.track_file_style_conditional.track_file_style_selector == "vlines_track_option": - + ## Vlines: + #if $track.track_file_style_conditional.track_file_style_selector == "vlines_track_option": [vlines_$counter] file = $track.track_file_style_conditional.track_input_bed_single type = vlines -file_type = bed -#end if -#if $track.track_file_style_conditional.track_file_style_selector == "spacer_option": + #end if -#if $track.track_file_style_conditional.spacer_height != "": + ## Hlines: + #if $track.track_file_style_conditional.track_file_style_selector == "hlines_track_option": +[hlines_$counter] + #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.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 +y_values = $track.track_file_style_conditional.y_values +show_data_range = $track.track_file_style_conditional.show_data +color = $track.track_file_style_conditional.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 + #if $track.track_file_style_conditional.invert_orientation: +orientation = inverted + #end if +overlay_previous = $track.track_file_style_conditional.overlay_select +file_type = hlines + ## 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 if + #end if + + ## Spacer + #if $track.track_file_style_conditional.track_file_style_selector == "spacer_option": +[spacer] + #if $track.track_file_style_conditional.spacer_height != "": +height = $track.track_file_style_conditional.spacer_height + #end if + #end if #end for -#if $x_axis.x_axis_select == "yes": -#if $x_axis.where == 'bottom': +#if $x_axis.x_axis_select == "true": + #if $x_axis.where == 'bottom': [x-axis] -#if $x_axis.fontsize: + #if $x_axis.fontsize: fontsize = $x_axis.fontsize -#end if -#if $x_axis.where: -where = $x_axis.where -#end if -#end if + #end if +where = bottom + #end if #end if </configfile> </configfiles> @@ -467,13 +491,15 @@ <param name="track_file_style_selector" type="select" label="Choose style of the track"> <option value="hic_matrix_option">TAD visualization</option> <option value="chrom_states_option">Chromatine states</option> - <option value="tad_score_track_option">TAD score</option> + <option value="bedgraph_matrix_track_option">TAD score</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</option> <option value="vlines_track_option">Vlines track</option> + <option value="hlines_track_option">Hlines track</option> <option value="spacer_option">Spacer</option> </param> <when value="hic_matrix_option"> @@ -487,37 +513,27 @@ <option value="log1p" selected="True" >log1p</option> <option value="log">log</option> <option value="-log">-log</option> - <option value="">no transformation</option> + <option value="no">no transformation</option> </param> <param name="height_matrix" type="float" value="" optional="True" label="height"/> - <param name="show_masked_bins" type="boolean" truevalue="yes" falsevalue="no" checked="false" + <param name="show_masked_bins" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Show masked bins" /> - <param name="boundaries_file" type="data" optional="True" format="bed" label="Boundaries file" multiple='True'/> <!-- multiple='True'--> + <param name="boundaries_file" type="data" optional="True" format="bed" label="Boundaries file" multiple="True"/> <param name="scale_factor" type="float" value="1.0" optional="True" label="Scale factor" help="if the values in the matrix need to be scaled the following parameter can be used" /> + <param name="rasterize" type="boolean" truevalue="true" falsevalue="false" checked="true" + label="Rasterize the heatmap" /> <expand macro="inverted_macro" /> <expand macro="spacer_macro" /> </when> - <when value="tad_score_track_option"> - <expand macro="plot_title" /> - <expand macro="track_input_bedgraph_macro" /> - <param name="color" type="color" value="#000000" label="Color of track" optional="True" /> - <param name="type_lines" type="boolean" truevalue="lines" falsevalue="" checked="false" - label="Set 'type' to 'lines'" help="if type is set as lines, then the TAD score lines are drawn instead - of the matrix set to lines if a heatmap representing the matrix is not wanted"/> - <param name="height_tad" type="float" value="0.2" optional="True" label="height"/> - <param name='show_data' type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Show visualization of data range" /> - <expand macro="spacer_macro" /> - - </when> <when value="chrom_states_option"> <expand macro="plot_title" /> - <expand macro="track_input_bed_macro" /> <expand macro="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="on" falsevalue="off" checked="true" + <param name="labels" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Plot labels" /> <expand macro="spacer_macro" /> @@ -528,22 +544,41 @@ <expand macro="track_input_bed_gtf_macro" /> <expand macro="color_bed_macro" /> <param name="height_bed" type="float" value="1.5" optional="True" label="height"/> - <param name="labels" type="boolean" truevalue="on" falsevalue="off" checked="true" + <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"/> <param name="display" type="select" label="display to use"> <option value="stacked" selected="True">stacked (no overlap even with the label)</option> - <option value="interlaced">interlaced (everything on 2 lines)</option> + <option value="interleaved">interleaved (everything on 2 lines)</option> <option value="collapsed">collapsed (everything on 1 line)</option> - <option value="domain">domain (only the first line of stacked)</option> + <option value="triangles">triangles (plot triangles between start and end)</option> </param> - <param name="global_max_row" type="boolean" truevalue="yes" falsevalue="no" checked="false" - label="Global max rows" /> - <param name="gene_rows" type="integer" value="" optional="True" label="Gene rows" /> + <param name="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" /> + <expand macro="overlay_macro" /> + <expand macro="inverted_macro" /> <expand macro="spacer_macro" /> </when> + <when value="link_track_option"> + <expand macro="plot_title" /> + <expand macro="track_input_link_macro" /> + <expand macro="links_color_macro" /> + <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="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" /> + </when> <when value="narrow_peak_track_option"> <expand macro="plot_title" /> <expand macro="track_input_narrow_peak_macro" /> @@ -555,22 +590,24 @@ <option value="box">box: Draw a box</option> </param> <when value="peak"> - <param name='use_summit' type="boolean" truevalue="yes" falsevalue="no" checked="true" + <param name="use_summit" type="boolean" truevalue="true" falsevalue="false" checked="true" optional="True" label="Use summit information to make the curve." /> - <param name='show_data' type="boolean" truevalue="yes" falsevalue="no" checked="false" + <param name="show_data" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Show visualization of data range" /> - <param name='width_adjust' type="float" value="1.5" optional="True" + <param name="width_adjust" type="float" value="1.5" optional="True" label="Factor to change the width of the curve."/> <expand macro="minmax_macro" /> </when> <when value="box"> - <param name='use_summit' type="boolean" truevalue="yes" falsevalue="no" checked="true" + <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="show_labels" type="boolean" truevalue="yes" falsevalue="no" checked="true" + <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" /> + <expand macro="overlay_macro" /> + <expand macro="inverted_macro" /> <expand macro="spacer_macro" /> </when> @@ -581,11 +618,14 @@ <expand macro="minmax_macro" /> <param name="height_bedgraph" type="float" value="1.5" optional="True" label="height"/> <expand macro="type_coverage_macro" /> - <param name='show_data' type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Show visualization of data range" /> + <param name="nans_to_zeros" type="boolean" truevalue="true" falsevalue="false" checked="false" + label="NAN's to zeros" /> + <param name="use_middle" type="boolean" truevalue="true" falsevalue="false" checked="false" + label="Use middle: Instead of using start and end, use the middle of intervals (useful for 4C-seq tracks)." /> + <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" /> - </when> <when value="bigwig_track_option"> <expand macro="plot_title" /> @@ -599,14 +639,13 @@ <expand macro="reading_bw_macro" /> <expand macro="type_coverage_macro" /> <expand macro="type_coverage_macro" /> - <param name="show_data" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Show visualization of data range"/> + <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" /> </when> - <when value="bedgraph_matrix_track_option"> <expand macro="plot_title" /> @@ -617,7 +656,13 @@ <param name="type_lines" type="boolean" truevalue="lines" falsevalue="" checked="false" label="Set 'type' to 'lines'" help="if type is set as lines, then the TAD score lines are drawn instead - of the matrix set to lines if a heatmap representing the matrix is not wanted"/> + 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" /> <expand macro="inverted_macro" /> <expand macro="spacer_macro" /> @@ -625,8 +670,21 @@ <when value="vlines_track_option"> <expand macro="track_input_bed_single_macro" /> </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"/> + <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" /> + </when> <when value="spacer_option"> - <expand macro="spacer_macro" /> + <param name="spacer_height" type="float" value="" optional="True" + label="Height of the spacer."/> </when> </conditional> @@ -635,17 +693,17 @@ <conditional name="x_axis"> <param name="x_axis_select" type="select" label="Configure x-axis"> - <option value="no" selected="True">No</option> - <option value="yes">Yes</option> + <option value="false" selected="True">No</option> + <option value="true">Yes</option> </param> - <when value="yes"> + <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="no" /> + <when value="false" /> </conditional> <param name="image_file_format" type="select" label="Image output format"> <option value="png">png</option> @@ -664,7 +722,7 @@ <test> <param name="region" value="chrX:3000000-3500000"/> <conditional name="x_axis"> - <param name="x_axis_select" value="yes" /> + <param name="x_axis_select" value="true" /> </conditional> <repeat name="tracks"> <conditional name="track_file_style_conditional"> @@ -675,7 +733,6 @@ <param name="depth" value="200000" /> <param name="transform" value="log1p" /> <param name="boundaries_file" value="domains.bed" /> - <param name="x_labels" value="True" /> </conditional> </repeat> <repeat name="tracks"> @@ -690,7 +747,7 @@ <param name="track_input_bed" value="tad_classification.bed" ftype="bed" /> <param name="title" value="TAD state" /> <param name="height_chrom" value="0.5" /> - <param name="labels" value="off" /> + <param name="labels" value="false" /> <conditional name="color_bed"> <param name="color_bed_select" value="bed_rgb" /> </conditional> @@ -698,10 +755,10 @@ </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> - <param name="track_file_style_selector" value="tad_score_track_option" /> - <param name="track_input_bedgraph" value="tad_score.gz" ftype="bedgraph" /> + <param name="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="height_tad" value="10" /> + <param name="height_bedgraph" value="10" /> </conditional> </repeat> <repeat name="tracks"> @@ -800,7 +857,9 @@ <param name="title" value="max num rows 3" /> <param name="height_bed" value="3" /> <param name="fontsize" value="8" /> - <param name="gene_rows" value="3" /> + <section name="bed_advanced"> + <param name="gene_rows" value="3" /> + </section> </conditional> </repeat> <repeat name="tracks"> @@ -816,14 +875,15 @@ <param name="title" value="bed6 global max row" /> <param name="height_bed" value="20" /> <param name="fontsize" value="10" /> - <param name="global_max_row" value="True" /> + <section name="bed_advanced"> + <param name="global_max_row" value="true" /> + </section> </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="vlines_track_option" /> <param name="track_input_bed_single" value="domains.bed" ftype="bed" /> - <param name="type" value="vlines" /> </conditional> </repeat> <param name="image_file_format" value="png" /> @@ -832,7 +892,7 @@ <test> <param name="region" value="chrX:3000000-3500000"/> <conditional name="x_axis"> - <param name="x_axis_select" value="yes" /> + <param name="x_axis_select" value="true" /> </conditional> <repeat name="tracks"> <conditional name="track_file_style_conditional"> @@ -847,13 +907,52 @@ </conditional> </conditional> </repeat> + <repeat name="tracks"> + <conditional name="track_file_style_conditional"> + <param name="track_file_style_selector" value="bigwig_track_option" /> + <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" /> + <param name="title" value="nans_to_zeros" /> + <param name="height_bigwig" value="4" /> + <param name="color" value="blue" /> + <section name="reading_bw_conditional"> + <param name="nans_to_zeros" value="true" /> + </section> + <param name="show_data" value="true" /> + <conditional name="type_conditional"> + <param name="type_selector" value="line_option" /> + <param name="width_line" value="1" /> + </conditional> + </conditional> + </repeat> + <repeat name="tracks"> + <conditional name="track_file_style_conditional"> + <param name="track_file_style_selector" value="hlines_track_option" /> + <param name="title" value="" /> + <param name="color" value="orange" /> + <param name="y_values" value="50" /> + <param name="line_width" value="2" /> + <param name="line_style" value="dashed" /> + <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="hlines_track_option" /> + <param name="title" value="hlines" /> + <param name="color" value="purple" /> + <param name="y_values" value="0, 10, 20, 100" /> + <param name="min_value" value="12" /> + <param name="show_data" value="true" /> + <param name="invert_orientation" value="true" /> + </conditional> + </repeat> <param name="image_file_format" value="png" /> <output name="outFileName" file="bigwig_multiple.png" ftype="png" compare="sim_size" delta="35000" /> </test> <test> <param name="region" value="chrX:3000000-3500000"/> <conditional name="x_axis"> - <param name="x_axis_select" value="yes" /> + <param name="x_axis_select" value="true" /> </conditional> <repeat name="tracks"> <conditional name="track_file_style_conditional"> @@ -872,7 +971,7 @@ <param name="track_input_bed" value="tad_classification.bed" ftype="bed" /> <param name="title" value="TAD state" /> <param name="height_chrom" value="0.5" /> - <param name="labels" value="off" /> + <param name="labels" value="false" /> <conditional name="color_bed"> <param name="color_bed_select" value="bed_rgb" /> </conditional> @@ -885,8 +984,8 @@ <param name="title" value="Kc DpnII (Li et al. 2015) inverted no transform" /> <param name="colormap" value="Reds" /> <param name="depth" value="200000" /> - <param name="transform" value="" /> - <param name="invert_orientation" value="yes" /> + <param name="transform" value="no" /> + <param name="invert_orientation" value="true" /> <param name="min_value" value="5" /> <param name="max_value" value="70" /> </conditional> @@ -905,7 +1004,7 @@ <param name="height_bedgraph" value="4" /> <param name="color" value="black" /> <conditional name="color_negative"> - <param name="color_negative_select" value="yes" /> + <param name="color_negative_select" value="true" /> <param name="color" value="red" /> </conditional> <conditional name="type_conditional"> @@ -1003,7 +1102,9 @@ <param name="title" value="bed6 global max row color from score" /> <param name="height_bed" value="20" /> <param name="fontsize" value="10" /> - <param name="global_max_row" value="True" /> + <section name="bed_advanced"> + <param name="global_max_row" value="true" /> + </section> <conditional name="color_bed"> <param name="color_bed_select" value="colormap" /> <param name="color" value="RdYlBu_r" /> @@ -1014,13 +1115,15 @@ <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 interlaced" /> + <param name="title" value="domains.bed using the 9th field for colors interleaved" /> <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="display" value="interlaced" /> + <param name="border_color" value="red" /> + <param name="labels" value="false" /> + <param name="display" value="interleaved" /> </conditional> </repeat> <param name="image_file_format" value="png" /> @@ -1029,7 +1132,7 @@ <test> <param name="region" value="X:2700000-3100000"/> <conditional name="x_axis"> - <param name="x_axis_select" value="yes" /> + <param name="x_axis_select" value="true" /> <param name="where" value="bottom" /> </conditional> <repeat name="tracks"> @@ -1064,7 +1167,7 @@ <test> <param name="region" value="X:3000000-3300000"/> <conditional name="x_axis"> - <param name="x_axis_select" value="yes" /> + <param name="x_axis_select" value="true" /> </conditional> <repeat name="tracks"> <conditional name="track_file_style_conditional"> @@ -1094,7 +1197,7 @@ <test> <param name="region" value="X:2760000-2802000"/> <conditional name="x_axis"> - <param name="x_axis_select" value="yes" /> + <param name="x_axis_select" value="true" /> <param name="where" value="bottom" /> </conditional> <repeat name="tracks"> @@ -1106,9 +1209,9 @@ <param name="height_narrow_peak" value="4" /> <conditional name="display"> <param name="display_selector" value="box" /> - <param name="use_summit" value="yes" /> + <param name="use_summit" value="true" /> </conditional> - <param name="show_labels" value="yes" /> + <param name="show_labels" value="true" /> </conditional> </repeat> <repeat name="tracks"> @@ -1120,12 +1223,12 @@ <param name="height_narrow_peak" value="4" /> <conditional name="display"> <param name="display_selector" value="peak" /> - <param name="use_summit" value="yes" /> - <param name="show_data" value="yes" /> + <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="no" /> + <param name="show_labels" value="false" /> <param name="spacer_height" value="0.5"/> </conditional> </repeat> @@ -1138,15 +1241,279 @@ <param name="height_narrow_peak" value="4" /> <conditional name="display"> <param name="display_selector" value="peak" /> - <param name="use_summit" value="no" /> - <param name="show_data" value="no" /> + <param name="use_summit" value="false" /> + <param name="show_data" value="false" /> </conditional> - <param name="show_labels" value="yes" /> + <param name="show_labels" value="true" /> </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> + <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="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="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="height_bed" value="10" /> + <section name="bed_advanced"> + <section name ="flybase"> + <param name="height_utr" value="0.75"/> + <param name="color_utr" value="#ff0000"/> + </section> + <section name ="gtf"> + <param name="prefered_name" value="gene_name"/> + <param name="merge_transcripts" value="true"/> + </section> + </section> + </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> + <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="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> + </repeat> + <repeat name="tracks"> + <conditional name="track_file_style_conditional"> + <param name="track_file_style_selector" value="gene_track_option" /> + <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" /> + <param name="title" value="genes.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"> + <param name="arrow_interval" value="10"/> + </section> + </section> + </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> + <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="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> + <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="height_bed" value="10" /> + <conditional name="color_bed"> + <param name="color_bed_select" value="manually" /> + <param name="color" value="red" /> + </conditional> + <param name="flybase" value="false" /> + <param name="spacer_height" value="1"/> + </conditional> + </repeat> + <repeat name="tracks"> + <conditional name="track_file_style_conditional"> + <param name="track_file_style_selector" value="gene_track_option" /> + <param name="track_input_bed" value="dm3_subset_BDGP5.78.gtf.gz" ftype="gtf" /> + <param name="title" value="test" /> + <param name="height_bed" value="10" /> + <conditional name="color_bed"> + <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> + </repeat> + <repeat name="tracks"> + <conditional name="track_file_style_conditional"> + <param name="track_file_style_selector" value="vlines_track_option" /> + <param name="track_input_bed_single" value="dm3_subset_BDGP5.78_asbed4.bed.gz" ftype="bed" /> + </conditional> + </repeat> + <param name="image_file_format" value="png" /> + <output name="outFileName" file="test_arrowhead_zoom.png" ftype="png" compare="sim_size" delta="35000" /> + </test> + <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="gene_track_option" /> + <param name="track_input_bed" value="domains.bed" ftype="bed" /> + <param name="height_bed" value="6" /> + <conditional name="color_bed"> + <param name="color_bed_select" value="manually" /> + <param name="color" value="yellow" /> + </conditional> + <param name="display" value="triangles" /> + <param name="spacer_height" value="1"/> + </conditional> + </repeat> + <repeat name="tracks"> + <conditional name="track_file_style_conditional"> + <param name="track_file_style_selector" value="bedgraph_track_option" /> + <param name="track_input_bedgraph" value="bedgraph_chrx_2e6_5e6.bg" ftype="bedgraph" /> + <param name="title" value="bedgraph" /> + <param name="height_bedgraph" value="4" /> + <param name="color" value="blue" /> + <conditional name="type_conditional"> + <param name="type_selector" value="line_option" /> + </conditional> + </conditional> + </repeat> + <repeat name="tracks"> + <conditional name="track_file_style_conditional"> + <param name="track_file_style_selector" value="bedgraph_track_option" /> + <param name="track_input_bedgraph" value="bedgraph_chrx_2e6_5e6.bg" ftype="bedgraph" /> + <param name="title" value="bedgraph" /> + <param name="height_bedgraph" value="4" /> + <param name="color" value="blue" /> + <param name="use_middle" value="true" /> + <conditional name="type_conditional"> + <param name="type_selector" value="line_option" /> + </conditional> + </conditional> + </repeat> + <param name="image_file_format" value="png" /> + <output name="outFileName" file="test_middle_triangle.png" ftype="png" compare="sim_size" delta="35000" /> + </test> + <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="hic_matrix_option" /> + <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.h5"/> + <param name="title" value="Kc DpnII (Li et al. 2015)" /> + <param name="colormap" value="RdYlBu_r" /> + <param name="depth" value="100000" /> + <param name="transform" value="log1p" /> + <param name="show_masked_bins" value="true" /> + <param name="scale_factor" value="2.0" /> + </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="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="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> + </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="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> + </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> + <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="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="Purples" /> + <param name="depth" value="190000" /> + <param name="transform" value="no" /> + </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="" /> + <param name="line_width" value="10" /> + <param name="links_type" value="loops" /> + <conditional name="color_link"> + <param name="color_link_select" value="manually" /> + <param name="color" value="red" /> + </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="link_track_option" /> + <param name="track_input_link" value="test.arcs" ftype="bed" /> + <param name="title" value="" /> + <param name="height" value="5" /> + <conditional name="color_link"> + <param name="color_link_select" value="colormap" /> + <param name="color" value="hot" /> + </conditional> + <param name="max_value" value="5"/> + <param name="invert_orientation" value="true" /> + </conditional> + </repeat> + <param name="image_file_format" value="png" /> + <output name="outFileName" file="test_link.png" ftype="png" compare="sim_size" delta="35000" /> + </test> </tests> <help><![CDATA[