Mercurial > repos > iuc > pygenometracks
diff pyGenomeTracks.xml @ 15:c7af51147b55 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068
| author | iuc |
|---|---|
| date | Wed, 01 Oct 2025 19:34:28 +0000 |
| parents | d640aa8a24ab |
| children |
line wrap: on
line diff
--- a/pyGenomeTracks.xml Fri May 26 07:54:18 2023 +0000 +++ b/pyGenomeTracks.xml Wed Oct 01 19:34:28 2025 +0000 @@ -4,6 +4,7 @@ <token name="@BINARY@">pyGenomeTracks</token> <import>macros.xml</import> </macros> + <expand macro="xrefs" /> <expand macro="requirements" /> <command detect_errors="exit_code"> <![CDATA[ @@ -218,15 +219,17 @@ ## 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): + #for $counter_bed, $data_bed in enumerate($track.track_file_style_conditional.bed_gtf.track_input_bed): [genes_${counter}_${counter_bed}] - #set ext = $data_bed.extension file = $data_bed - #if $ext == 'gtf': -prefered_name = $track.track_file_style_conditional.bed_style.bed_advanced.gtf.prefered_name - #if $track.track_file_style_conditional.bed_style.bed_advanced.gtf.merge_transcripts.merge_transcripts_select == 'true': + #if $track.track_file_style_conditional.bed_gtf.input_bed_or_gtf == "bed": +file_type = bed + #else: +file_type = gtf +prefered_name = $track.track_file_style_conditional.bed_gtf.prefered_name + #if $track.track_file_style_conditional.bed_gtf.merge_transcripts.merge_transcripts_select == 'true': merge_transcripts = true -merge_overlapping_exons = $track.track_file_style_conditional.bed_style.bed_advanced.gtf.merge_transcripts.merge_overlapping_exons +merge_overlapping_exons = $track.track_file_style_conditional.bed_gtf.merge_transcripts.merge_overlapping_exons #end if #end if #if $track.track_file_style_conditional.title: @@ -247,66 +250,109 @@ #end if #end if #end if - #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 -style = $track.track_file_style_conditional.bed_style.bed_style_select - #if $track.track_file_style_conditional.bed_style.bed_style_select == 'UCSC': -arrow_interval = $track.track_file_style_conditional.bed_style.bed_advanced.arrow_interval - #if $track.track_file_style_conditional.bed_style.bed_advanced.backbone_color_bed.backbone_color_bed_select == 'manually': -color_backbone = $track.track_file_style_conditional.bed_style.bed_advanced.backbone_color_bed.color - #else -color_backbone = $track.track_file_style_conditional.bed_style.bed_advanced.backbone_color_bed.backbone_color_bed_select +display = $track.track_file_style_conditional.display_cond.display + #if $track.track_file_style_conditional.display_cond.display in ['stacked', 'interleaved', 'collapsed']: +style = $track.track_file_style_conditional.display_cond.bed_style.bed_style_select + #if $track.track_file_style_conditional.display_cond.bed_style.bed_style_select in ['UCSC', 'exonarrows', 'flybase']: + #if $track.track_file_style_conditional.display_cond.bed_style.border_color_bed.border_color_bed_select == 'manually': +border_color = $track.track_file_style_conditional.display_cond.bed_style.border_color_bed.color + #else +border_color = $track.track_file_style_conditional.display_cond.bed_style.border_color_bed.border_color_bed_select + #end if #end if - #else: -height_utr = $track.track_file_style_conditional.bed_style.bed_advanced.height_utr - #if $track.track_file_style_conditional.bed_style.bed_advanced.color_utr.color_utr_select == 'manually': -color_utr = $track.track_file_style_conditional.bed_style.bed_advanced.color_utr.color - #elif $track.track_file_style_conditional.bed_style.bed_advanced.color_utr.color_utr_select == 'bed_rgb': -color_utr = bed_rgb + #if $track.track_file_style_conditional.display_cond.bed_style.bed_style_select in ['UCSC', 'exonarrows']: +arrow_interval = $track.track_file_style_conditional.display_cond.bed_style.bed_advanced.arrow_interval + #if $track.track_file_style_conditional.display_cond.bed_style.bed_advanced.color_arrow.color_arrow_select == "manually": +color_arrow = $track.track_file_style_conditional.display_cond.bed_style.bed_advanced.color_arrow.color + #else +color_arrow = $track.track_file_style_conditional.display_cond.bed_style.bed_advanced.color_arrow.color_arrow_select + #end if + #end if + #if $track.track_file_style_conditional.display_cond.bed_style.bed_style_select == 'UCSC': + #if $track.track_file_style_conditional.display_cond.bed_style.bed_advanced.backbone_color_bed.backbone_color_bed_select == 'manually': +color_backbone = $track.track_file_style_conditional.display_cond.bed_style.bed_advanced.backbone_color_bed.color + #else +color_backbone = $track.track_file_style_conditional.display_cond.bed_style.bed_advanced.backbone_color_bed.backbone_color_bed_select + #end if #else: - ## This is 'like' - #if $track.track_file_style_conditional.color_bed.color_bed_select == "bed_rgb": + #if $track.track_file_style_conditional.display_cond.bed_style.bed_advanced.color_utr.color_utr_select == 'manually': +color_utr = $track.track_file_style_conditional.display_cond.bed_style.bed_advanced.color_utr.color + #elif $track.track_file_style_conditional.display_cond.bed_style.bed_advanced.color_utr.color_utr_select == 'bed_rgb': color_utr = bed_rgb #else: + ## This is 'like' + #if $track.track_file_style_conditional.color_bed.color_bed_select == "bed_rgb": +color_utr = bed_rgb + #else: color_utr = $track.track_file_style_conditional.color_bed.color + #end if + #end if + #if $track.track_file_style_conditional.display_cond.bed_style.bed_style_select in ['flybase', 'tssarrow']: +height_utr = $track.track_file_style_conditional.display_cond.bed_style.bed_advanced.height_utr + #end if + #if $track.track_file_style_conditional.display_cond.bed_style.bed_style_select == 'exonarrows': +height_intron = $track.track_file_style_conditional.display_cond.bed_style.bed_advanced.height_intron + #end if + #if $track.track_file_style_conditional.display_cond.bed_style.bed_style_select == 'tssarrow' and $track.track_file_style_conditional.display_cond.bed_style.bed_advanced.arrow_length != '': +arrow_length = $track.track_file_style_conditional.display_cond.bed_style.bed_advanced.arrow_length + #end if + #if $track.track_file_style_conditional.display_cond.bed_style.bed_style_select == 'flybase': +arrowhead_included = $track.track_file_style_conditional.display_cond.bed_style.arrowhead_included +arrowhead_fraction = $track.track_file_style_conditional.display_cond.bed_style.arrowhead_fraction + #if $track.track_file_style_conditional.display_cond.bed_style.bed_advanced.backbone_color_bed.backbone_color_bed_select == 'manually': +color_backbone = $track.track_file_style_conditional.display_cond.bed_style.bed_advanced.backbone_color_bed.color + #else +color_backbone = $track.track_file_style_conditional.display_cond.bed_style.bed_advanced.backbone_color_bed.backbone_color_bed_select + #end if #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 + #if $track.track_file_style_conditional.display_cond.bed_style.bed_style_select in ['UCSC', 'exonarrows', 'tssarrow']: +arrowhead_fraction = $track.track_file_style_conditional.display_cond.bed_style.bed_advanced.arrowhead_fraction + #end if + #if $track.track_file_style_conditional.display_cond.bed_style.bed_advanced.gene_rows: +gene_rows = $track.track_file_style_conditional.display_cond.bed_style.bed_advanced.gene_rows #end if - #if $track.track_file_style_conditional.bed_style.bed_style_select == 'flybase': -arrowhead_included = $track.track_file_style_conditional.bed_style.arrowhead_included -arrowhead_fraction = $track.track_file_style_conditional.bed_style.arrowhead_fraction - #if $track.track_file_style_conditional.bed_style.bed_advanced.backbone_color_bed.backbone_color_bed_select == 'manually': -color_backbone = $track.track_file_style_conditional.bed_style.bed_advanced.backbone_color_bed.color - #else -color_backbone = $track.track_file_style_conditional.bed_style.bed_advanced.backbone_color_bed.backbone_color_bed_select +global_max_row = $track.track_file_style_conditional.display_cond.bed_style.bed_advanced.global_max_row +max_labels = $track.track_file_style_conditional.display_cond.bed_style.bed_advanced.max_labels +line_width = $track.track_file_style_conditional.display_cond.bed_style.bed_advanced.line_width +labels = $track.track_file_style_conditional.display_cond.labels.plot_labels + #if $track.track_file_style_conditional.display_cond.labels.plot_labels == 'true': +all_labels_inside = $track.track_file_style_conditional.display_cond.labels.all_labels_inside +labels_in_margin = $track.track_file_style_conditional.display_cond.labels.labels_in_margin +fontstyle = $track.track_file_style_conditional.display_cond.labels.fontstyle + #if $track.track_file_style_conditional.display_cond.labels.fontsize: +fontsize = $track.track_file_style_conditional.display_cond.labels.fontsize #end if #end if #end if -display = $track.track_file_style_conditional.display + #if $track.track_file_style_conditional.display_cond.display in ['triangle', 'squares']: + #if $track.track_file_style_conditional.display_cond.border_color_bed.border_color_bed_select == 'manually': +border_color = $track.track_file_style_conditional.display_cond.border_color_bed.color + #else +border_color = $track.track_file_style_conditional.display_cond.border_color_bed.border_color_bed_select + #end if + #end if + #if $track.track_file_style_conditional.display_cond.display in ['inversions', 'deletions', 'triangles', 'squares']: +line_width = $track.track_file_style_conditional.display_cond.line_width + #end if + #if $track.track_file_style_conditional.display_cond.display in ['inversions', 'deletions']: +labels = $track.track_file_style_conditional.display_cond.labels.plot_labels + #if $track.track_file_style_conditional.display_cond.labels.plot_labels == 'true': +fontstyle = $track.track_file_style_conditional.display_cond.labels.fontstyle + #if $track.track_file_style_conditional.display_cond.labels.fontsize: +fontsize = $track.track_file_style_conditional.display_cond.labels.fontsize + #end if + #end if + #end if + #if $track.track_file_style_conditional.display_cond.display == 'deletions': +backbone_color = $track.track_file_style_conditional.display_cond.backbone_color + #end if + #if $track.track_file_style_conditional.display_cond.display == 'inversions': +arrowhead_fraction = $track.track_file_style_conditional.display_cond.arrowhead_fraction + #end if #if $track.track_file_style_conditional.height_bed: height = $track.track_file_style_conditional.height_bed #end if -labels = $track.track_file_style_conditional.labels.plot_labels - #if $track.track_file_style_conditional.labels.plot_labels == 'true': -all_labels_inside = $track.track_file_style_conditional.labels.all_labels_inside -labels_in_margin = $track.track_file_style_conditional.labels.labels_in_margin -fontstyle = $track.track_file_style_conditional.labels.fontstyle - #if $track.track_file_style_conditional.labels.fontsize: -fontsize = $track.track_file_style_conditional.labels.fontsize - #end if - #end if -file_type = $ext - #if $track.track_file_style_conditional.bed_style.bed_advanced.gene_rows: -gene_rows = $track.track_file_style_conditional.bed_style.bed_advanced.gene_rows - #end if -global_max_row = $track.track_file_style_conditional.bed_style.bed_advanced.global_max_row -max_labels = $track.track_file_style_conditional.bed_style.bed_advanced.max_labels -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 @@ -769,6 +815,7 @@ species_order_only = $track.track_file_style_conditional.species_order_only #end if display_ref_seq = $track.track_file_style_conditional.display_ref_seq +rasterize = $track.track_file_style_conditional.rasterize file_type = maf ## If spacer is asked a new section is created: #if $track.track_file_style_conditional.spacer_height != "": @@ -920,8 +967,32 @@ </when> <when value="gene_track_option"> <expand macro="plot_title" /> - - <expand macro="track_input_bed_gtf_macro" /> + <conditional name="bed_gtf"> + <param name="input_bed_or_gtf" type="select" label="Use bed or gtf input:"> + <option value="bed" selected="True">bed</option> + <option value="gtf">gtf</option> + </param> + <when value="bed"> + <expand macro="track_input_bed_macro" /> + </when> + <when value="gtf"> + <!-- I call it track_input_bed to make it the same name as the bed input --> + <param name="track_input_bed" type="data" format="gtf" label="Track file(s) gtf format" multiple="True"/> + <param name="prefered_name" type="text" value="transcript_name" label="attribute to use as label" + help="Usually transcript_name or gene_name"/> + <conditional name="merge_transcripts"> + <param name="merge_transcripts_select" type="select" label="Merge all transcripts of each gene in a single entry"> + <option value="false" selected="True">No</option> + <option value="true">Yes</option> + </param> + <when value="true"> + <param name="merge_overlapping_exons" type="boolean" truevalue="true" falsevalue="false" checked="true" + label="Merge overlapping exons" help="Usually it makes prettier plots" /> + </when> + <when value="false" /> + </conditional> + </when> + </conditional> <conditional name="color_bed"> <param name="color_bed_select" type="select" label="Define color:"> <option value="manually" selected="True">manually</option> @@ -941,74 +1012,49 @@ <expand macro="minmax_macro" /> </when> </conditional> - <expand macro="border_color_bed_macro" /> <param name="height_bed" type="float" value="1.5" optional="True" label="height"/> - <conditional name="labels"> - <param name="plot_labels" type="select" label="Plot labels"> - <option value="true" selected="True">yes</option> - <option value="false">no</option> + <conditional name="display_cond"> + <param name="display" type="select" label="display to use"> + <option value="stacked" selected="True">stacked (no overlap even with the label)</option> + <option value="interleaved">interleaved (everything on 2 lines)</option> + <option value="collapsed">collapsed (everything on 1 line)</option> + <option value="triangles">triangles (plot triangles between start and end)</option> + <option value="squares">squares (plot squares on the diagonal)</option> + <option value="deletions">deletions (plot a horizontal line with V for each region of your bed)</option> + <option value="inversions">inversions (plot arrows around each region of your bed)</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."/> - <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" /> - <param name="fontstyle" type="select" label="Fontstyle"> - <option value="normal" selected="True">normal</option> - <option value="italic">italic</option> - <option value="oblique">oblique</option> - </param> + <when value="stacked"> + <expand macro="bed_style_macro" /> + </when> + <when value="interleaved"> + <expand macro="bed_style_macro" /> </when> - <when value="false"/> - </conditional> - <param name="display" type="select" label="display to use"> - <option value="stacked" selected="True">stacked (no overlap even with the label)</option> - <option value="interleaved">interleaved (everything on 2 lines)</option> - <option value="collapsed">collapsed (everything on 1 line)</option> - <option value="triangles">triangles (plot triangles between start and end)</option> - <option value="squares">squares (plot squares on the diagonal)</option> - </param> - <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."/> + <when value="collapsed"> + <expand macro="bed_style_macro" /> + </when> + <when value="triangles"> + <expand macro="border_color_bed_macro" /> + <param name="line_width" type="float" value="0.5" label="width of lines" /> + </when> + <when value="squares"> + <expand macro="border_color_bed_macro" /> + <param name="line_width" type="float" value="0.5" label="width of lines" /> + </when> + <when value="deletions"> + <param name="line_width" type="float" value="0.5" label="width of lines" /> + <param name="backbone_color" type="color" value="#000000" label="Color of the horizontal line"/> + <expand macro="delinv_labels"/> + </when> + <when value="inversions"> <param name="arrowhead_fraction" type="float" value="0.004" min="0" max="1" - label="Size of arrowhead relative to the plotted region" - help="This size is also used to put space between the bed regions and their labels."/> - <section name="bed_advanced" title="Configure other bed parameters" expanded="False"> - <expand macro="utr_macro" /> - <expand macro="bed_advanced_macro" /> - <expand macro="backbone_color_bed_macro" /> - </section> - </when> - <when value="UCSC"> - <section name="bed_advanced" title="Configure other bed parameters" expanded="False"> - <param name="arrow_interval" type="integer" value="2" min="0" label="interval between 2 arrows on introns in UCSC style"/> - <expand macro="bed_advanced_macro" /> - <expand macro="backbone_color_bed_macro" /> - </section> - </when> - <when value="tssarrow"> - <section name="bed_advanced" title="Configure other bed parameters" expanded="False"> - <param name="arrow_length" type="integer" optional="true" label="arrow length" help="the length of the arrow in bp (default is 4% of the plotted region)"/> - <expand macro="utr_macro" /> - <expand macro="bed_advanced_macro" /> - </section> + label="Parameter to control the size of the arrows"/> + <param name="line_width" type="float" value="0.5" label="width of lines" /> + <expand macro="delinv_labels"/> </when> </conditional> <expand macro="overlay_macro" /> <expand macro="inverted_macro" /> <expand macro="spacer_macro" /> - </when> <when value="link_track_option"> <expand macro="plot_title" /> @@ -1313,6 +1359,8 @@ label="Display only the species specified above"/> <param name="display_ref_seq" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Display the sequence of the reference"/> + <param name="rasterize" type="boolean" truevalue="true" falsevalue="false" checked="false" + label="Rasterize the line and blocks of the maf track"/> <expand macro="inverted_macro" /> <expand macro="overlay_macro" /> <expand macro="spacer_macro" /> @@ -1460,11 +1508,16 @@ <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" /> + <conditional name="bed_gtf"> + <param name="input_bed_or_gtf" value="bed"/> + <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" /> + </conditional> <param name="title" value="genes" /> <param name="height_bed" value="5" /> - <conditional name="labels"> - <param name="fontsize" value="10" /> + <conditional name="display_cond"> + <conditional name="labels"> + <param name="fontsize" value="10" /> + </conditional> </conditional> </conditional> </repeat> @@ -1477,16 +1530,21 @@ <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" /> + <conditional name="bed_gtf"> + <param name="input_bed_or_gtf" value="bed"/> + <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" /> + </conditional> <param name="title" value="max num rows 3" /> <param name="height_bed" value="3" /> - <conditional name="labels"> - <param name="fontsize" value="8" /> - </conditional> - <conditional name="bed_style"> - <section name="bed_advanced"> - <param name="gene_rows" value="3" /> - </section> + <conditional name="display_cond"> + <conditional name="labels"> + <param name="fontsize" value="8" /> + </conditional> + <conditional name="bed_style"> + <section name="bed_advanced"> + <param name="gene_rows" value="3" /> + </section> + </conditional> </conditional> </conditional> </repeat> @@ -1499,16 +1557,21 @@ <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="gene_track_option" /> - <param name="track_input_bed" value="dm3_genes.bed6.gz" ftype="bed" /> + <conditional name="bed_gtf"> + <param name="input_bed_or_gtf" value="bed"/> + <param name="track_input_bed" value="dm3_genes.bed6.gz" ftype="bed" /> + </conditional> <param name="title" value="bed6 global max row" /> <param name="height_bed" value="20" /> - <conditional name="labels"> - <param name="fontsize" value="10" /> - </conditional> - <conditional name="bed_style"> - <section name="bed_advanced"> - <param name="global_max_row" value="true" /> - </section> + <conditional name="display_cond"> + <conditional name="labels"> + <param name="fontsize" value="10" /> + </conditional> + <conditional name="bed_style"> + <section name="bed_advanced"> + <param name="global_max_row" value="true" /> + </section> + </conditional> </conditional> </conditional> </repeat> @@ -1519,7 +1582,7 @@ </conditional> </repeat> <param name="image_file_format" value="png" /> - <output name="outFileName" file="master_TADs_plot.png" ftype="png" compare="sim_size" delta="100" /> + <output name="outFileName" file="master_TADs_plot.png" ftype="png" compare="image_diff" /> </test> <!--test 2--> <test> @@ -1595,7 +1658,7 @@ </conditional> </repeat> <param name="image_file_format" value="png" /> - <output name="outFileName" file="bigwig_multiple.png" ftype="png" compare="sim_size" delta="100" /> + <output name="outFileName" file="bigwig_multiple.png" ftype="png" compare="image_diff" /> </test> <!--test 3--> <test> @@ -1740,30 +1803,40 @@ <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" /> + <conditional name="bed_gtf"> + <param name="input_bed_or_gtf" value="bed"/> + <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" /> + </conditional> <param name="title" value="genes in ucsc" /> <param name="height_bed" value="5" /> - <conditional name="labels"> - <param name="fontsize" value="10" /> - </conditional> - <conditional name="bed_style"> - <param name="bed_style_select" value="UCSC"/> + <conditional name="display_cond"> + <conditional name="labels"> + <param name="fontsize" value="10" /> + </conditional> + <conditional name="bed_style"> + <param name="bed_style_select" value="UCSC"/> + </conditional> </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.bed6.gz" ftype="bed" /> + <conditional name="bed_gtf"> + <param name="input_bed_or_gtf" value="bed"/> + <param name="track_input_bed" value="dm3_genes.bed6.gz" ftype="bed" /> + </conditional> <param name="title" value="bed6 global max row color from score" /> <param name="height_bed" value="20" /> - <conditional name="labels"> - <param name="fontsize" value="10" /> - </conditional> - <conditional name="bed_style"> - <section name="bed_advanced"> - <param name="global_max_row" value="true" /> - </section> + <conditional name="display_cond"> + <conditional name="labels"> + <param name="fontsize" value="10" /> + </conditional> + <conditional name="bed_style"> + <section name="bed_advanced"> + <param name="global_max_row" value="true" /> + </section> + </conditional> </conditional> <conditional name="color_bed"> <param name="color_bed_select" value="colormap" /> @@ -1776,60 +1849,81 @@ <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" /> + <conditional name="bed_gtf"> + <param name="input_bed_or_gtf" value="bed"/> + <param name="track_input_bed" value="domains.bed" ftype="bed" /> + </conditional> <param name="title" value="domains.bed using the 9th field for colors interleaved border=red" /> <param name="height_bed" value="2" /> <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 name="display_cond"> + <conditional name="bed_style"> + <conditional name="border_color_bed"> + <param name="border_color_bed_select" value="manually" /> + <param name="color" value="red" /> + </conditional> + </conditional> + <conditional name="labels"> + <param name="plot_labels" value="false" /> + </conditional> + <param name="display" value="interleaved" /> </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" /> + <conditional name="bed_gtf"> + <param name="input_bed_or_gtf" value="bed"/> + <param name="track_input_bed" value="domains.bed" ftype="bed" /> + </conditional> <param name="title" value="domains.bed using the 9th field for colors interleaved border=bed_rgb" /> <param name="height_bed" value="2" /> <conditional name="color_bed"> <param name="color_bed_select" value="bed_rgb" /> </conditional> - <conditional name="border_color_bed"> - <param name="border_color_bed_select" value="bed_rgb" /> + <conditional name="display_cond"> + <conditional name="bed_style"> + <conditional name="border_color_bed"> + <param name="border_color_bed_select" value="bed_rgb" /> + </conditional> + </conditional> + <conditional name="labels"> + <param name="plot_labels" value="false" /> + </conditional> + <param name="display" value="interleaved" /> </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" /> + <conditional name="bed_gtf"> + <param name="input_bed_or_gtf" value="bed"/> + <param name="track_input_bed" value="domains.bed" ftype="bed" /> + </conditional> <param name="title" value="domains.bed using the 9th field for colors interleaved border=none" /> <param name="height_bed" value="2" /> <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 name="display_cond"> + <conditional name="bed_style"> + <conditional name="border_color_bed"> + <param name="border_color_bed_select" value="none" /> + </conditional> + </conditional> + <conditional name="labels"> + <param name="plot_labels" value="false" /> + </conditional> + <param name="display" value="interleaved" /> </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="100" /> + <output name="outFileName" file="master_TADs_BW_plot.png" ftype="png" compare="image_diff" /> </test> <!--test 4--> <test> @@ -1838,7 +1932,7 @@ <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="(bigwig color=blue 2000 bins) overlayed with (bigwig mean color=red alpha = 0.5 max over 300 bins)" /> + <param name="title" value="(bigwig color=blue 2000 bins) overlayed with (bigwig color=red alpha = 0.5 max over 300 bins)" /> <param name="height_bigwig" value="7" /> <param name="color" value="#00b0f0" /> <section name="reading_bw_conditional"> @@ -1853,8 +1947,8 @@ <param name="title" value="" /> <param name="color" value="#ff0000" /> <param name="alpha" value="0.5" /> - <param name="summary_method" value="max" /> <section name="reading_bw_conditional"> + <param name="summary_method" value="max" /> <param name="number_of_bins" value="300"/> </section> <param name="overlay_select" value="share-y"/> @@ -1867,7 +1961,7 @@ </conditional> </repeat> <param name="image_file_format" value="png" /> - <output name="outFileName" file="test_alpha.png" ftype="png" compare="sim_size" delta="100" /> + <output name="outFileName" file="test_alpha.png" ftype="png" compare="image_diff" /> </test> <!--test 5--> <test> @@ -1881,12 +1975,19 @@ <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" /> + <conditional name="bed_gtf"> + <param name="input_bed_or_gtf" value="gtf"/> + <param name="track_input_bed" value="dm3_subset_BDGP5.78.gtf.gz" ftype="gtf" /> + </conditional> <param name="title" value="test" /> <param name="height_bed" value="10" /> - <param name="color" value="#000000" /> - <conditional name="bed_style"> - <param name="bed_style_select" value="UCSC"/> + <conditional name="color_bed"> + <param name="color" value="#000000" /> + </conditional> + <conditional name="display_cond"> + <conditional name="bed_style"> + <param name="bed_style_select" value="UCSC"/> + </conditional> </conditional> <param name="spacer_height" value="1"/> </conditional> @@ -1894,18 +1995,25 @@ <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" /> + <conditional name="bed_gtf"> + <param name="input_bed_or_gtf" value="bed"/> + <param name="track_input_bed" value="dm3_subset_BDGP5.78_asbed4.bed.gz" ftype="bed" /> + </conditional> <param name="title" value="test" /> <param name="height_bed" value="10" /> - <param name="color" value="#000000" /> - <conditional name="bed_style"> - <param name="bed_style_select" value="UCSC"/> + <conditional name="color_bed"> + <param name="color" value="#000000" /> + </conditional> + <conditional name="display_cond"> + <conditional name="bed_style"> + <param name="bed_style_select" value="UCSC"/> + </conditional> </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="100" /> + <output name="outFileName" file="test_gtf_bed4.png" ftype="png" compare="image_diff" /> </test> <!--test 6--> <test> @@ -1978,7 +2086,7 @@ </conditional> </repeat> <param name="image_file_format" value="png" /> - <output name="outFileName" file="test_narrowPeak.png" ftype="png" compare="sim_size" delta="100" /> + <output name="outFileName" file="test_narrowPeak.png" ftype="png" compare="image_diff" /> </test> <!--test 7--> <test> @@ -1992,7 +2100,10 @@ <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" /> + <conditional name="bed_gtf"> + <param name="input_bed_or_gtf" value="gtf"/> + <param name="track_input_bed" value="dm3_subset_BDGP5.78.gtf.gz" ftype="gtf" /> + </conditional> <param name="title" value="gtf default" /> <param name="height_bed" value="10" /> </conditional> @@ -2000,55 +2111,64 @@ <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" /> + <conditional name="bed_gtf"> + <param name="input_bed_or_gtf" value="gtf"/> + <param name="track_input_bed" value="dm3_subset_BDGP5.78.gtf.gz" ftype="gtf" /> + <param name="prefered_name" value="gene_name"/> + <conditional name="merge_transcripts"> + <param name="merge_transcripts_select" value="true"/> + <param name="merge_overlapping_exons" value="false"/> + </conditional> + </conditional> <param name="title" value="gtf merge transcripts, use gene_name, red 0.75 UTR" /> <param name="height_bed" value="10" /> - <conditional name="bed_style"> - <section name="bed_advanced"> - <param name="height_utr" value="0.75"/> - <conditional name="color_utr"> - <param name="color_utr_select" value="manually"/> - <param name="color" value="#ff0000"/> - </conditional> - <section name ="gtf"> - <param name="prefered_name" value="gene_name"/> - <conditional name="merge_transcripts"> - <param name="merge_transcripts_select" value="true"/> - <param name="merge_overlapping_exons" value="false"/> + <conditional name="display_cond"> + <conditional name="bed_style"> + <section name="bed_advanced"> + <param name="height_utr" value="0.75"/> + <conditional name="color_utr"> + <param name="color_utr_select" value="manually"/> + <param name="color" value="#ff0000"/> </conditional> </section> - </section> + </conditional> </conditional> </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="gene_track_option" /> - <param name="track_input_bed" value="dm3_subset_BDGP5.78.gtf.gz" ftype="gtf" /> + <conditional name="bed_gtf"> + <param name="input_bed_or_gtf" value="gtf"/> + <param name="track_input_bed" value="dm3_subset_BDGP5.78.gtf.gz" ftype="gtf" /> + <param name="prefered_name" value="gene_name"/> + <conditional name="merge_transcripts"> + <param name="merge_transcripts_select" value="true"/> + <param name="merge_overlapping_exons" value="true"/> + </conditional> + </conditional> <param name="title" value="same but merge overlapping exons" /> <param name="height_bed" value="10" /> - <conditional name="bed_style"> - <section name="bed_advanced"> - <param name="height_utr" value="0.75"/> - <conditional name="color_utr"> - <param name="color_utr_select" value="manually"/> - <param name="color" value="#ff0000"/> - </conditional> - <section name ="gtf"> - <param name="prefered_name" value="gene_name"/> - <conditional name="merge_transcripts"> - <param name="merge_transcripts_select" value="true"/> - <param name="merge_overlapping_exons" value="true"/> + <conditional name="display_cond"> + <conditional name="bed_style"> + <section name="bed_advanced"> + <param name="height_utr" value="0.75"/> + <conditional name="color_utr"> + <param name="color_utr_select" value="manually"/> + <param name="color" value="#ff0000"/> </conditional> </section> - </section> - </conditional> + </conditional> + </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" /> + <conditional name="bed_gtf"> + <param name="input_bed_or_gtf" value="bed"/> + <param name="track_input_bed" value="dm3_genes_withrgbandscore.bed.gz" ftype="bed" /> + </conditional> <param name="title" value="genes with scores" /> <param name="height_bed" value="10" /> <conditional name="color_bed"> @@ -2060,57 +2180,72 @@ <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" /> + <conditional name="bed_gtf"> + <param name="input_bed_or_gtf" value="bed"/> + <param name="track_input_bed" value="dm3_genes_withrgbandscore.bed.gz" ftype="bed" /> + </conditional> <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> + <conditional name="display_cond"> + <conditional name="bed_style"> + <section name="bed_advanced"> + <conditional name="color_utr"> + <param name="color_utr_select" value="bed_rgb"/> + </conditional> + </section> + </conditional> </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" /> + <conditional name="bed_gtf"> + <param name="input_bed_or_gtf" value="bed"/> + <param name="track_input_bed" value="dm3_genes_withrgbandscore.bed.gz" ftype="bed" /> + </conditional> <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 name="display_cond"> + <conditional name="labels"> + <param name="plot_labels" value="true" /> + <param name="labels_in_margin" value="true" /> + </conditional> </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" /> + <conditional name="bed_gtf"> + <param name="input_bed_or_gtf" value="bed"/> + <param name="track_input_bed" value="dm3_genes_withrgbandscore.bed.gz" ftype="bed" /> + </conditional> <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> - </conditional> - <conditional name="labels"> - <param name="plot_labels" value="true" /> - <param name="all_labels_inside" value="true" /> + <conditional name="display_cond"> + <conditional name="bed_style"> + <section name="bed_advanced"> + <conditional name="color_utr"> + <param name="color_utr_select" value="like"/> + </conditional> + </section> + </conditional> + <conditional name="labels"> + <param name="plot_labels" value="true" /> + <param name="all_labels_inside" value="true" /> + </conditional> </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="100" /> + <output name="outFileName" file="test_gtf_flybase_param.png" ftype="png" compare="image_diff" /> </test> <!--test 8--> <test> @@ -2124,35 +2259,72 @@ <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" /> + <conditional name="bed_gtf"> + <param name="input_bed_or_gtf" value="bed"/> + <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" /> + </conditional> + <param name="title" value="global max row max 15 labels" /> <param name="height_bed" value="10" /> - <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 name="display_cond"> + <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> </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" /> + <conditional name="bed_gtf"> + <param name="input_bed_or_gtf" value="bed"/> + <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" /> + </conditional> + <param name="title" value="arrow_interval 10 line_width 2 change color_arrow" /> <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"/> - <param name="line_width" value="2"/> - </section> + <conditional name="display_cond"> + <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"/> + <conditional name="color_arrow"> + <param name="color" value="#00ffff"/> + </conditional> + </section> + </conditional> + </conditional> + </conditional> + </repeat> + <repeat name="tracks"> + <conditional name="track_file_style_conditional"> + <param name="track_file_style_selector" value="gene_track_option" /> + <conditional name="bed_gtf"> + <param name="input_bed_or_gtf" value="bed"/> + <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" /> + </conditional> + <param name="title" value="same as above but arrowhead_fraction = 0.02" /> + <param name="height_bed" value="10" /> + <conditional name="display_cond"> + <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"/> + <conditional name="color_arrow"> + <param name="color" value="#00ffff"/> + </conditional> + <param name="arrowhead_fraction" value="0.02"/> + </section> + </conditional> </conditional> </conditional> </repeat> <param name="image_file_format" value="png" /> - <output name="outFileName" file="test_ucsc_param.png" ftype="png" compare="sim_size" delta="100" /> + <output name="outFileName" file="test_ucsc_param.png" ftype="png" compare="image_diff" /> </test> <!--test 9--> <test> @@ -2166,42 +2338,57 @@ <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" /> + <conditional name="bed_gtf"> + <param name="input_bed_or_gtf" value="gtf"/> + <param name="track_input_bed" value="dm3_subset_BDGP5.78.gtf.gz" ftype="gtf" /> + </conditional> <param name="title" value="defaut arrowhead fontstyle italic" /> <param name="height_bed" value="10" /> <param name="spacer_height" value="1"/> - <conditional name="labels"> - <param name="fontstyle" value="italic"/> + <conditional name="display_cond"> + <conditional name="labels"> + <param name="fontstyle" value="italic"/> + </conditional> </conditional> </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="gene_track_option" /> - <param name="track_input_bed" value="dm3_subset_BDGP5.78.gtf.gz" ftype="gtf" /> + <conditional name="bed_gtf"> + <param name="input_bed_or_gtf" value="gtf"/> + <param name="track_input_bed" value="dm3_subset_BDGP5.78.gtf.gz" ftype="gtf" /> + </conditional> <param name="title" value="arrowhead_fraction 0.1 fontstyle oblique" /> <param name="height_bed" value="10" /> <param name="spacer_height" value="1"/> - <conditional name="labels"> - <param name="fontstyle" value="oblique"/> - </conditional> - <conditional name="bed_style"> - <param name="arrowhead_fraction" value="0.1"/> + <conditional name="display_cond"> + <conditional name="labels"> + <param name="fontstyle" value="oblique"/> + </conditional> + <conditional name="bed_style"> + <param name="arrowhead_fraction" value="0.1"/> + </conditional> </conditional> </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="gene_track_option" /> - <param name="track_input_bed" value="dm3_subset_BDGP5.78_asbed4.bed.gz" ftype="bed" /> + <conditional name="bed_gtf"> + <param name="input_bed_or_gtf" value="bed"/> + <param name="track_input_bed" value="dm3_subset_BDGP5.78_asbed4.bed.gz" ftype="bed" /> + </conditional> <param name="title" value="genes without orientation" /> <param name="height_bed" value="10" /> <conditional name="color_bed"> <param name="color_bed_select" value="manually" /> <param name="color" value="red" /> </conditional> - <conditional name="bed_style"> - <param name="bed_style_select" value="UCSC"/> + <conditional name="display_cond"> + <conditional name="bed_style"> + <param name="bed_style_select" value="UCSC"/> + </conditional> </conditional> <param name="spacer_height" value="1"/> </conditional> @@ -2209,7 +2396,10 @@ <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" /> + <conditional name="bed_gtf"> + <param name="input_bed_or_gtf" value="gtf"/> + <param name="track_input_bed" value="dm3_subset_BDGP5.78.gtf.gz" ftype="gtf" /> + </conditional> <param name="title" value="arrowhead included" /> <param name="height_bed" value="10" /> <conditional name="color_bed"> @@ -2217,8 +2407,10 @@ <param name="color" value="red" /> </conditional> <param name="spacer_height" value="1"/> - <conditional name="bed_style"> - <param name="arrowhead_included" value="true"/> + <conditional name="display_cond"> + <conditional name="bed_style"> + <param name="arrowhead_included" value="true"/> + </conditional> </conditional> </conditional> </repeat> @@ -2242,7 +2434,7 @@ </conditional> </repeat> <param name="image_file_format" value="png" /> - <output name="outFileName" file="test_arrowhead_zoom.png" ftype="png" compare="sim_size" delta="100" /> + <output name="outFileName" file="test_arrowhead_zoom.png" ftype="png" compare="image_diff" /> </test> <!--test 10--> <test> @@ -2256,13 +2448,19 @@ <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" /> + <conditional name="bed_gtf"> + <param name="input_bed_or_gtf" value="bed"/> + <param name="track_input_bed" value="domains.bed" ftype="bed" /> + </conditional> <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" /> + <conditional name="display_cond"> + <param name="display" value="triangles" /> + <param name="line_width" value="3"/> + </conditional> <param name="spacer_height" value="1"/> </conditional> </repeat> @@ -2292,7 +2490,7 @@ </conditional> </repeat> <param name="image_file_format" value="png" /> - <output name="outFileName" file="test_middle_triangle.png" ftype="png" compare="sim_size" delta="100" /> + <output name="outFileName" file="test_middle_triangle.png" ftype="png" compare="image_diff" /> </test> <!--test 11--> <test> @@ -2351,7 +2549,7 @@ </conditional> </repeat> <param name="image_file_format" value="png" /> - <output name="outFileName" file="test_TADs_bdgm.png" ftype="png" compare="sim_size" delta="100" /> + <output name="outFileName" file="test_TADs_bdgm.png" ftype="png" compare="image_diff" /> </test> <!--test 12--> <test> @@ -2403,7 +2601,7 @@ </conditional> </repeat> <param name="image_file_format" value="png" /> - <output name="outFileName" file="test_link.png" ftype="png" compare="sim_size" delta="100" /> + <output name="outFileName" file="test_link.png" ftype="png" compare="image_diff" /> </test> <!--test 13--> <test> @@ -2462,7 +2660,7 @@ </conditional> </repeat> <param name="image_file_format" value="png" /> - <output name="outFileName" file="test_link2.png" ftype="png" compare="sim_size" delta="100" /> + <output name="outFileName" file="test_link2.png" ftype="png" compare="image_diff" /> </test> <!--test 14--> <test> @@ -2502,7 +2700,7 @@ </conditional> </repeat> <param name="image_file_format" value="png" /> - <output name="outFileName" file="test_scale_bar.png" ftype="png" compare="sim_size" delta="100" /> + <output name="outFileName" file="test_scale_bar.png" ftype="png" compare="image_diff" /> </test> <!--test 15--> <test> @@ -2516,69 +2714,124 @@ <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" /> + <conditional name="bed_gtf"> + <param name="input_bed_or_gtf" value="bed"/> + <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" /> + </conditional> <param name="title" value="flybase backbone blue" /> <param name="height_bed" value="10" /> - <conditional name="bed_style"> - <param name="bed_style_select" value="flybase"/> - <section name="bed_advanced"> - <conditional name="backbone_color_bed"> - <param name="backbone_color_bed_select" value="manually" /> + <conditional name="display_cond"> + <conditional name="bed_style"> + <param name="bed_style_select" value="flybase"/> + <section name="bed_advanced"> + <conditional name="backbone_color_bed"> + <param name="backbone_color_bed_select" value="manually" /> + <param name="color" value="blue" /> + </conditional> + </section> + </conditional> + </conditional> + </conditional> + </repeat> + <repeat name="tracks"> + <conditional name="track_file_style_conditional"> + <param name="track_file_style_selector" value="gene_track_option" /> + <conditional name="bed_gtf"> + <param name="input_bed_or_gtf" value="bed"/> + <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" /> + </conditional> + <param name="title" value="UCSC backbone blue" /> + <param name="height_bed" value="10" /> + <conditional name="display_cond"> + <conditional name="bed_style"> + <param name="bed_style_select" value="UCSC"/> + <section name="bed_advanced"> + <param name="arrow_interval" value="10"/> + <conditional name="backbone_color_bed"> + <param name="backbone_color_bed_select" value="manually" /> <param name="color" value="blue" /> - </conditional> - </section> + </conditional> + </section> + </conditional> </conditional> </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="gene_track_option" /> - <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" /> - <param name="title" value="UCSC backbone blue" /> + <conditional name="bed_gtf"> + <param name="input_bed_or_gtf" value="bed"/> + <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" /> + </conditional> + <param name="title" value="tssarrow" /> <param name="height_bed" value="10" /> - <conditional name="bed_style"> - <param name="bed_style_select" value="UCSC"/> - <section name="bed_advanced"> - <param name="arrow_interval" value="10"/> - <conditional name="backbone_color_bed"> - <param name="backbone_color_bed_select" value="manually" /> - <param name="color" value="blue" /> - </conditional> - </section> + <conditional name="display_cond"> + <conditional name="bed_style"> + <param name="bed_style_select" value="tssarrow"/> + </conditional> + </conditional> + </conditional> + </repeat> + <repeat name="tracks"> + <conditional name="track_file_style_conditional"> + <param name="track_file_style_selector" value="gene_track_option" /> + <conditional name="bed_gtf"> + <param name="input_bed_or_gtf" value="bed"/> + <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" /> + </conditional> + <param name="title" value="tssarrow 20kb increase arrowhead" /> + <param name="height_bed" value="10" /> + <conditional name="display_cond"> + <conditional name="bed_style"> + <param name="bed_style_select" value="tssarrow"/> + <section name="bed_advanced"> + <param name="arrow_length" value="20000"/> + <param name="arrowhead_fraction" value="0.01"/> + </section> + </conditional> </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 name="bed_gtf"> + <param name="input_bed_or_gtf" value="bed"/> + <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" /> + </conditional> + <param name="title" value="exonarrows" /> + <conditional name="color_bed"> + <param name="color_bed_select" value="manually" /> + <param name="color" value="red"/> </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 name="display_cond"> + <conditional name="bed_style"> + <param name="bed_style_select" value="exonarrows"/> + <conditional name="border_color_bed"> + <param name="border_color_bed_select" value="manually"/> + <param name="color" value="red"/> + </conditional> + <section name="bed_advanced"> + <param name="line_width" value="2" /> + <conditional name="color_utr"> + <param name="color_utr_select" value="manually"/> + <param name="color" value="blue"/> + </conditional> + <conditional name="color_arrow"> + <param name="color" value="white"/> + </conditional> + </section> + </conditional> </conditional> </conditional> </repeat> <param name="image_file_format" value="png" /> - <output name="outFileName" file="test_tssarrow.png" ftype="png" compare="sim_size" delta="100" /> + <output name="outFileName" file="test_tssarrow.png" ftype="png" compare="image_diff" /> </test> <!--test 16--> <test> - <param name="region" value="X:2700000-3100000"/> + <param name="region" value="chrX:2700000-3100000"/> <section name="global_args"> <param name="decreasingXAxis" value="true"/> </section> @@ -2586,7 +2839,7 @@ <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="(bigwig color=blue 2000 bins) overlayed with (bigwig mean color=red alpha = 0.5 max over 300 bins)" /> + <param name="title" value="(bigwig color=blue 2000 bins) overlayed with (bigwig color=red alpha = 0.5 max over 300 bins)" /> <param name="height_bigwig" value="7" /> <param name="color" value="#00b0f0" /> <section name="reading_bw_conditional"> @@ -2601,8 +2854,8 @@ <param name="title" value="" /> <param name="color" value="#ff0000" /> <param name="alpha" value="0.5" /> - <param name="summary_method" value="max" /> <section name="reading_bw_conditional"> + <param name="summary_method" value="max" /> <param name="number_of_bins" value="300"/> </section> <param name="overlay_select" value="share-y"/> @@ -2615,7 +2868,7 @@ </conditional> </repeat> <param name="image_file_format" value="png" /> - <output name="outFileName" file="test_alpha_dec.png" ftype="png" compare="sim_size" delta="1000" /> + <output name="outFileName" file="test_alpha_dec.png" ftype="png" compare="image_diff" /> </test> <!--test 17--> <test> @@ -2738,7 +2991,7 @@ </conditional> </repeat> <param name="image_file_format" value="png" /> - <output name="outFileName" file="test_log.png" ftype="png" compare="sim_size" delta="100" /> + <output name="outFileName" file="test_log.png" ftype="png" compare="image_diff" /> </test> <!--test 18--> <test> @@ -2816,7 +3069,7 @@ </conditional> </repeat> <param name="image_file_format" value="png" /> - <output name="outFileName" file="test_operation.png" ftype="png" compare="sim_size" delta="100" /> + <output name="outFileName" file="test_operation.png" ftype="png" compare="image_diff" /> </test> <!--test 19--> <test> @@ -2947,7 +3200,7 @@ </conditional> </repeat> <param name="image_file_format" value="png" /> - <output name="outFileName" file="test_log_grid.png" ftype="png" compare="sim_size" delta="100" /> + <output name="outFileName" file="test_log_grid.png" ftype="png" compare="image_diff" /> </test> <!--test 20--> <test> @@ -2968,7 +3221,7 @@ <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="depth = 300000; transform = log1p; min_value = 5 (next track: overlay_previous = share-y links_type = loops)" /> + <param name="title" value="depth = 300000 transform = log1p min_value = 5 (next track: overlay_previous = share-y links_type = loops)" /> <param name="depth" value="300000" /> <param name="transform" value="log1p" /> <param name="min_value" value="5" /> @@ -3012,7 +3265,7 @@ <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="depth = 300000; transform = log1p; min_value = 5 (next track: overlay_previous = share-y links_type = loops)" /> + <param name="title" value="depth = 300000 transform = log1p min_value = 5 (next track: overlay_previous = share-y links_type = loops)" /> <param name="depth" value="300000" /> <param name="transform" value="log1p" /> <param name="min_value" value="5" /> @@ -3057,7 +3310,7 @@ </conditional> </repeat> <param name="image_file_format" value="png" /> - <output name="outFileName" file="test_arcs_use_middle.png" ftype="png" compare="sim_size" delta="1200" /> + <output name="outFileName" file="test_arcs_use_middle.png" ftype="png" compare="image_diff" /> </test> <!--test 21--> <test> @@ -3135,7 +3388,7 @@ </conditional> </repeat> <param name="image_file_format" value="png" /> - <output name="outFileName" file="master_scale_bar_startend.png" ftype="png" compare="sim_size" delta="100" /> + <output name="outFileName" file="master_scale_bar_startend.png" ftype="png" compare="image_diff" /> </test> <!--test 22--> <test> @@ -3172,7 +3425,7 @@ </conditional> </repeat> <param name="image_file_format" value="png" /> - <output name="outFileName" file="master_fasta.png" ftype="png" compare="sim_size" delta="100" /> + <output name="outFileName" file="master_fasta.png" ftype="png" compare="image_diff" /> </test> <!--test 23--> <test> @@ -3266,7 +3519,7 @@ </conditional> </repeat> <param name="image_file_format" value="png" /> - <output name="outFileName" file="test_matrix_square.png" ftype="png" compare="sim_size" delta="1200" /> + <output name="outFileName" file="test_matrix_square.png" ftype="png" compare="image_diff" /> </test> <!--test 24--> <test> @@ -3313,7 +3566,6 @@ <param name="species_order" value="hg19"/> <param name="species_labels" value="Human"/> <param name="species_order_only" value="true"/> - <param name="spacer_height" value="1"/> </conditional> </repeat> <repeat name="tracks"> @@ -3323,7 +3575,7 @@ </conditional> </repeat> <param name="image_file_format" value="png" /> - <output name="outFileName" file="test_maf.png" ftype="png" compare="sim_size" delta="1200" /> + <output name="outFileName" file="test_maf.png" ftype="png" compare="image_diff" /> </test> <!--test 25--> <test> @@ -3352,7 +3604,117 @@ </conditional> </repeat> <param name="image_file_format" value="png" /> - <output name="outFileName" file="test_vhighlight.png" ftype="png" compare="sim_size" delta="1200" /> + <output name="outFileName" file="test_vhighlight.png" ftype="png" compare="image_diff" /> + </test> + <!--test 26--> + <test> + <param name="region" value="chrX:3060000-3080000"/> + <repeat name="tracks"> + <conditional name="track_file_style_conditional"> + <param name="track_file_style_selector" value="gene_track_option" /> + <conditional name="bed_gtf"> + <param name="input_bed_or_gtf" value="bed"/> + <param name="track_input_bed" value="dm3_genes_withrgbandscore.bed.gz" ftype="bed" /> + </conditional> + <param name="title" value="default inversions overlayed with empty deletion" /> + <param name="height_bed" value="2" /> + <conditional name="display_cond"> + <param name="display" value = "inversions"/> + </conditional> + </conditional> + </repeat> + <repeat name="tracks"> + <conditional name="track_file_style_conditional"> + <param name="track_file_style_selector" value="gene_track_option" /> + <conditional name="bed_gtf"> + <param name="input_bed_or_gtf" value="bed"/> + <param name="track_input_bed" value="empty.bed" ftype="bed" /> + </conditional> + <param name="title" value="" /> + <conditional name="display_cond"> + <param name="display" value = "deletions"/> + </conditional> + <param name="overlay_select" value="share-y" /> + <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" /> + <conditional name="bed_gtf"> + <param name="input_bed_or_gtf" value="bed"/> + <param name="track_input_bed" value="dm3_genes_withrgbandscore.bed.gz" ftype="bed" /> + </conditional> + <param name="title" value="inversions rgb no labels" /> + <param name="height_bed" value="2" /> + <conditional name="color_bed"> + <param name="color_bed_select" value="bed_rgb" /> + </conditional> + <conditional name="display_cond"> + <param name="display" value = "inversions"/> + <conditional name="labels"> + <param name="plot_labels" value = "false"/> + </conditional> + </conditional> + </conditional> + </repeat> + <repeat name="tracks"> + <conditional name="track_file_style_conditional"> + <param name="track_file_style_selector" value="gene_track_option" /> + <conditional name="bed_gtf"> + <param name="input_bed_or_gtf" value="bed"/> + <param name="track_input_bed" value="dm3_genes_withrgbandscore.bed.gz" ftype="bed" /> + </conditional> + <param name="title" value="deletions colormap no labels" /> + <param name="height_bed" value="2" /> + <conditional name="color_bed"> + <param name="color_bed_select" value="colormap" /> + <param name="color" value="viridis"/> + </conditional> + <conditional name="display_cond"> + <param name="display" value = "deletions"/> + <conditional name="labels"> + <param name="plot_labels" value = "false"/> + </conditional> + </conditional> + <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" /> + <conditional name="bed_gtf"> + <param name="input_bed_or_gtf" value="bed"/> + <param name="track_input_bed" value="dm3_genes_withrgbandscore.bed.gz" ftype="bed" /> + </conditional> + <param name="title" value="default deletions" /> + <param name="height_bed" value="2" /> + <conditional name="display_cond"> + <param name="display" value = "deletions"/> + </conditional> + </conditional> + </repeat> + <repeat name="tracks"> + <conditional name="track_file_style_conditional"> + <param name="track_file_style_selector" value="gene_track_option" /> + <conditional name="bed_gtf"> + <param name="input_bed_or_gtf" value="bed"/> + <param name="track_input_bed" value="dm3_genes_withrgbandscore.bed.gz" ftype="bed" /> + </conditional> + <param name="title" value="squares border_color orange line_width 3" /> + <param name="height_bed" value="10" /> + <conditional name="display_cond"> + <param name="display" value="squares"/> + <param name="line_width" value="3"/> + <conditional name="border_color_bed"> + <param name="border_color_bed_select" value="manually"/> + <param name="color" value="orange"/> + </conditional> + </conditional> + </conditional> + </repeat> + <param name="image_file_format" value="png" /> + <output name="outFileName" file="test_bed_invdelsquares.png" ftype="png" compare="image_diff" /> </test> </tests> <help><![CDATA[