| Previous changeset 7:326a3db8d9d1 (2020-04-17) Next changeset 9:2824d77cd8f8 (2020-11-18) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" |
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modified:
macros.xml pyGenomeTracks.xml test-data/master_TADs_plot.png test-data/testpyGT.sh |
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added:
test-data/GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz test-data/bedgraph2_X_2.5e6_3.5e6.bdg test-data/compare_images.py test-data/compare_images.sh test-data/test17.ini test-data/test18.ini test-data/test19.ini test-data/test20.ini test-data/test_alpha_dec.png test-data/test_arcs_use_middle.png test-data/test_log.png test-data/test_log_grid.png test-data/test_operation.png test-data/test_wide.arcs test.bed |
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| diff -r 326a3db8d9d1 -r 4ac4e7083b7e macros.xml --- a/macros.xml Fri Apr 17 11:57:44 2020 -0400 +++ b/macros.xml Tue Jul 21 03:32:48 2020 -0400 |
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| @@ -1,6 +1,6 @@ <macros> <token name="@THREADS@">\${GALAXY_SLOTS:-4}</token> - <token name="@WRAPPER_VERSION@">3.3</token> + <token name="@WRAPPER_VERSION@">3.5</token> <xml name="requirements"> <requirements> <requirement type="package" version="@WRAPPER_VERSION@">pygenometracks</requirement> @@ -114,6 +114,43 @@ <when value="fill_option" /> </conditional> </xml> + <xml name="logScale_coverage_macro"> + <conditional name="logScale_conditional"> + <param name="transform_selector" type="select" label="Choose a transformation"> + <option value="no">no transformation</option> + <option value="log1p">log1p</option> + <option value="log">log</option> + <option value="log2">log2</option> + <option value="log10">log10</option> + <option value="-log">-log</option> + </param> + <when value="no"/> + <when value="log1p"> + <param name="y_axis_values" type="boolean" truevalue="original" falsevalue="transformed" checked="false" + label="Use original values instead of transformed values." /> + </when> + <when value="log"> + <param name="log_pseudocount" type="float" value="0" label="pseudo count to add before applying log" /> + <param name="y_axis_values" type="boolean" truevalue="original" falsevalue="transformed" checked="false" + label="Use original values instead of transformed values." /> + </when> + <when value="log2"> + <param name="log_pseudocount" type="float" value="0" label="pseudo count to add before applying log2" /> + <param name="y_axis_values" type="boolean" truevalue="original" falsevalue="transformed" checked="false" + label="Use original values instead of transformed values." /> + </when> + <when value="log10"> + <param name="log_pseudocount" type="float" value="0" label="pseudo count to add before applying log10" /> + <param name="y_axis_values" type="boolean" truevalue="original" falsevalue="transformed" checked="false" + label="Use original values instead of transformed values." /> + </when> + <when value="-log"> + <param name="log_pseudocount" type="float" value="0" label="pseudo count to add before applying -log" /> + <param name="y_axis_values" type="boolean" truevalue="original" falsevalue="transformed" checked="false" + label="Use original values instead of transformed values." /> + </when> + </conditional> + </xml> <xml name="border_color_bed_macro"> <conditional name="border_color_bed"> <param name="border_color_bed_select" type="select" label="Define border color:"> |
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| diff -r 326a3db8d9d1 -r 4ac4e7083b7e pyGenomeTracks.xml --- a/pyGenomeTracks.xml Fri Apr 17 11:57:44 2020 -0400 +++ b/pyGenomeTracks.xml Tue Jul 21 03:32:48 2020 -0400 |
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| b'@@ -7,7 +7,7 @@\n <expand macro="requirements" />\n <command detect_errors="exit_code">\n <![CDATA[\n- ## First symlink data of hic or bed/gtf to have the good extension\n+ ## First symlink data of hic to have the good extension\n #for $counter, $track in enumerate($tracks):\n #if $track.track_file_style_conditional.track_file_style_selector == "hic_matrix_option":\n #for $counter_matrix, $data_matrix in enumerate($track.track_file_style_conditional.matrix_h5_cooler_multiple):\n@@ -15,12 +15,6 @@\n ln -s $data_matrix ${counter}_${counter_matrix}.$ext &&\n #end for\n #end if\n- #if $track.track_file_style_conditional.track_file_style_selector == "gene_track_option":\n- #for $counter_bed, $data_bed in enumerate($track.track_file_style_conditional.track_input_bed):\n- #set ext = $data_bed.extension\n- ln -s $data_bed ${counter}_${counter_bed}.$ext &&\n- #end for\n- #end if\n #end for\n \n \n@@ -38,6 +32,7 @@\n --trackLabelFraction $global_args.trackLabelFraction\n --trackLabelHAlign $global_args.trackLabelHAlign\n --outFileName plot.$image_file_format\n+ $global_args.decreasingXAxis\n && mv plot.$image_file_format plot\n ]]>\n </command>\n@@ -144,7 +139,7 @@\n #for $counter_bed, $data_bed in enumerate($track.track_file_style_conditional.track_input_bed):\n [genes_${counter}_${counter_bed}]\n #set ext = $data_bed.extension\n-file = ${counter}_${counter_bed}.$ext\n+file = $data_bed\n #if $ext == \'gtf\':\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@@ -196,7 +191,7 @@\n all_labels_inside = $track.track_file_style_conditional.labels.all_labels_inside\n labels_in_margin = $track.track_file_style_conditional.labels.labels_in_margin\n #end if\n-file_type = bed\n+file_type = $ext\n #if $track.track_file_style_conditional.fontsize:\n fontsize = $track.track_file_style_conditional.fontsize\n #end if\n@@ -245,6 +240,7 @@\n #if $track.track_file_style_conditional.ylim != "":\n ylim = $track.track_file_style_conditional.ylim\n #end if\n+use_middle = $track.track_file_style_conditional.use_middle\n #if $track.track_file_style_conditional.invert_orientation:\n orientation = inverted\n #end if\n@@ -330,6 +326,7 @@\n max_value = $track.track_file_style_conditional.max_value\n #end if\n show_data_range = $track.track_file_style_conditional.show_data\n+grid = $track.track_file_style_conditional.grid\n nans_to_zeros = $track.track_file_style_conditional.nans_to_zeros\n use_middle = $track.track_file_style_conditional.use_middle\n #set $columns = len(open(str($track.track_file_style_conditional.track_input_bedgraph)).readline().split(\'\\t\'))\n@@ -345,6 +342,25 @@\n #elif $track.track_file_style_conditional.type_conditional.type_selector == \'point_option\':\n type = points:$track.track_file_style_conditional.type_conditional.width_point\n #end if\n+ #if $track.track_file_style_conditional.logScale_conditional.transform_selector != \'no\':\n+transform = $track.track_file_style_conditional.logScale_conditional.transform_selector\n+y_axis_values = $track.track_file_style_conditional.logScale_conditional.y_axis_values\n+ #if $track.track_file_style_conditional.logScale_conditional.transform_selector != \'log1p\':\n+log_pseudocount = $track.track_file_style_conditional.logScale_conditional.log_pseudocount\n+ #end if\n+ #end if\n+ #end if\n+ #if $track.track_file_style_conditional.reading_bdg_as_bw.summary_method != \'no\':\n+summary_method = $track.track_file_style_conditional.reading_bdg_as_bw.summary_method\n+ #if $track.track_file_style_conditional.reading_bdg_as_bw.number_of_bins:\n+number_of_bins = $tra'..b'oops" />\n+ <param name="overlay_select" value="share-y" />\n+ </conditional>\n+ </repeat>\n+ <repeat name="tracks">\n+ <conditional name="track_file_style_conditional">\n+ <param name="track_file_style_selector" value="link_track_option" />\n+ <param name="track_input_link" value="test_wide.arcs" ftype="bed" />\n+ <conditional name="color_link">\n+ <param name="color" value="RdYlGn" />\n+ </conditional>\n+ <param name="line_width" value="3" />\n+ <param name="invert_orientation" value="true" />\n+ <param name="title" value="links line_width = 3 color RdYlGn" />\n+ </conditional>\n+ </repeat>\n+ <repeat name="tracks">\n+ <conditional name="track_file_style_conditional">\n+ <param name="track_file_style_selector" value="spacer_option" />\n+ <param name="spacer_height" value="1" />\n+ </conditional>\n+ </repeat>\n+ <repeat name="tracks">\n+ <conditional name="track_file_style_conditional">\n+ <param name="track_file_style_selector" value="hic_matrix_option" />\n+ <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.h5"/>\n+ <param name="title" value="depth = 300000; transform = log1p; min_value = 5 (next track: overlay_previous = share-y links_type = loops)" />\n+ <param name="depth" value="300000" />\n+ <param name="transform" value="log1p" />\n+ <param name="min_value" value="5" />\n+ <param name="show_masked_bins" value="false" />\n+ </conditional>\n+ </repeat>\n+ <repeat name="tracks">\n+ <conditional name="track_file_style_conditional">\n+ <param name="track_file_style_selector" value="link_track_option" />\n+ <param name="track_input_link" value="test_wide.arcs" ftype="bed" />\n+ <conditional name="color_link">\n+ <param name="color" value="red" />\n+ </conditional>\n+ <param name="line_width" value="5" />\n+ <param name="links_type" value="loops" />\n+ <param name="overlay_select" value="share-y" />\n+ </conditional>\n+ </repeat>\n+ <repeat name="tracks">\n+ <conditional name="track_file_style_conditional">\n+ <param name="track_file_style_selector" value="link_track_option" />\n+ <param name="track_input_link" value="test_wide.arcs" ftype="bed" />\n+ <conditional name="color_link">\n+ <param name="color" value="RdYlGn" />\n+ </conditional>\n+ <param name="line_width" value="3" />\n+ <param name="invert_orientation" value="true" />\n+ <param name="use_middle" value="true" />\n+ <param name="title" value="links line_width = 3 color RdYlGn use_middle = true" />\n+ </conditional>\n+ </repeat>\n+ <repeat name="tracks">\n+ <conditional name="track_file_style_conditional">\n+ <param name="track_file_style_selector" value="vlines_track_option" />\n+ <param name="track_input_bed_single" value="tad_classification.bed" ftype="bed" />\n+ <param name="line_width" value="3" />\n+ </conditional>\n+ </repeat>\n+ <param name="image_file_format" value="png" />\n+ <output name="outFileName" file="test_arcs_use_middle.png" ftype="png" compare="sim_size" delta="35000" />\n+ </test>\n </tests>\n <help><![CDATA[\n \n' |
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| diff -r 326a3db8d9d1 -r 4ac4e7083b7e test-data/GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz |
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| Binary file test-data/GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz has changed |
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| diff -r 326a3db8d9d1 -r 4ac4e7083b7e test-data/bedgraph2_X_2.5e6_3.5e6.bdg --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bedgraph2_X_2.5e6_3.5e6.bdg Tue Jul 21 03:32:48 2020 -0400 |
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| diff -r 326a3db8d9d1 -r 4ac4e7083b7e test-data/compare_images.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/compare_images.py Tue Jul 21 03:32:48 2020 -0400 |
| [ |
| @@ -0,0 +1,12 @@ +import os + +from matplotlib.testing.compare import compare_images + +pngs = [f for f in os.listdir('test-data') if f.endswith('.png')] + +for png in pngs: + print(png) + res = compare_images(os.path.join('test-data', png), + os.path.join('outputs', png), + 17) + print(res) |
| b |
| diff -r 326a3db8d9d1 -r 4ac4e7083b7e test-data/compare_images.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/compare_images.sh Tue Jul 21 03:32:48 2020 -0400 |
| b |
| @@ -0,0 +1,5 @@ +. <(planemo conda_env pyGenomeTracks.xml) +# After +# planemo t --no_cleanup --galaxy_python_version 3.8 --galaxy_root $galaxyF --job_output_files outputs +python test-data/compare_images.py +conda_env_deactivate |
| b |
| diff -r 326a3db8d9d1 -r 4ac4e7083b7e test-data/master_TADs_plot.png |
| b |
| Binary file test-data/master_TADs_plot.png has changed |
| b |
| diff -r 326a3db8d9d1 -r 4ac4e7083b7e test-data/test17.ini --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test17.ini Tue Jul 21 03:32:48 2020 -0400 |
| [ |
| @@ -0,0 +1,67 @@ +[test bedgraph] +file = GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz +color = blue +height = 5 +title = bedgraph color = blue transform = no +transform = no + +[test bedgraph] +file = GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz +color = blue +height = 5 +title = bedgraph color = blue transform = log +transform = log + +[test bedgraph] +file = GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz +color = red +height = 5 +title = bedgraph color = red transform = log min_value = 1 +min_value = 1 +transform = log + +[test bedgraph] +file = GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz +color = green +height = 5 +title = bedgraph color = green transform = log log_pseudocount = 2 min_value = 0 +transform = log +log_pseudocount = 2 +min_value = 0 + +[test bedgraph with operation] +file = GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz +color = green +height = 5 +title = bedgraph color = green operation = log(2+file) min_value = 0.7 +operation = log(2+file) +min_value = 0.7 + +[test bedgraph] +file = GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz +color = black +height = 5 +title = bedgraph color = black transform = log2 log_pseudocount = 1 min_value = 0 +transform = log2 +log_pseudocount = 1 +min_value = 0 + +[test bedgraph] +file = GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz +color = black +height = 5 +title = bedgraph color = black operation = log2(1+file) min_value = 0 +operation = log2(1+file) +min_value = 0 + +[test bedgraph] +file = GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz +color = black +height = 5 +title = bedgraph color = black transform = log2 log_pseudocount = 1 min_value = 0 y_axis_values = original +transform = log2 +log_pseudocount = 1 +min_value = 0 +y_axis_values = original + +[x-axis] \ No newline at end of file |
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| diff -r 326a3db8d9d1 -r 4ac4e7083b7e test-data/test18.ini --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test18.ini Tue Jul 21 03:32:48 2020 -0400 |
| [ |
| @@ -0,0 +1,47 @@ +[x-axis] +where = top + +[test file] +file = bedgraph_chrx_2e6_5e6.bg +color = blue +height = 4 +title = file summary_method = mean number_of_bins=20 +summary_method = mean +number_of_bins=20 +min_value = 0 +max_value = 30 + +[test file] +file = bedgraph2_X_2.5e6_3.5e6.bdg +color = red +height = 4 +title = second_file summary_method = mean +summary_method = mean +min_value = 0 +max_value = 30 + + +[spacer] +height = 0.5 + +[test op0] +file = bedgraph_chrx_2e6_5e6.bg +color = blue +height = 4 +title = operation = log1p(file) (no summary_method) +operation = log1p(file) + + +[spacer] +height = 0.5 + +[test op1] +file = bedgraph_chrx_2e6_5e6.bg +second_file = bedgraph2_X_2.5e6_3.5e6.bdg +color = blue +negative_color = red +height = 8 +title = operation = file - second_file +operation = file - second_file +min_value = -30 +max_value = 30 |
| b |
| diff -r 326a3db8d9d1 -r 4ac4e7083b7e test-data/test19.ini --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test19.ini Tue Jul 21 03:32:48 2020 -0400 |
| [ |
| @@ -0,0 +1,75 @@ +[test bedgraph] +file = GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz +color = blue +height = 5 +title = bedgraph color = blue transform = no +transform = no +grid = true + +[test bedgraph] +file = GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz +color = blue +height = 5 +title = bedgraph color = blue transform = log +transform = log +grid = true + +[test bedgraph] +file = GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz +color = red +height = 5 +title = bedgraph color = red transform = log min_value = 1 +min_value = 1 +transform = log +grid = true + +[test bedgraph] +file = GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz +color = green +height = 5 +title = bedgraph color = green transform = log log_pseudocount = 2 min_value = 0 +transform = log +log_pseudocount = 2 +min_value = 0 +grid = true + +[test bedgraph with operation] +file = GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz +color = green +height = 5 +title = bedgraph color = green operation = log(2+file) min_value = 0.7 +operation = log(2+file) +min_value = 0.7 +grid = true + +[test bedgraph] +file = GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz +color = black +height = 5 +title = bedgraph color = black transform = log2 log_pseudocount = 1 min_value = 0 +transform = log2 +log_pseudocount = 1 +min_value = 0 +grid = true + +[test bedgraph] +file = GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz +color = black +height = 5 +title = bedgraph color = black operation = log2(1+file) min_value = 0 +operation = log2(1+file) +min_value = 0 +grid = true + +[test bedgraph] +file = GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz +color = black +height = 5 +title = bedgraph color = black transform = log2 log_pseudocount = 1 min_value = 0 y_axis_values = original +transform = log2 +log_pseudocount = 1 +min_value = 0 +y_axis_values = original +grid = true + +[x-axis] \ No newline at end of file |
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| diff -r 326a3db8d9d1 -r 4ac4e7083b7e test-data/test20.ini --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test20.ini Tue Jul 21 03:32:48 2020 -0400 |
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| @@ -0,0 +1,61 @@ +[x-axis] +where = top + +[spacer] +height = 0.05 +[hic matrix] +file = Li_et_al_2015.h5 +title = depth = 300000; transform = log1p; min_value = 5 (next track: overlay_previous = share-y links_type = loops) +depth = 300000 +min_value = 5 +transform = log1p +file_type = hic_matrix +show_masked_bins = false + +[test arcs overlay] +file = test_wide.arcs +color = red +line_width = 5 +links_type = loops +overlay_previous = share-y + +[test arcs] +file = test_wide.arcs +line_width = 3 +color = RdYlGn +title = links line_width = 3 color RdYlGn +height = 3 +orientation = inverted + +[spacer] +height = 1 + +[hic matrix] +file = Li_et_al_2015.h5 +title = depth = 300000; transform = log1p; min_value = 5 (next track: overlay_previous = share-y links_type = loops) +depth = 300000 +min_value = 5 +transform = log1p +file_type = hic_matrix +show_masked_bins = false + +[test arcs overlay] +file = test_wide.arcs +color = red +line_width = 5 +links_type = loops +overlay_previous = share-y + +[test arcs] +file = test_wide.arcs +line_width = 3 +color = RdYlGn +title = links line_width = 3 color RdYlGn use_middle = true +use_middle = true +height = 3 +orientation = inverted + +[vlines] +file = tad_classification.bed +type = vlines +line_width = 3 |
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| diff -r 326a3db8d9d1 -r 4ac4e7083b7e test-data/test_alpha_dec.png |
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| diff -r 326a3db8d9d1 -r 4ac4e7083b7e test-data/test_arcs_use_middle.png |
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| diff -r 326a3db8d9d1 -r 4ac4e7083b7e test-data/test_log.png |
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| diff -r 326a3db8d9d1 -r 4ac4e7083b7e test-data/test_operation.png |
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| diff -r 326a3db8d9d1 -r 4ac4e7083b7e test-data/test_wide.arcs --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_wide.arcs Tue Jul 21 03:32:48 2020 -0400 |
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| @@ -0,0 +1,3 @@ +chrX 3000000 3005000 chrX 3010000 3018000 1 +chrX 3030000 3032000 chrX 3080000 3090000 0.5 +chrX 3030000 3040000 chrX 3200000 3280000 2 |
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| diff -r 326a3db8d9d1 -r 4ac4e7083b7e test-data/testpyGT.sh --- a/test-data/testpyGT.sh Fri Apr 17 11:57:44 2020 -0400 +++ b/test-data/testpyGT.sh Tue Jul 21 03:32:48 2020 -0400 |
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| @@ -1,18 +1,23 @@ . <(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/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 conda_env_deactivate |
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| diff -r 326a3db8d9d1 -r 4ac4e7083b7e test.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test.bed Tue Jul 21 03:32:48 2020 -0400 |
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| @@ -0,0 +1,1 @@ +X 3000000 3500000 |
