| Previous changeset 8:4ac4e7083b7e (2020-07-21) Next changeset 10:a1abfa420d9d (2022-02-13) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" |
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modified:
macros.xml pyGenomeTracks.xml test-data/bigwig_multiple.png test-data/master_TADs_BW_plot.png test-data/master_TADs_plot.png test-data/test_TADs_bdgm.png test-data/test_alpha.png test-data/test_alpha_dec.png test-data/test_arcs_use_middle.png test-data/test_arrowhead_zoom.png test-data/test_gtf_bed4.png test-data/test_gtf_flybase_param.png test-data/test_link.png test-data/test_link2.png test-data/test_log.png test-data/test_log_grid.png test-data/test_middle_triangle.png test-data/test_narrowPeak.png test-data/test_operation.png test-data/test_scale_bar.png test-data/test_tssarrow.png test-data/test_ucsc_param.png test-data/testpyGT.sh |
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added:
test-data/master_scale_bar_startend.png test-data/test21.ini |
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removed:
test.bed |
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| diff -r 4ac4e7083b7e -r 2824d77cd8f8 macros.xml --- a/macros.xml Tue Jul 21 03:32:48 2020 -0400 +++ b/macros.xml Wed Nov 18 21:33:46 2020 +0000 |
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| @@ -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> |
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| diff -r 4ac4e7083b7e -r 2824d77cd8f8 pyGenomeTracks.xml --- a/pyGenomeTracks.xml Tue Jul 21 03:32:48 2020 -0400 +++ b/pyGenomeTracks.xml Wed Nov 18 21:33:46 2020 +0000 |
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| b'@@ -21,11 +21,17 @@\n sed \'/^$/d\' \'$tracks_config\' &&\n @BINARY@\n --tracks \'$tracks_config\'\n- #if $region and $region is not None:\n- --region \'$region\'\n+ --region \'$region\'\n+ #if $global_args.title != \'\':\n+ --title \'$global_args.title\'\n #end if\n- #if $global_args.title is not None:\n- --title \'$global_args.title\'\n+ #if $global_args.plotWidth != \'\':\n+ --plotWidth $global_args.plotWidth\n+ #else:\n+ --width $global_args.width\n+ #end if\n+ #if $global_args.height != \'\':\n+ --height \'$global_args.height\'\n #end if\n --fontSize $global_args.fontsize\n --dpi $global_args.dpi\n@@ -557,11 +563,17 @@\n #end if\n alpha = $track.track_file_style_conditional.alpha\n line_width = $track.track_file_style_conditional.line_width\n- #if $track.track_file_style_conditional.x_center != "":\n-x_center = $track.track_file_style_conditional.x_center\n+ #if $track.track_file_style_conditional.scalebar_pos.x_center != "":\n+x_center = $track.track_file_style_conditional.scalebar_pos.x_center\n+ #end if\n+ #if $track.track_file_style_conditional.scalebar_pos.size != "":\n+size = $track.track_file_style_conditional.scalebar_pos.size\n #end if\n- #if $track.track_file_style_conditional.size != "":\n-size = $track.track_file_style_conditional.size\n+ #if $track.track_file_style_conditional.scalebar_pos.scalebar_start_position != "":\n+scalebar_start_position = $track.track_file_style_conditional.scalebar_pos.scalebar_start_position\n+ #end if\n+ #if $track.track_file_style_conditional.scalebar_pos.scalebar_end_position != "":\n+scalebar_end_position = $track.track_file_style_conditional.scalebar_pos.scalebar_end_position\n #end if\n where = $track.track_file_style_conditional.sb_where\n #if $track.track_file_style_conditional.fontsize != "":\n@@ -580,12 +592,19 @@\n <inputs>\n <!--Arguments for pgt-->\n <param argument="--region" type="text" label="Region of the genome to limit the operation" optional="false"\n- help="The format is chr:start-end. Also valid is just to specify a chromosome, for example chr10:10-500" />\n+ help="The format is chr:start-end, for example chr10:10-500">\n+ <validator type="expression" message="Region should be like chr10:10-500">\'^[a-zA-Z0-9_]:\\d+-\\d+$\'</validator>\n+ </param>\n <section name="global_args" title="Configure figure parameters" expanded="False">\n <param argument="--title" type="text" label="Plot title" help="If set, you may need to start by a spacer track"/> \n <param argument="--fontsize" type="integer" label="Font size for the labels of the plot" value="12"/>\n <param argument="--dpi" type="integer" label="Resolution (dpi)" value="72"\n help="Resolution for the image in case the ouput is a raster graphics image (e.g png, jpg)"/>\n+ <param argument="--width" type="float" label="Figure width in cm" value="40"/>\n+ <param argument="--plotWidth" type="float" label="Width in centimeters of the plotting (central) part" optional="true"\n+ help="This will overwrite what has been defined as a figure width."/>\n+ <param argument="--height" type="float" label="Figure height in centimeters" optional="true"\n+ 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."/>\n <param argument="--trackLabelFraction" type="float" label="Proportion of space dedicated to track labels" value="0.05"\n min="0" max="1"/> \n <param argument="--trackLabelHAlign" type="select" label="Horizontal alignment of track labels">\n@@ -964,10 +983,14 @@\n '..b' </repeat>\n+ <param name="image_file_format" value="png" />\n+ <output name="outFileName" file="master_scale_bar_startend.png" ftype="png" compare="sim_size" delta="100" />\n </test>\n </tests>\n <help><![CDATA[\n@@ -2619,10 +2725,12 @@\n Currently, it is possible to plot:\n \n - bigwig\n- - bed (many options)\n+ - bed/gtf (many options)\n - bedgraph\n- - links (represented as arcs)\n- - Hi-C matrices\n+ - epilogos\n+ - narrow peaks\n+ - links\n+ - Hi-C matrices (cool or HiCExplorer h5)\n \n _________________\n \n@@ -2631,17 +2739,21 @@\n \n This tool takes various types of tracks as input:\n \n+ - **Hi-C tracks:**\n+ - **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.\n+ - **TAD score:** display TAD seperation score computed by HiCExplorer\'s ``hicFindTADs``.\n - **Chromatin states:** display blocks of different colors following a bed file.\n- - **Gene track / Bed Track:** display genes or bed files. Labels like gene names can be toggled on or off.\n+ - **Gene track / Bed Track:** display genes or annotations in bed/gtf files. Labels like gene names can be toggled on or off.\n+ - **Link track:** display links (pair of coordinates) as arcs, triangles or loops.\n+ - **NarrowPeak track:** display narrowPeak (encode format) as boxes or as curve (reconstructed peak).\n - **Bigwig track:** generic bigwig track plotting.\n - **Bedgraph track:** generic bedgraph track plotting.\n - **Bedgraph matrix track** is used to specifically plot bm files computed by HiCExplorer\'s ``hicFindTADs`` (TAD seperation scores).\n - **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``.\n+ - **Hlines:** horizontal lines drawn either by themselves or on top of other tracks.\n - **Spacer:** Add some space between two tracks.\n- - **Hi-C tracks:**\n- - **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.\n- - **TAD score:** display TAD seperation score computed by HiCExplorer\'s ``hicFindTADs``.\n-\n+ - **X-axis:** Plot x-axis scale wherever you want.\n+ - **Scale bar track:** Plot scale bar.\n \n For each track, parameters for the color, the width or the font size can be defined.\n \n@@ -2651,7 +2763,7 @@\n ------\n \n **pyGenomeTracks** output is similar to a genome browser screen-shot that besides the usual genes, and score data (like bigwig or bedgraph files)\n-also contains Hi-C data. The plot is composed of tracks that need to be specified.\n+may also contains Hi-C data. The plot is composed of tracks that need to be specified.\n Below is represented the 85 Mb to 110 Mb region from human chromosome 2 visualized using **pyGenomeTracks**.\n TADs were computed by HiCExplorer\'s ``hicFindTADs``. The additional tracks added correspond to:\n TAD-separation score (as reported by HiCExplorer\'s ``hicFindTADs``), chromatin states,\n@@ -2663,8 +2775,9 @@\n \n _________________\n \n-| For more information about pyGenomeTracks please consider our documentation on github_\n+| For more information about pyGenomeTracks please consider our documentation on readthedocs_ or github_\n \n+.. _readthedocs: https://pygenometracks.readthedocs.io\n .. _github: https://github.com/deeptools/pyGenomeTracks\n .. _`Nothjunge et al. (2017)`: https://www.nature.com/articles/s41467-017-01724-9\n ]]></help>\n' |
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| diff -r 4ac4e7083b7e -r 2824d77cd8f8 test-data/test21.ini --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test21.ini Wed Nov 18 21:33:46 2020 +0000 |
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| @@ -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] |
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| diff -r 4ac4e7083b7e -r 2824d77cd8f8 test-data/testpyGT.sh --- 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 |
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| @@ -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 |
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| diff -r 4ac4e7083b7e -r 2824d77cd8f8 test.bed --- a/test.bed Tue Jul 21 03:32:48 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,1 +0,0 @@ -X 3000000 3500000 |
