Mercurial > repos > iuc > pygenometracks
changeset 9:2824d77cd8f8 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
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--- a/macros.xml Tue Jul 21 03:32:48 2020 -0400 +++ b/macros.xml Wed Nov 18 21:33:46 2020 +0000 @@ -1,6 +1,6 @@ <macros> <token name="@THREADS@">\${GALAXY_SLOTS:-4}</token> - <token name="@WRAPPER_VERSION@">3.5</token> + <token name="@WRAPPER_VERSION@">3.6</token> <xml name="requirements"> <requirements> <requirement type="package" version="@WRAPPER_VERSION@">pygenometracks</requirement> @@ -11,7 +11,8 @@ <xml name="citations"> <citations> - <citation type="doi">10.5281/zenodo.1133705</citation> + <citation type="doi">10.1038/s41467-017-02525-w</citation> + <citation type="doi">10.1093/bioinformatics/btaa692</citation> <yield /> </citations> </xml>
--- a/pyGenomeTracks.xml Tue Jul 21 03:32:48 2020 -0400 +++ b/pyGenomeTracks.xml Wed Nov 18 21:33:46 2020 +0000 @@ -21,11 +21,17 @@ sed '/^$/d' '$tracks_config' && @BINARY@ --tracks '$tracks_config' - #if $region and $region is not None: - --region '$region' + --region '$region' + #if $global_args.title != '': + --title '$global_args.title' #end if - #if $global_args.title is not None: - --title '$global_args.title' + #if $global_args.plotWidth != '': + --plotWidth $global_args.plotWidth + #else: + --width $global_args.width + #end if + #if $global_args.height != '': + --height '$global_args.height' #end if --fontSize $global_args.fontsize --dpi $global_args.dpi @@ -557,11 +563,17 @@ #end if alpha = $track.track_file_style_conditional.alpha line_width = $track.track_file_style_conditional.line_width - #if $track.track_file_style_conditional.x_center != "": -x_center = $track.track_file_style_conditional.x_center + #if $track.track_file_style_conditional.scalebar_pos.x_center != "": +x_center = $track.track_file_style_conditional.scalebar_pos.x_center + #end if + #if $track.track_file_style_conditional.scalebar_pos.size != "": +size = $track.track_file_style_conditional.scalebar_pos.size #end if - #if $track.track_file_style_conditional.size != "": -size = $track.track_file_style_conditional.size + #if $track.track_file_style_conditional.scalebar_pos.scalebar_start_position != "": +scalebar_start_position = $track.track_file_style_conditional.scalebar_pos.scalebar_start_position + #end if + #if $track.track_file_style_conditional.scalebar_pos.scalebar_end_position != "": +scalebar_end_position = $track.track_file_style_conditional.scalebar_pos.scalebar_end_position #end if where = $track.track_file_style_conditional.sb_where #if $track.track_file_style_conditional.fontsize != "": @@ -580,12 +592,19 @@ <inputs> <!--Arguments for pgt--> <param argument="--region" type="text" label="Region of the genome to limit the operation" optional="false" - help="The format is chr:start-end. Also valid is just to specify a chromosome, for example chr10:10-500" /> + help="The format is chr:start-end, for example chr10:10-500"> + <validator type="expression" message="Region should be like chr10:10-500">'^[a-zA-Z0-9_]:\d+-\d+$'</validator> + </param> <section name="global_args" title="Configure figure parameters" expanded="False"> <param argument="--title" type="text" label="Plot title" help="If set, you may need to start by a spacer track"/> <param argument="--fontsize" type="integer" label="Font size for the labels of the plot" value="12"/> <param argument="--dpi" type="integer" label="Resolution (dpi)" value="72" help="Resolution for the image in case the ouput is a raster graphics image (e.g png, jpg)"/> + <param argument="--width" type="float" label="Figure width in cm" value="40"/> + <param argument="--plotWidth" type="float" label="Width in centimeters of the plotting (central) part" optional="true" + help="This will overwrite what has been defined as a figure width."/> + <param argument="--height" type="float" label="Figure height in centimeters" optional="true" + help="If not given, the figure height is computed based on the heights of the tracks. If given, the track height are proportionally scaled to match the desired figure height."/> <param argument="--trackLabelFraction" type="float" label="Proportion of space dedicated to track labels" value="0.05" min="0" max="1"/> <param argument="--trackLabelHAlign" type="select" label="Horizontal alignment of track labels"> @@ -964,10 +983,14 @@ <param name="color" type="color" label="Color of the scale bar" optional="True" /> <param name="alpha" type="float" value="1" min="0" max="1" label="level of transparency (alpha)" help="1 is opaque and 0 is totally transparent"/> <param name="line_width" type="float" value="0.5" label="width of lines"/> - <param name="x_center" type="integer" label="coordinate where the scale bar should be plotted (center)" optional="True" - help="If not set it will be in the middle of the plotted area."/> - <param name="size" type="integer" label="size of the scale bar" optional="True" - help="If not set it will be the higher number that begins with 1, 2 or 5 followed by 0s that is less than half the plotted area."/> + <section name="scalebar_pos" title="Set the scalebar position" expanded="true" help="You can optionally define one or multiple parameters below."> + <param name="scalebar_start_position" type="integer" label="coordinate where the scale bar should begin." optional="True"/> + <param name="scalebar_end_position" type="integer" label="coordinate where the scale bar should end." optional="True"/> + <param name="x_center" type="integer" label="coordinate where the scale bar should be plotted (center)" optional="True" + help="If not set and cannot be deduced from others it will be in the middle of the plotted area."/> + <param name="size" type="integer" label="size of the scale bar" optional="True" + help="If not set and cannot be deduced from others it will be the higher number that begins with 1, 2 or 5 followed by 0s that is less than half the plotted area."/> + </section> <param name="sb_where" type="select" label="where the size of the scale bar should appear relative to the bar"> <option value="left" selected="True">left</option> <option value="right">right</option> @@ -1174,7 +1197,7 @@ </conditional> </repeat> <param name="image_file_format" value="png" /> - <output name="outFileName" file="master_TADs_plot.png" ftype="png" compare="sim_size" delta="35000" /> + <output name="outFileName" file="master_TADs_plot.png" ftype="png" compare="sim_size" delta="100" /> </test> <!--test 2--> <test> @@ -1238,7 +1261,7 @@ </conditional> </repeat> <param name="image_file_format" value="png" /> - <output name="outFileName" file="bigwig_multiple.png" ftype="png" compare="sim_size" delta="35000" /> + <output name="outFileName" file="bigwig_multiple.png" ftype="png" compare="sim_size" delta="100" /> </test> <!--test 3--> <test> @@ -1469,7 +1492,7 @@ </conditional> </repeat> <param name="image_file_format" value="png" /> - <output name="outFileName" file="master_TADs_BW_plot.png" ftype="png" compare="sim_size" delta="35000" /> + <output name="outFileName" file="master_TADs_BW_plot.png" ftype="png" compare="sim_size" delta="100" /> </test> <!--test 4--> <test> @@ -1507,7 +1530,7 @@ </conditional> </repeat> <param name="image_file_format" value="png" /> - <output name="outFileName" file="test_alpha.png" ftype="png" compare="sim_size" delta="35000" /> + <output name="outFileName" file="test_alpha.png" ftype="png" compare="sim_size" delta="100" /> </test> <!--test 5--> <test> @@ -1545,7 +1568,7 @@ </conditional> </repeat> <param name="image_file_format" value="png" /> - <output name="outFileName" file="test_gtf_bed4.png" ftype="png" compare="sim_size" delta="35000" /> + <output name="outFileName" file="test_gtf_bed4.png" ftype="png" compare="sim_size" delta="100" /> </test> <!--test 6--> <test> @@ -1619,7 +1642,7 @@ </conditional> </repeat> <param name="image_file_format" value="png" /> - <output name="outFileName" file="test_narrowPeak.png" ftype="png" compare="sim_size" delta="35000" /> + <output name="outFileName" file="test_narrowPeak.png" ftype="png" compare="sim_size" delta="100" /> </test> <!--test 7--> <test> @@ -1724,7 +1747,7 @@ </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" /> + <output name="outFileName" file="test_gtf_flybase_param.png" ftype="png" compare="sim_size" delta="100" /> </test> <!--test 8--> <test> @@ -1766,7 +1789,7 @@ </conditional> </repeat> <param name="image_file_format" value="png" /> - <output name="outFileName" file="test_ucsc_param.png" ftype="png" compare="sim_size" delta="35000" /> + <output name="outFileName" file="test_ucsc_param.png" ftype="png" compare="sim_size" delta="100" /> </test> <!--test 9--> <test> @@ -1825,7 +1848,7 @@ </conditional> </repeat> <param name="image_file_format" value="png" /> - <output name="outFileName" file="test_arrowhead_zoom.png" ftype="png" compare="sim_size" delta="35000" /> + <output name="outFileName" file="test_arrowhead_zoom.png" ftype="png" compare="sim_size" delta="100" /> </test> <!--test 10--> <test> @@ -1875,7 +1898,7 @@ </conditional> </repeat> <param name="image_file_format" value="png" /> - <output name="outFileName" file="test_middle_triangle.png" ftype="png" compare="sim_size" delta="35000" /> + <output name="outFileName" file="test_middle_triangle.png" ftype="png" compare="sim_size" delta="100" /> </test> <!--test 11--> <test> @@ -1932,7 +1955,7 @@ </conditional> </repeat> <param name="image_file_format" value="png" /> - <output name="outFileName" file="test_TADs_bdgm.png" ftype="png" compare="sim_size" delta="35000" /> + <output name="outFileName" file="test_TADs_bdgm.png" ftype="png" compare="sim_size" delta="100" /> </test> <!--test 12--> <test> @@ -1982,7 +2005,7 @@ </conditional> </repeat> <param name="image_file_format" value="png" /> - <output name="outFileName" file="test_link.png" ftype="png" compare="sim_size" delta="35000" /> + <output name="outFileName" file="test_link.png" ftype="png" compare="sim_size" delta="100" /> </test> <!--test 13--> <test> @@ -2035,7 +2058,7 @@ </conditional> </repeat> <param name="image_file_format" value="png" /> - <output name="outFileName" file="test_link2.png" ftype="png" compare="sim_size" delta="35000" /> + <output name="outFileName" file="test_link2.png" ftype="png" compare="sim_size" delta="100" /> </test> <!--test 14--> <test> @@ -2065,15 +2088,17 @@ <param name="color" value="red"/> <param name="alpha" value="0.5"/> <param name="line_width" value="2"/> - <param name="x_center" value="3200000"/> - <param name="size" value="100002"/> + <section name="scalebar_pos"> + <param name="x_center" value="3200000"/> + <param name="size" value="100002"/> + </section> <param name="sb_where" value="right"/> <param name="fontsize" value="8"/> <param name="spacer_height" value="4"/> </conditional> </repeat> <param name="image_file_format" value="png" /> - <output name="outFileName" file="test_scale_bar.png" ftype="png" compare="sim_size" delta="35000" /> + <output name="outFileName" file="test_scale_bar.png" ftype="png" compare="sim_size" delta="100" /> </test> <!--test 15--> <test> @@ -2132,7 +2157,7 @@ </conditional> </repeat> <param name="image_file_format" value="png" /> - <output name="outFileName" file="test_tssarrow.png" ftype="png" compare="sim_size" delta="35000" /> + <output name="outFileName" file="test_tssarrow.png" ftype="png" compare="sim_size" delta="100" /> </test> <!--test 16--> <test> @@ -2173,7 +2198,7 @@ </conditional> </repeat> <param name="image_file_format" value="png" /> - <output name="outFileName" file="test_alpha_dec.png" ftype="png" compare="sim_size" delta="35000" /> + <output name="outFileName" file="test_alpha_dec.png" ftype="png" compare="sim_size" delta="1000" /> </test> <!--test 17--> <test> @@ -2296,7 +2321,7 @@ </conditional> </repeat> <param name="image_file_format" value="png" /> - <output name="outFileName" file="test_log.png" ftype="png" compare="sim_size" delta="35000" /> + <output name="outFileName" file="test_log.png" ftype="png" compare="sim_size" delta="100" /> </test> <!--test 18--> <test> @@ -2374,7 +2399,7 @@ </conditional> </repeat> <param name="image_file_format" value="png" /> - <output name="outFileName" file="test_operation.png" ftype="png" compare="sim_size" delta="35000" /> + <output name="outFileName" file="test_operation.png" ftype="png" compare="sim_size" delta="100" /> </test> <!--test 19--> <test> @@ -2505,7 +2530,7 @@ </conditional> </repeat> <param name="image_file_format" value="png" /> - <output name="outFileName" file="test_log_grid.png" ftype="png" compare="sim_size" delta="35000" /> + <output name="outFileName" file="test_log_grid.png" ftype="png" compare="sim_size" delta="100" /> </test> <!--test 20--> <test> @@ -2555,6 +2580,7 @@ <param name="line_width" value="3" /> <param name="invert_orientation" value="true" /> <param name="title" value="links line_width = 3 color RdYlGn" /> + <param name="height" value="3" /> </conditional> </repeat> <repeat name="tracks"> @@ -2597,6 +2623,7 @@ <param name="invert_orientation" value="true" /> <param name="use_middle" value="true" /> <param name="title" value="links line_width = 3 color RdYlGn use_middle = true" /> + <param name="height" value="3" /> </conditional> </repeat> <repeat name="tracks"> @@ -2607,7 +2634,86 @@ </conditional> </repeat> <param name="image_file_format" value="png" /> - <output name="outFileName" file="test_arcs_use_middle.png" ftype="png" compare="sim_size" delta="35000" /> + <output name="outFileName" file="test_arcs_use_middle.png" ftype="png" compare="sim_size" delta="1200" /> + </test> + <!--test 21--> + <test> + <param name="region" value="X:3000000-3600000"/> + <section name="global_args"> + <param name="trackLabelFraction" value="0.3"/> + <param name="plotWidth" value="12"/> + <param name="dpi" value="20"/> + </section> + <repeat name="tracks"> + <conditional name="track_file_style_conditional"> + <param name="track_file_style_selector" value="scale_bar_option" /> + <param name="title" value="scalebar where = right" /> + <param name="where" value="right" /> + <param name="spacer_height" value="0.5"/> + </conditional> + </repeat> + <repeat name="tracks"> + <conditional name="track_file_style_conditional"> + <param name="track_file_style_selector" value="scale_bar_option" /> + <param name="title" value="scalebar scalebar_start_position = 3200000" /> + <section name="scalebar_pos"> + <param name="scalebar_start_position" value="3200000"/> + </section> + <param name="spacer_height" value="0.5"/> + </conditional> + </repeat> + <repeat name="tracks"> + <conditional name="track_file_style_conditional"> + <param name="track_file_style_selector" value="scale_bar_option" /> + <param name="title" value="scalebar scalebar_start_position = 3200000 scalebar_end_position = 3250000" /> + <section name="scalebar_pos"> + <param name="scalebar_start_position" value="3200000"/> + <param name="scalebar_start_position" value="3250000"/> + </section> + <param name="spacer_height" value="0.5"/> + </conditional> + </repeat> + <repeat name="tracks"> + <conditional name="track_file_style_conditional"> + <param name="track_file_style_selector" value="scale_bar_option" /> + <param name="title" value="scalebar scalebar_start_position = 3200000 x_center = 3250000" /> + <section name="scalebar_pos"> + <param name="scalebar_start_position" value="3200000"/> + <param name="x_center" value="3250000"/> + </section> + <param name="spacer_height" value="0.5"/> + </conditional> + </repeat> + <repeat name="tracks"> + <conditional name="track_file_style_conditional"> + <param name="track_file_style_selector" value="scale_bar_option" /> + <param name="title" value="scalebar scalebar_start_position = 3200000 size = 50000" /> + <section name="scalebar_pos"> + <param name="scalebar_start_position" value="3200000"/> + <param name="size" value="50000"/> + </section> + <param name="spacer_height" value="0.5"/> + </conditional> + </repeat> + <repeat name="tracks"> + <conditional name="track_file_style_conditional"> + <param name="track_file_style_selector" value="scale_bar_option" /> + <param name="title" value="scalebar scalebar_end_position = 3200000 size = 50000" /> + <section name="scalebar_pos"> + <param name="scalebar_end_position" value="3200000"/> + <param name="size" value="50000"/> + </section> + <param name="spacer_height" value="0.5"/> + </conditional> + </repeat> + <repeat name="tracks"> + <conditional name="track_file_style_conditional"> + <param name="track_file_style_selector" value="xaxis_option" /> + <param name="xaxis_where" value="bottom" /> + </conditional> + </repeat> + <param name="image_file_format" value="png" /> + <output name="outFileName" file="master_scale_bar_startend.png" ftype="png" compare="sim_size" delta="100" /> </test> </tests> <help><![CDATA[ @@ -2619,10 +2725,12 @@ Currently, it is possible to plot: - bigwig - - bed (many options) + - bed/gtf (many options) - bedgraph - - links (represented as arcs) - - Hi-C matrices + - epilogos + - narrow peaks + - links + - Hi-C matrices (cool or HiCExplorer h5) _________________ @@ -2631,17 +2739,21 @@ This tool takes various types of tracks as input: + - **Hi-C tracks:** + - **TAD vizualisation:** corrected Hi-C contact matrix to plot a contact heatmap. It is recommended to follow HiCExplorer's ``hicPlotMatrix`` instructions. Boundaries file can used, which is the output of HiCExplorer's ``hicFindTADs`` in bed format. If selected, TADs will be drawn directly on the contact heatmap. + - **TAD score:** display TAD seperation score computed by HiCExplorer's ``hicFindTADs``. - **Chromatin states:** display blocks of different colors following a bed file. - - **Gene track / Bed Track:** display genes or bed files. Labels like gene names can be toggled on or off. + - **Gene track / Bed Track:** display genes or annotations in bed/gtf files. Labels like gene names can be toggled on or off. + - **Link track:** display links (pair of coordinates) as arcs, triangles or loops. + - **NarrowPeak track:** display narrowPeak (encode format) as boxes or as curve (reconstructed peak). - **Bigwig track:** generic bigwig track plotting. - **Bedgraph track:** generic bedgraph track plotting. - **Bedgraph matrix track** is used to specifically plot bm files computed by HiCExplorer's ``hicFindTADs`` (TAD seperation scores). - **Vlines:** vertical lines drawn on top of all tracks following a bed file. It is used as a visual support where regions start / end over all tracks, for example to display TAD boundaries computed by HiCExplorer's ``hicFindTADs``. + - **Hlines:** horizontal lines drawn either by themselves or on top of other tracks. - **Spacer:** Add some space between two tracks. - - **Hi-C tracks:** - - **TAD vizualisation:** corrected Hi-C contact matrix to plot a contact heatmap. It is recommended to follow HiCExplorer's ``hicPlotMatrix`` instructions. Boundaries file can used, which is the output of HiCExplorer's ``hicFindTADs`` in bed format. If selected, TADs will be drawn directly on the contact heatmap. - - **TAD score:** display TAD seperation score computed by HiCExplorer's ``hicFindTADs``. - + - **X-axis:** Plot x-axis scale wherever you want. + - **Scale bar track:** Plot scale bar. For each track, parameters for the color, the width or the font size can be defined. @@ -2651,7 +2763,7 @@ ------ **pyGenomeTracks** output is similar to a genome browser screen-shot that besides the usual genes, and score data (like bigwig or bedgraph files) -also contains Hi-C data. The plot is composed of tracks that need to be specified. +may also contains Hi-C data. The plot is composed of tracks that need to be specified. Below is represented the 85 Mb to 110 Mb region from human chromosome 2 visualized using **pyGenomeTracks**. TADs were computed by HiCExplorer's ``hicFindTADs``. The additional tracks added correspond to: TAD-separation score (as reported by HiCExplorer's ``hicFindTADs``), chromatin states, @@ -2663,8 +2775,9 @@ _________________ -| For more information about pyGenomeTracks please consider our documentation on github_ +| For more information about pyGenomeTracks please consider our documentation on readthedocs_ or github_ +.. _readthedocs: https://pygenometracks.readthedocs.io .. _github: https://github.com/deeptools/pyGenomeTracks .. _`Nothjunge et al. (2017)`: https://www.nature.com/articles/s41467-017-01724-9 ]]></help>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test21.ini Wed Nov 18 21:33:46 2020 +0000 @@ -0,0 +1,46 @@ + +[sb1] +file_type = scalebar +title = scalebar where = right +where = right + +[spacer] + +[sb2] +file_type = scalebar +title = scalebar scalebar_start_position = 3200000 +scalebar_start_position = 3200000 + +[spacer] + +[sb3] +file_type = scalebar +title = scalebar scalebar_start_position = 3200000 scalebar_end_position = 3250000 +scalebar_end_position = 3250000 +scalebar_start_position = 3200000 + +[spacer] + +[sb4] +file_type = scalebar +title = scalebar scalebar_start_position = 3200000 x_center = 3250000 +x_center = 3250000 +scalebar_start_position = 3200000 + +[spacer] + +[sb5] +file_type = scalebar +title = scalebar scalebar_start_position = 3200000 size = 50000 +size = 50000 +scalebar_start_position = 3200000 + +[spacer] + +[sb6] +file_type = scalebar +title = scalebar scalebar_end_position = 3200000 size = 50000 +size = 50000 +scalebar_end_position = 3200000 + +[x-axis]
--- a/test-data/testpyGT.sh Tue Jul 21 03:32:48 2020 -0400 +++ b/test-data/testpyGT.sh Wed Nov 18 21:33:46 2020 +0000 @@ -1,23 +1,24 @@ . <(planemo conda_env pyGenomeTracks.xml) -# pgt --tracks test-data/test1.ini --region chrX:3000000-3500000 -o test-data/master_TADs_plot.png -# pgt --tracks test-data/test2.ini --region chrX:3000000-3500000 -o test-data/bigwig_multiple.png -# pgt --tracks test-data/test3.ini --region chrX:3000000-3500000 -o test-data/master_TADs_BW_plot.png -# pgt --tracks test-data/test4.ini --region X:2700000-3100000 -o test-data/test_alpha.png -# pgt --tracks test-data/test5.ini --region X:3000000-3300000 -o test-data/test_gtf_bed4.png -# pgt --tracks test-data/test6.ini --region X:2760000-2802000 -o test-data/test_narrowPeak.png -# pgt --tracks test-data/test7.ini --region chrX:3300000-3500000 -o test-data/test_gtf_flybase_param.png -# pgt --tracks test-data/test8.ini --region chrX:3300000-3500000 -o test-data/test_ucsc_param.png -# pgt --tracks test-data/test9.ini --region X:3133000-3138000 -o test-data/test_arrowhead_zoom.png -# pgt --tracks test-data/test10.ini --region X:3340000-3380000 -o test-data/test_middle_triangle.png -# pgt --tracks test-data/test11.ini --region chrX:3250000-3400000 -o test-data/test_TADs_bdgm.png -# pgt --tracks test-data/test12.ini --region chrX:3000000-3300000 -o test-data/test_link.png -# pgt --tracks test-data/test13.ini --region chrX:3000000-3300000 -o test-data/test_link2.png -# pgt --tracks test-data/test14.ini --region chrX:3000000-3300000 --title "Scale bar" --trackLabelFraction 0.5 --trackLabelHAlign center -o test-data/test_scale_bar.png -# pgt --tracks test-data/test15.ini --region chrX:3300000-3500000 -o test-data/test_tssarrow.png -# pgt --tracks test-data/test4.ini --region chrX:2700000-3100000 --decreasingXAxis -o test-data/test_alpha_dec.png -# pgt --tracks test-data/test17.ini --region chr2:73,800,000-75,744,000 -o test-data/test_log.png -# pgt --tracks test-data/test18.ini --region chrX:2700000-3100000 -o test-data/test_operation.png -# pgt --tracks test-data/test19.ini --region chr2:73,800,000-75,744,000 -o test-data/test_log_grid.png -pgt --tracks test-data/test20.ini --region chrX:3000000-3300000 -o test-data/test_arcs_use_middle.png +pgt --tracks test-data/test1.ini --region chrX:3000000-3500000 --fontSize 12 -o test-data/master_TADs_plot.png +pgt --tracks test-data/test2.ini --region chrX:3000000-3500000 --fontSize 12 -o test-data/bigwig_multiple.png +pgt --tracks test-data/test3.ini --region chrX:3000000-3500000 --fontSize 12 -o test-data/master_TADs_BW_plot.png +pgt --tracks test-data/test4.ini --region X:2700000-3100000 --fontSize 12 -o test-data/test_alpha.png +pgt --tracks test-data/test5.ini --region X:3000000-3300000 --fontSize 12 -o test-data/test_gtf_bed4.png +pgt --tracks test-data/test6.ini --region X:2760000-2802000 --fontSize 12 -o test-data/test_narrowPeak.png +pgt --tracks test-data/test7.ini --region chrX:3300000-3500000 --fontSize 12 -o test-data/test_gtf_flybase_param.png +pgt --tracks test-data/test8.ini --region chrX:3300000-3500000 --fontSize 12 -o test-data/test_ucsc_param.png +pgt --tracks test-data/test9.ini --region X:3133000-3138000 --fontSize 12 -o test-data/test_arrowhead_zoom.png +pgt --tracks test-data/test10.ini --region X:3340000-3380000 --fontSize 12 -o test-data/test_middle_triangle.png +pgt --tracks test-data/test11.ini --region chrX:3250000-3400000 --fontSize 12 -o test-data/test_TADs_bdgm.png +pgt --tracks test-data/test12.ini --region chrX:3000000-3300000 --fontSize 12 -o test-data/test_link.png +pgt --tracks test-data/test13.ini --region chrX:3000000-3300000 --fontSize 12 -o test-data/test_link2.png +pgt --tracks test-data/test14.ini --region chrX:3000000-3300000 --fontSize 12 --title "Scale bar" --trackLabelFraction 0.5 --trackLabelHAlign center -o test-data/test_scale_bar.png +pgt --tracks test-data/test15.ini --region chrX:3300000-3500000 --fontSize 12 -o test-data/test_tssarrow.png +pgt --tracks test-data/test4.ini --region chrX:2700000-3100000 --fontSize 12 --decreasingXAxis -o test-data/test_alpha_dec.png +pgt --tracks test-data/test17.ini --region chr2:73,800,000-75,744,000 --fontSize 12 -o test-data/test_log.png +pgt --tracks test-data/test18.ini --region chrX:2700000-3100000 --fontSize 12 -o test-data/test_operation.png +pgt --tracks test-data/test19.ini --region chr2:73,800,000-75,744,000 --fontSize 12 -o test-data/test_log_grid.png +pgt --tracks test-data/test20.ini --region chrX:3000000-3300000 --fontSize 12 -o test-data/test_arcs_use_middle.png +pgt --tracks test-data/test21.ini --region X:3000000-3600000 --fontSize 12 --trackLabelFraction 0.3 --plotWidth 12 --dpi 20 -o test-data/master_scale_bar_startend.png conda_env_deactivate