| Previous changeset 6:5cec5fb749f0 (2020-02-11) Next changeset 8:4ac4e7083b7e (2020-07-21) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" |
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modified:
macros.xml pyGenomeTracks.xml test-data/master_TADs_BW_plot.png test-data/master_TADs_plot.png test-data/test3.ini test-data/test6.ini test-data/test7.ini test-data/test_arrowhead_zoom.png test-data/test_gtf_bed4.png test-data/test_gtf_flybase_param.png test-data/test_narrowPeak.png test-data/test_ucsc_param.png test-data/testpyGT.sh |
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added:
test-data/dm3_genes_withrgbandscore.bed.gz test-data/test13.ini test-data/test14.ini test-data/test15.ini test-data/test_link2.png test-data/test_scale_bar.png test-data/test_tssarrow.png |
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| diff -r 5cec5fb749f0 -r 326a3db8d9d1 macros.xml --- a/macros.xml Tue Feb 11 10:20:24 2020 -0500 +++ b/macros.xml Fri Apr 17 11:57:44 2020 -0400 |
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| b'@@ -1,6 +1,6 @@\n <macros>\n <token name="@THREADS@">\\${GALAXY_SLOTS:-4}</token>\n- <token name="@WRAPPER_VERSION@">3.2.1</token>\n+ <token name="@WRAPPER_VERSION@">3.3</token>\n <xml name="requirements">\n <requirements>\n <requirement type="package" version="@WRAPPER_VERSION@">pygenometracks</requirement>\n@@ -15,159 +15,6 @@\n <yield />\n </citations>\n </xml>\n-\n- <xml name="colormap">\n- <param argument="--colorMap" name="colormap" type="select" optional="True" label="Color map to use for the heatmap" help=" Available color map names can be found here: https://matplotlib.org/examples/color/colormaps_reference.html">\n- <option value="RdYlBu">RdYlBu</option>\n- <option value="Accent">Accent</option>\n- <option value="Spectral">Spectral</option>\n- <option value="Set1">Set1</option>\n- <option value="Set2">Set2</option>\n- <option value="Set3">Set3</option>\n- <option value="Dark2">Dark2</option>\n- <option value="Reds">Reds</option>\n- <option value="Oranges">Oranges</option>\n- <option value="Greens">Greens</option>\n- <option value="Blues">Blues</option>\n- <option value="Greys">Greys</option>\n- <option value="Purples">Purples</option>\n- <option value="Paired">Paired</option>\n- <option value="Pastel1">Pastel1</option>\n- <option value="Pastel2">Pastel2</option>\n- <option value="spring">spring</option>\n- <option value="summer">summer</option>\n- <option value="autumn">autumn</option>\n- <option value="winter">winter</option>\n- <option value="hot">hot</option>\n- <option value="coolwarm">coolwarm</option>\n- <option value="cool">cool</option>\n- <option value="seismic">seismic</option>\n- <option value="terrain">terrain</option>\n- <option value="ocean">ocean</option>\n- <option value="rainbow">rainbow</option>\n- <option value="bone">bone</option>\n- <option value="flag">flag</option>\n- <option value="prism">prism</option>\n- <option value="cubehelix">cubehelix</option>\n- <option value="binary">binary</option>\n- <option value="pink">pink</option>\n- <option value="gray">gray</option>\n- <option value="copper">copper</option>\n- <option value="BrBG">BrBG</option>\n- <option value="BuGn">BuGn</option>\n- <option value="BuPu">BuPu</option>\n- <option value="GnBu">GnBu</option>\n- <option value="OrRd">OrRd</option>\n- <option value="PiYG">PiYG</option>\n- <option value="PRGn">PRGn</option>\n- <option value="PuOr">PuOr</option>\n- <option value="PuRd">PuRd</option>\n- <option value="PuBu">PuBu</option>\n- <option value="RdBu">RdBu</option>\n- <option value="RdGy">RdGy</option>\n- <option value="RdPu">RdPu</option>\n- <option value="YlGn">YlGn</option>\n- <option value="PuBuGn">PuBuGn</option>\n- <option value="RdYlGn">RdYlGn</option>\n- <option value="YlGnBu">YlGnBu</option>\n- <option value="YlOrBr">YlOrBr</option>\n- <option value="YlOrRd">YlOrRd</option>\n- <option value="gist_gray">gist_gray</option>\n- <option value="gist_stern">gist_stern</option>\n- <option value="gist_earth">gist_earth</option>\n- <option value="gist_yarg">gist_yarg</option>\n- <option value="gist_ncar">gist_ncar</option>\n- <option value="gist_rainbow">gist_rainbow</option>\n- <option value="gist_heat">gist_heat</option>\n- <option value="gnuplot">gnuplot</option>\n- <option value="gnuplot2">gnuplot2</option>\n- <option value="CMRmap">CMRmap</option>\n- '..b' <option value="Reds_r">Reds reversed</option>\n+ <option value="Oranges_r">Oranges reversed</option>\n+ <option value="Greens_r">Greens reversed</option>\n+ <option value="Blues_r">Blues reversed</option>\n+ <option value="Greys_r">Greys reversed</option>\n+ <option value="Purples_r">Purples reversed</option>\n+ <option value="Paired_r">Paired reversed</option>\n+ <option value="Pastel1_r">Pastel1 reversed</option>\n+ <option value="Pastel2_r">Pastel2 reversed</option>\n+ <option value="spring_r">spring reversed</option>\n+ <option value="summer_r">summer reversed</option>\n+ <option value="autumn_r">autumn reversed</option>\n+ <option value="winter_r">winter reversed</option>\n+ <option value="hot_r">hot reversed</option>\n+ <option value="coolwarm_r">coolwarm reversed</option>\n+ <option value="cool_r">cool reversed</option>\n+ <option value="seismic_r">seismic reversed</option>\n+ <option value="terrain_r">terrain reversed</option>\n+ <option value="ocean_r">ocean reversed</option>\n+ <option value="rainbow_r">rainbow reversed</option>\n+ <option value="bone_r">bone reversed</option>\n+ <option value="flag_r">flag reversed</option>\n+ <option value="prism_r">prism reversed</option>\n+ <option value="cubehelix_r">cubehelix reversed</option>\n+ <option value="binary_r">binary reversed</option>\n+ <option value="pink_r">pink reversed</option>\n+ <option value="gray_r">gray reversed</option>\n+ <option value="copper_r">copper reversed</option>\n+ <option value="BrBG_r">BrBG reversed</option>\n+ <option value="BuGn_r">BuGn reversed</option>\n+ <option value="BuPu_r">BuPu reversed</option>\n+ <option value="GnBu_r">GnBu reversed</option>\n+ <option value="OrRd_r">OrRd reversed</option>\n+ <option value="PiYG_r">PiYG reversed</option>\n+ <option value="PRGn_r">PRGn reversed</option>\n+ <option value="PuOr_r">PuOr reversed</option>\n+ <option value="PuRd_r">PuRd reversed</option>\n+ <option value="PuBu_r">PuBu reversed</option>\n+ <option value="RdBu_r">RdBu reversed</option>\n+ <option value="RdGy_r">RdGy reversed</option>\n+ <option value="RdPu_r">RdPu reversed</option>\n+ <option value="YlGn_r">YlGn reversed</option>\n+ <option value="PuBuGn_r">PuBuGn reversed</option>\n+ <option value="RdYlBu_r">RdYlBu reversed</option>\n+ <option value="RdYlGn_r">RdYlGn reversed</option>\n+ <option value="YlGnBu_r">YlGnBu reversed</option>\n+ <option value="YlOrBr_r">YlOrBr reversed</option>\n+ <option value="YlOrRd_r">YlOrRd reversed</option>\n+ <option value="gist_gray_r">gist_gray reversed</option>\n+ <option value="gist_stern_r">gist_stern reversed</option>\n+ <option value="gist_earth_r">gist_earth reversed</option>\n+ <option value="gist_yarg_r">gist_yarg reversed</option>\n+ <option value="gist_ncar_r">gist_ncar reversed</option>\n+ <option value="gist_rainbow_r">gist_rainbow reversed</option>\n+ <option value="gist_heat_r">gist_heat reversed</option>\n+ <option value="gnuplot_r">gnuplot reversed</option>\n+ <option value="gnuplot2_r">gnuplot2 reversed</option>\n+ <option value="CMRmap_r">CMRmap reversed</option>\n+ <option value="bwr_r">bwr reversed</option>\n+ <option value="hsv_r">hsv reversed</option>\n+ <option value="brg_r">brg reversed</option>\n+ <option value="jet_r">jet reversed</option>\n+ <option value="afmhot_r">afmhot reversed</option>\n+ <option value="viridis_r">viridis reversed</option>\n+ <option value="plasma_r">plasma reversed</option>\n+ <option value="inferno_r">inferno reversed</option>\n+ <option value="magma_r">magma reversed</option>\n+ <option value="cividis_r">cividis reversed</option>\n </xml>\n </macros>\n' 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| diff -r 5cec5fb749f0 -r 326a3db8d9d1 pyGenomeTracks.xml --- a/pyGenomeTracks.xml Tue Feb 11 10:20:24 2020 -0500 +++ b/pyGenomeTracks.xml Fri Apr 17 11:57:44 2020 -0400 |
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| b'@@ -30,24 +30,20 @@\n #if $region and $region is not None:\n --region \'$region\'\n #end if\n+ #if $global_args.title is not None:\n+ --title \'$global_args.title\'\n+ #end if\n+ --fontSize $global_args.fontsize\n+ --dpi $global_args.dpi\n+ --trackLabelFraction $global_args.trackLabelFraction\n+ --trackLabelHAlign $global_args.trackLabelHAlign\n --outFileName plot.$image_file_format\n && mv plot.$image_file_format plot\n ]]>\n </command>\n <configfiles>\n <configfile name="tracks_config">\n-## First the xaxis if where = top\n-#if $x_axis.x_axis_select == "true":\n- #if $x_axis.where == \'top\':\n-[x-axis]\n- #if $x_axis.fontsize:\n-fontsize = $x_axis.fontsize\n- #end if\n-where = top\n- #end if\n-#end if\n-\n-## Then each track:\n+## Each track:\n #for $counter, $track in enumerate($tracks):\n ## Hi-C Track\n #if $track.track_file_style_conditional.track_file_style_selector == "hic_matrix_option":\n@@ -124,8 +120,10 @@\n #elif $track.track_file_style_conditional.color_bed.color:\n color = $track.track_file_style_conditional.color_bed.color\n #end if\n- #if $track.track_file_style_conditional.border_color:\n-border_color = $track.track_file_style_conditional.border_color\n+ #if $track.track_file_style_conditional.border_color_bed.border_color_bed_select == \'manually\':\n+border_color = $track.track_file_style_conditional.border_color_bed.color\n+ #else\n+border_color = $track.track_file_style_conditional.border_color_bed.border_color_bed_select\n #end if\n display = collapsed\n #if $track.track_file_style_conditional.height_chrom:\n@@ -148,8 +146,8 @@\n #set ext = $data_bed.extension\n file = ${counter}_${counter_bed}.$ext\n #if $ext == \'gtf\':\n-prefered_name = $track.track_file_style_conditional.bed_advanced.gtf.prefered_name\n-merge_transcripts = $track.track_file_style_conditional.bed_advanced.gtf.merge_transcripts\n+prefered_name = $track.track_file_style_conditional.bed_style.bed_advanced.gtf.prefered_name\n+merge_transcripts = $track.track_file_style_conditional.bed_style.bed_advanced.gtf.merge_transcripts\n #end if\n #if $track.track_file_style_conditional.title:\n title = $track.track_file_style_conditional.title\n@@ -161,33 +159,53 @@\n #elif $track.track_file_style_conditional.color_bed.color:\n color = $track.track_file_style_conditional.color_bed.color\n #end if\n- #if $track.track_file_style_conditional.border_color:\n-border_color = $track.track_file_style_conditional.border_color\n+ #if $track.track_file_style_conditional.border_color_bed.border_color_bed_select == \'manually\':\n+border_color = $track.track_file_style_conditional.border_color_bed.color\n+ #else\n+border_color = $track.track_file_style_conditional.border_color_bed.border_color_bed_select\n #end if\n- #if $track.track_file_style_conditional.flybase:\n-style = flybase\n-height_utr = $track.track_file_style_conditional.bed_advanced.flybase.height_utr\n-color_utr = $track.track_file_style_conditional.bed_advanced.flybase.color_utr\n- #else\n-style = UCSC\n-arrow_interval = $track.track_file_style_conditional.bed_advanced.ucsc.arrow_interval\n+style = $track.track_file_style_conditional.bed_style.bed_style_select\n+ #if $track.track_file_style_conditional.bed_style.bed_style_select == \'UCSC\':\n+arrow_interval = $track.track_file_style_conditional.bed_style.bed_advanced.arrow_interval\n+ #else:\n+height_utr = $track.track_file_style_conditional.bed_style.bed_advanced.height_utr\n+ #if $track.track_file_style_conditional.bed_style.bed_advanced.color_utr.color_utr_select == \'manually\':\n+color_utr = $track.track_file_style_conditional.bed_style.bed_advanced.color_utr.color\n+ #elif $track.track_file_style_conditional.bed_style.bed_advanced.color_utr.color_utr_select == \'bed_rgb\':\n+color_utr = bed_rgb\n+ #else:\n+ #if $track.track_file_'..b'\n+ <param name="color" value="red"/>\n+ <param name="alpha" value="0.5"/>\n+ <param name="line_width" value="2"/>\n+ <param name="x_center" value="3200000"/>\n+ <param name="size" value="100002"/>\n+ <param name="sb_where" value="right"/>\n+ <param name="fontsize" value="8"/>\n+ <param name="spacer_height" value="4"/>\n+ </conditional>\n+ </repeat>\n+ <param name="image_file_format" value="png" />\n+ <output name="outFileName" file="test_scale_bar.png" ftype="png" compare="sim_size" delta="35000" />\n+ </test>\n+ <!--test 15-->\n+ <test>\n+ <param name="region" value="chrX:3300000-3500000"/>\n+ <repeat name="tracks">\n+ <conditional name="track_file_style_conditional">\n+ <param name="track_file_style_selector" value="xaxis_option" />\n+ <param name="xaxis_where" value="bottom" />\n+ </conditional>\n+ </repeat>\n+ <repeat name="tracks">\n+ <conditional name="track_file_style_conditional">\n+ <param name="track_file_style_selector" value="gene_track_option" />\n+ <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" />\n+ <param name="title" value="flybase" />\n+ <param name="height_bed" value="10" />\n+ </conditional>\n+ </repeat>\n+ <repeat name="tracks">\n+ <conditional name="track_file_style_conditional">\n+ <param name="track_file_style_selector" value="gene_track_option" />\n+ <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" />\n+ <param name="title" value="UCSC" />\n+ <param name="height_bed" value="10" />\n+ <conditional name="bed_style">\n+ <param name="bed_style_select" value="UCSC"/>\n+ <section name="bed_advanced">\n+ <param name="arrow_interval" value="10"/>\n+ </section>\n+ </conditional>\n+ </conditional>\n+ </repeat>\n+ <repeat name="tracks">\n+ <conditional name="track_file_style_conditional">\n+ <param name="track_file_style_selector" value="gene_track_option" />\n+ <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" />\n+ <param name="title" value="tssarrow" />\n+ <param name="height_bed" value="10" />\n+ <conditional name="bed_style">\n+ <param name="bed_style_select" value="tssarrow"/>\n+ </conditional>\n+ </conditional>\n+ </repeat>\n+ <repeat name="tracks">\n+ <conditional name="track_file_style_conditional">\n+ <param name="track_file_style_selector" value="gene_track_option" />\n+ <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" />\n+ <param name="title" value="tssarrow 5kb" />\n+ <param name="height_bed" value="10" />\n+ <conditional name="bed_style">\n+ <param name="bed_style_select" value="tssarrow"/>\n+ <section name="bed_advanced">\n+ <param name="arrow_length" value="5000"/>\n+ </section>\n+ </conditional>\n+ </conditional>\n+ </repeat>\n+ <param name="image_file_format" value="png" />\n+ <output name="outFileName" file="test_tssarrow.png" ftype="png" compare="sim_size" delta="35000" />\n+ </test>\n </tests>\n <help><![CDATA[\n \n' |
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| diff -r 5cec5fb749f0 -r 326a3db8d9d1 test-data/dm3_genes_withrgbandscore.bed.gz |
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| Binary file test-data/dm3_genes_withrgbandscore.bed.gz has changed |
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| diff -r 5cec5fb749f0 -r 326a3db8d9d1 test-data/master_TADs_BW_plot.png |
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| Binary file test-data/master_TADs_BW_plot.png has changed |
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| diff -r 5cec5fb749f0 -r 326a3db8d9d1 test-data/master_TADs_plot.png |
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| Binary file test-data/master_TADs_plot.png has changed |
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| diff -r 5cec5fb749f0 -r 326a3db8d9d1 test-data/test13.ini --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test13.ini Fri Apr 17 11:57:44 2020 -0400 |
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| @@ -0,0 +1,49 @@ +[links_1] +file = test.arcs +title = default +height = 1.5 +color = #000000 +alpha = 1.0 +line_width = 0.5 +line_style = solid +links_type = arcs +compact_arcs_level = 0 +overlay_previous = no +file_type = links +[links_2] +file = test.arcs +title = ylim 20kb +height = 1.5 +color = #000000 +alpha = 1.0 +line_width = 0.5 +line_style = solid +links_type = arcs +compact_arcs_level = 0 +ylim = 20000.0 +overlay_previous = no +file_type = links +[links_3] +file = test.arcs +title = compacted +height = 1.5 +color = #000000 +alpha = 1.0 +line_width = 0.5 +line_style = solid +links_type = arcs +compact_arcs_level = 1 +overlay_previous = no +file_type = links +[links_4] +file = test.arcs +title = highly compacted +height = 1.5 +color = #000000 +alpha = 1.0 +line_width = 0.5 +line_style = solid +links_type = arcs +compact_arcs_level = 2 +overlay_previous = no +file_type = links |
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| diff -r 5cec5fb749f0 -r 326a3db8d9d1 test-data/test14.ini --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test14.ini Fri Apr 17 11:57:44 2020 -0400 |
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| @@ -0,0 +1,23 @@ +[spacer] +height = 1.0 +[scale_bar] +title = default +color = #000000 +alpha = 1.0 +line_width = 0.5 +where = left +file_type = scalebar +[spacer] +height = 1.0 +[scale_bar] +title = scalebar where = right x_center = 3200000 size = 100002 fontsize = 8 line_width =2 color = red alpha = 0.5 +color = red +alpha = 0.5 +line_width = 2.0 +x_center = 3200000 +size = 100002 +where = right +fontsize = 8.0 +file_type = scalebar +[spacer] +height = 4.0 \ No newline at end of file |
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| diff -r 5cec5fb749f0 -r 326a3db8d9d1 test-data/test15.ini --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test15.ini Fri Apr 17 11:57:44 2020 -0400 |
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| @@ -0,0 +1,67 @@ +[x-axis] +where = bottom +[genes_1_0] +file = dm3_genes.bed.gz +title = flybase +color = #000000 +border_color = #000000 +style = flybase +height_utr = 1.0 +color_utr = grey +arrowhead_included = false +display = stacked +height = 10.0 +labels = true +file_type = bed +global_max_row = false +max_labels = 60 +line_width = 0.5 +overlay_previous = no +[genes_2_0] +file = dm3_genes.bed.gz +title = UCSC +color = #000000 +border_color = #000000 +style = UCSC +arrow_interval = 10 +display = stacked +height = 10.0 +labels = true +file_type = bed +global_max_row = false +max_labels = 60 +line_width = 0.5 +overlay_previous = no +[genes_3_0] +file = dm3_genes.bed.gz +title = tssarrow +color = #000000 +border_color = #000000 +style = tssarrow +height_utr = 1.0 +color_utr = grey +display = stacked +height = 10.0 +labels = true +file_type = bed +global_max_row = false +max_labels = 60 +line_width = 0.5 +overlay_previous = no +[genes_4_0] +file = dm3_genes.bed.gz +title = tssarrow 5kb +color = #000000 +border_color = #000000 +style = tssarrow +height_utr = 1.0 +color_utr = grey +arrow_length = 5000 +display = stacked +height = 10.0 +labels = true +file_type = bed +global_max_row = false +max_labels = 60 +line_width = 0.5 +overlay_previous = no \ No newline at end of file |
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| diff -r 5cec5fb749f0 -r 326a3db8d9d1 test-data/test3.ini --- a/test-data/test3.ini Tue Feb 11 10:20:24 2020 -0500 +++ b/test-data/test3.ini Fri Apr 17 11:57:44 2020 -0400 |
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| @@ -149,7 +149,7 @@ overlay_previous = no [genes_12_0] file = test-data/domains.bed -title = domains.bed using the 9th field for colors interleaved +title = domains.bed using the 9th field for colors interleaved border=red color = bed_rgb border_color = red style = flybase @@ -164,4 +164,40 @@ max_labels = 60 line_width = 0.5 arrowhead_included = false +overlay_previous = no +[genes_13_0] +file = test-data/domains.bed +title = domains.bed using the 9th field for colors interleaved border=bed_rgb +color = bed_rgb +border_color = bed_rgb +style = flybase +height_utr = 1.0 +color_utr = grey +display = interleaved +height = 2.0 +labels = false +file_type = bed +fontsize = 10 +global_max_row = false +max_labels = 60 +line_width = 0.5 +arrowhead_included = false +overlay_previous = no +[genes_14_0] +file = test-data/domains.bed +title = domains.bed using the 9th field for colors interleaved border=none +color = bed_rgb +border_color = none +style = flybase +height_utr = 1.0 +color_utr = grey +display = interleaved +height = 2.0 +labels = false +file_type = bed +fontsize = 10 +global_max_row = false +max_labels = 60 +line_width = 0.5 +arrowhead_included = false overlay_previous = no \ No newline at end of file |
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| diff -r 5cec5fb749f0 -r 326a3db8d9d1 test-data/test6.ini --- a/test-data/test6.ini Tue Feb 11 10:20:24 2020 -0500 +++ b/test-data/test6.ini Fri Apr 17 11:57:44 2020 -0400 |
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| @@ -10,6 +10,17 @@ overlay_previous = no [narrow_peak_1_0] file = test-data/test2.narrowPeak +title = box line_width = 2 +color = #9bbb59 +type = box +use_summit = true +height = 4.0 +show_labels = true +line_width = 2 +file_type = narrow_peak +overlay_previous = no +[narrow_peak_2_0] +file = test-data/test2.narrowPeak title = peak width 3 color = #c0504d type = peak @@ -23,7 +34,7 @@ overlay_previous = no [spacer] height = 0.5 -[narrow_peak_2_0] +[narrow_peak_3_0] file = test-data/test2.narrowPeak title = peak no data range color = #000000 |
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| diff -r 5cec5fb749f0 -r 326a3db8d9d1 test-data/test7.ini --- a/test-data/test7.ini Tue Feb 11 10:20:24 2020 -0500 +++ b/test-data/test7.ini Fri Apr 17 11:57:44 2020 -0400 |
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| @@ -35,4 +35,74 @@ max_labels = 60 line_width = 0.5 arrowhead_included = false +overlay_previous = no +[genes_2_0] +file = test-data/dm3_genes_withrgbandscore.bed.gz +title = genes with scores +color = cool_r +border_color = #000000 +style = flybase +height_utr = 1.0 +color_utr = grey +display = stacked +height = 10.0 +labels = true +file_type = bed +global_max_row = false +max_labels = 60 +line_width = 0.5 +arrowhead_included = false +overlay_previous = no +[genes_3_0] +file = test-data/dm3_genes_withrgbandscore.bed.gz +title = genes with utr as bed_rgb +color = black +border_color = #000000 +style = flybase +height_utr = 1.0 +color_utr = bed_rgb +display = stacked +height = 10.0 +labels = true +file_type = bed +global_max_row = false +max_labels = 60 +line_width = 0.5 +arrowhead_included = false +overlay_previous = no +[genes_3_0] +file = test-data/dm3_genes_withrgbandscore.bed.gz +title = genes with coding as bed_rgb - labels_in_margin +color = bed_rgb +border_color = #000000 +style = flybase +height_utr = 1.0 +color_utr = grey +display = stacked +height = 10.0 +labels = true +labels_in_margin = true +file_type = bed +global_max_row = false +max_labels = 60 +line_width = 0.5 +arrowhead_included = false +overlay_previous = no +[genes_4_0] +file = test-data/dm3_genes_withrgbandscore.bed.gz +title = genes bed_rgb like - all_labels_inside +color = bed_rgb +border_color = #000000 +style = flybase +height_utr = 1.0 +color_utr = bed_rgb +display = stacked +height = 10.0 +labels = true +all_labels_inside = true +file_type = bed +global_max_row = false +max_labels = 60 +line_width = 0.5 +arrowhead_included = false overlay_previous = no \ No newline at end of file |
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| diff -r 5cec5fb749f0 -r 326a3db8d9d1 test-data/testpyGT.sh --- a/test-data/testpyGT.sh Tue Feb 11 10:20:24 2020 -0500 +++ b/test-data/testpyGT.sh Fri Apr 17 11:57:44 2020 -0400 |
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| @@ -11,5 +11,8 @@ 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 conda_env_deactivate |
