| Previous changeset 4:c237ba772225 (2019-09-19) Next changeset 6:5cec5fb749f0 (2020-02-11) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" |
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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_alpha.png test-data/test_gtf_bed4.png test-data/test_narrowPeak.png |
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added:
test-data/test.arcs test-data/test1.ini test-data/test10.ini test-data/test11.ini test-data/test12.ini test-data/test2.ini test-data/test3.ini test-data/test4.ini test-data/test5.ini test-data/test6.ini test-data/test7.ini test-data/test8.ini test-data/test9.ini test-data/test_TADs_bdgm.png test-data/test_arrowhead_zoom.png test-data/test_gtf_flybase_param.png test-data/test_link.png test-data/test_middle_triangle.png test-data/test_ucsc_param.png test-data/testpyGT.sh |
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| diff -r c237ba772225 -r eca03db4f612 macros.xml --- a/macros.xml Thu Sep 19 17:18:54 2019 -0400 +++ b/macros.xml Wed Jan 08 09:15:19 2020 -0500 |
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| b'@@ -1,10 +1,9 @@\n <macros>\n <token name="@THREADS@">\\${GALAXY_SLOTS:-4}</token>\n- <token name="@WRAPPER_VERSION@">3.1.1</token>\n+ <token name="@WRAPPER_VERSION@">3.2.1</token>\n <xml name="requirements">\n <requirements>\n <requirement type="package" version="@WRAPPER_VERSION@">pygenometracks</requirement>\n- <!--<requirement type="package" version="3.7">python</requirement>-->\n <yield />\n </requirements>\n <version_command><![CDATA[@BINARY@ --version | tail -n 1 ]]></version_command>\n@@ -165,8 +164,8 @@\n help="The format is chr:start-end. Also valid is just to specify a chromosome, for example chr10:10-500" />\n </xml>\n \n- <xml name=\'matrix_h5_cooler_multiple_macro\'>\n- <param name=\'matrix_h5_cooler_multiple\' type="data" format="h5,cool"\n+ <xml name="matrix_h5_cooler_multiple_macro">\n+ <param name="matrix_h5_cooler_multiple" type="data" format="h5,cool"\n label="Matricies to compute on" multiple="true"/>\n </xml>\n <token name="@REFERENCES@">\n@@ -187,35 +186,38 @@\n </token>\n \n <xml name="track_input_bed_macro">\n- <param name="track_input_bed" type="data" format="bed" label="Track file bed format" multiple=\'True\'/>\n+ <param name="track_input_bed" type="data" format="bed" label="Track file bed format" multiple="True"/>\n </xml>\n <xml name="track_input_bed_gtf_macro">\n- <param name="track_input_bed" type="data" format="bed,gtf" label="Track file bed or gtf format" multiple=\'True\'/>\n+ <param name="track_input_bed" type="data" format="bed,gtf" label="Track file bed or gtf format" multiple="True"/>\n </xml>\n <xml name="track_input_narrow_peak_macro">\n- <param name="track_input_narrow_peak" type="data" format="encodepeak,bed" label="Track file encodepeak or format" multiple=\'True\'/>\n+ <param name="track_input_narrow_peak" type="data" format="encodepeak,bed" label="Track file encodepeak or format" multiple="True"/>\n </xml>\n <xml name="track_input_bed_single_macro">\n <param name="track_input_bed_single" type="data" format="bed" label="Track file bed format"/>\n </xml>\n <xml name="track_input_bedgraph_macro">\n- <param name="track_input_bedgraph" type="data" format="bedgraph" label="Track file bedgraph format" multiple=\'True\'/>\n+ <param name="track_input_bedgraph" type="data" format="bedgraph" label="Track file bedgraph format" multiple="True"/>\n </xml>\n <xml name="track_input_bigwig_macro">\n- <param name="track_input_bigwig" type="data" format="bigwig" label="Track file bigwig format" multiple=\'True\'/>\n+ <param name="track_input_bigwig" type="data" format="bigwig" label="Track file bigwig format" multiple="True"/>\n </xml>\n <xml name="track_input_bedgraph_matrix_macro">\n- <param name="track_input_bedgraph_matrix" type="data" format="bedgraph" label="Track file bigwig format" multiple=\'True\'/>\n+ <param name="track_input_bedgraph_matrix" type="data" format="bedgraph" label="Track file bigwig format" multiple="True"/>\n+ </xml>\n+ <xml name="track_input_link_macro">\n+ <param name="track_input_link" type="data" format="bed,interval" label="Track file for links" multiple="False"/>\n </xml>\n <xml name="plot_title">\n- <param name="title" type="text" optional="true" label="Plot title" multiple=\'True\'/>\n+ <param name="title" type="text" optional="true" label="Plot title" multiple="True"/>\n </xml>\n <xml name="spacer_macro">\n <param name="spacer_height" type="float" value="" optional="True"\n label="Include spacer at the end of the track" help="Height of the spacer." />\n </xml>\n <xml name="inverted_macro">\n- <param name="invert_orientation" type="boolean" truevalue="yes" falsevalue="no" checked="false"\n+ <param name="invert_orientation" type="boolean" truevalue="true" falsevalue="false" checked="false"\n '..b'="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" selected="True">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+ </param>\n+ </when>\n+ </conditional>\n+ </xml>\n </macros>\n' |
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| diff -r c237ba772225 -r eca03db4f612 pyGenomeTracks.xml --- a/pyGenomeTracks.xml Thu Sep 19 17:18:54 2019 -0400 +++ b/pyGenomeTracks.xml Wed Jan 08 09:15:19 2020 -0500 |
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| b'@@ -1,4 +1,4 @@\n-<tool id="pygenomeTracks" name="@BINARY@" version="@WRAPPER_VERSION@.1">\n+<tool id="pygenomeTracks" name="@BINARY@" version="@WRAPPER_VERSION@">\n <description>plot genomic data tracks</description>\n <macros>\n <token name="@BINARY@">pyGenomeTracks</token>\n@@ -7,6 +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 #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@@ -35,426 +36,449 @@\n </command>\n <configfiles>\n <configfile name="tracks_config">\n-#if $x_axis.x_axis_select == "yes":\n-#if $x_axis.where == \'top\':\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+ #if $x_axis.fontsize:\n fontsize = $x_axis.fontsize\n-#end if\n-#if $x_axis.where:\n-where = $x_axis.where\n+ #end if\n+where = top\n+ #end if\n #end if\n-#end if\n-#end if\n+\n+## Then each track:\n #for $counter, $track in enumerate($tracks):\n-#if $track.track_file_style_conditional.track_file_style_selector == "hic_matrix_option":\n-\n-#for $counter_matrix, $data_matrix in enumerate($track.track_file_style_conditional.matrix_h5_cooler_multiple):\n+ ## Hi-C Track\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 [hic_section_${counter}_${counter_matrix}]\n-#set ext = $data_matrix.extension\n+ #set ext = $data_matrix.extension\n file = ${counter}_${counter_matrix}.$ext\n file_type = hic_matrix\n-#if $track.track_file_style_conditional.title:\n+ #if $track.track_file_style_conditional.title:\n title = $track.track_file_style_conditional.title\n-#else:\n+ #else:\n title = $data_matrix.name\n-#end if\n-#if $track.track_file_style_conditional.depth:\n+ #end if\n+ #if $track.track_file_style_conditional.depth:\n depth = $track.track_file_style_conditional.depth\n-#end if\n-#if $track.track_file_style_conditional.colormap:\n+ #end if\n+ #if $track.track_file_style_conditional.colormap:\n colormap = $track.track_file_style_conditional.colormap\n-#end if\n-#if $track.track_file_style_conditional.min_value:\n+ #end if\n+ #if $track.track_file_style_conditional.min_value:\n min_value = $track.track_file_style_conditional.min_value\n-#end if\n-#if $track.track_file_style_conditional.max_value:\n+ #end if\n+ #if $track.track_file_style_conditional.max_value:\n max_value = $track.track_file_style_conditional.max_value\n-#end if\n-#if $track.track_file_style_conditional.transform != "":\n+ #end if\n transform = $track.track_file_style_conditional.transform\n-#end if\n-#if $track.track_file_style_conditional.height_matrix != "":\n+ #if $track.track_file_style_conditional.height_matrix != "":\n height = $track.track_file_style_conditional.height_matrix\n-#end if\n-\n-#if $track.track_file_style_conditional.show_masked_bins:\n+ #end if\n+ #if $track.track_file_style_conditional.show_masked_bins:\n show_masked_bins = $track.track_file_style_conditional.show_masked_bins\n-#end if\n-#if $track.track_file_style_conditional.invert_orientation:\n+ #end if\n+ #if $track.track_file_style_conditional.invert_orientation:\n orientation = inverted\n-#end if\n-#if $track.track_file_style_conditional.scale_factor:\n-scale factor = $track.track_file_style_conditional.scale_factor\n-#end if\n-\n-#if str($track.track_file_style_conditional.boundaries_file) != "None":\n-#if len($track.track_file_style_conditional.boundaries_file)>$counter_matrix:\n-#set boundary_file = $track.track_file_style_conditional.boundaries_file[$counter_matrix]\n-#els'..b' <param name="title" value="TAD separation score (Ramirez et al.)" />\n+ <param name="height_bedgraph" value="10" />\n+ <param name="type_lines" value="lines" />\n+ <param name="pos_score_in_bin" value="block" />\n+ <param name="plot_horizontal_lines" value="true" />\n+ <param name="show_data" value="true" />\n+ </conditional>\n+ </repeat>\n+ <repeat name="tracks">\n+ <conditional name="track_file_style_conditional">\n+ <param name="track_file_style_selector" value="bedgraph_matrix_track_option" />\n+ <param name="track_input_bedgraph_matrix" value="tad_score.gz" ftype="bedgraph" />\n+ <param name="title" value="TAD separation score (Ramirez et al.)" />\n+ <param name="height_bedgraph" value="10" />\n+ <param name="type_lines" value="lines" />\n+ <param name="pos_score_in_bin" value="center" />\n+ <param name="plot_horizontal_lines" value="false" />\n+ </conditional>\n+ </repeat>\n+ <param name="image_file_format" value="png" />\n+ <output name="outFileName" file="test_TADs_bdgm.png" ftype="png" compare="sim_size" delta="35000" />\n+ </test>\n+ <test>\n+ <param name="region" value="chrX:3000000-3300000"/>\n+ <conditional name="x_axis">\n+ <param name="x_axis_select" value="true" />\n+ </conditional>\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="Kc DpnII (Li et al. 2015)" />\n+ <param name="colormap" value="Purples" />\n+ <param name="depth" value="190000" />\n+ <param name="transform" value="no" />\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.arcs" ftype="bed" />\n+ <param name="title" value="" />\n+ <param name="line_width" value="10" />\n+ <param name="links_type" value="loops" />\n+ <conditional name="color_link">\n+ <param name="color_link_select" value="manually" />\n+ <param name="color" value="red" />\n+ </conditional>\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.arcs" ftype="bed" />\n+ <param name="title" value="" />\n+ <param name="height" value="5" />\n+ <conditional name="color_link">\n+ <param name="color_link_select" value="colormap" />\n+ <param name="color" value="hot" />\n+ </conditional>\n+ <param name="max_value" value="5"/>\n+ <param name="invert_orientation" value="true" />\n+ </conditional>\n+ </repeat>\n+ <param name="image_file_format" value="png" />\n+ <output name="outFileName" file="test_link.png" ftype="png" compare="sim_size" delta="35000" />\n+ </test>\n </tests>\n <help><![CDATA[\n \n' |
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| diff -r c237ba772225 -r eca03db4f612 test-data/bigwig_multiple.png |
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| Binary file test-data/bigwig_multiple.png has changed |
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| diff -r c237ba772225 -r eca03db4f612 test-data/master_TADs_BW_plot.png |
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| diff -r c237ba772225 -r eca03db4f612 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 c237ba772225 -r eca03db4f612 test-data/test.arcs --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test.arcs Wed Jan 08 09:15:19 2020 -0500 |
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| @@ -0,0 +1,3 @@ +chrX 3000000 3000001 chrX 3010000 3010001 1 +chrX 3030000 3030001 chrX 3080000 3080001 0.5 +chrX 3030000 3030001 chrX 3200000 3200001 2 |
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| diff -r c237ba772225 -r eca03db4f612 test-data/test1.ini --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test1.ini Wed Jan 08 09:15:19 2020 -0500 |
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| @@ -0,0 +1,162 @@ +[x-axis] +where = top +[hic_section_0_0] +file = test-data/Li_et_al_2015.h5 +file_type = hic_matrix +title = Kc DpnII (Li et al. 2015) +depth = 200000 +colormap = RdYlBu_r +transform = log1p +scale_factor = 1.0 +rasterize = true +[tads_0_0] +file = test-data/domains.bed +file_type = domains +border_color = black +color = none +overlay_previous = share-y +[spacer] +height = 0.05 +[chrom states_2] +file = test-data/tad_classification.bed +title = TAD state +color = bed_rgb +border_color = #000000 +display = collapsed +height = 0.5 +line_width = 0.5 +file_type = bed +[bedgraph_matrix_3] +file = test-data/tad_score.gz +title = TAD separation score (Ramirez et al.) +height = 10.0 +file_type = bedgraph_matrix +show_data_range = false +plot_horizontal_lines = false +pos_score_in_bin = center +[spacer] +height = 1.0 +[bedgraph_5] +file = test-data/bedgraph_chrx_2e6_5e6.bg +title = bedgraph +color = blue +alpha = 1.0 +height = 4.0 +show_data_range = false +nans_to_zeros = false +use_middle = false +file_type = bedgraph +type = fill +overlay_previous = no +[bigwig_6] +file = test-data/bigwig_chrx_2e6_5e6.bw +title = rep 1 test fill +color = blue +alpha = 1.0 +height = 4.0 +summary_method = mean +nans_to_zeros = false +type = fill +show_data_range = false +file_type = bigwig +overlay_previous = no +[bigwig_7] +file = test-data/bigwig_chrx_2e6_5e6.bw +title = rep 1 test line +color = red +alpha = 1.0 +height = 4.0 +summary_method = mean +nans_to_zeros = false +type = line:1.0 +show_data_range = false +file_type = bigwig +overlay_previous = no +[bigwig_8] +file = test-data/bigwig_chrx_2e6_5e6.bw +title = rep 1 test lw=0.2 +color = red +alpha = 1.0 +height = 4.0 +summary_method = mean +nans_to_zeros = false +type = line:0.1 +show_data_range = false +file_type = bigwig +overlay_previous = no +[bigwig_9] +file = test-data/bigwig_chrx_2e6_5e6.bw +title = rep 1 test point:0.5 +color = black +alpha = 1.0 +height = 4.0 +summary_method = mean +nans_to_zeros = false +type = points:0.5 +show_data_range = false +file_type = bigwig +overlay_previous = no +[spacer] +height = 0.5 +[genes_11_0] +file = test-data/dm3_genes.bed.gz +title = genes +color = #000000 +border_color = #000000 +style = flybase +height_utr = 1.0 +color_utr = grey +display = stacked +height = 5.0 +labels = true +file_type = bed +fontsize = 10 +global_max_row = false +max_labels = 60 +line_width = 0.5 +arrowhead_included = false +overlay_previous = no +[spacer] +height = 1.0 +[genes_13_0] +file = test-data/dm3_genes.bed.gz +title = max num rows 3 +color = #000000 +border_color = #000000 +style = flybase +height_utr = 1.0 +color_utr = grey +display = stacked +height = 3.0 +labels = true +file_type = bed +fontsize = 8 +gene_rows = 3 +global_max_row = false +max_labels = 60 +line_width = 0.5 +arrowhead_included = false +overlay_previous = no +[spacer] +height = 1.0 +[genes_15_0] +file = test-data/dm3_genes.bed6.gz +title = bed6 global max row +color = #000000 +border_color = #000000 +style = flybase +height_utr = 1.0 +color_utr = grey +display = stacked +height = 20.0 +labels = true +file_type = bed +fontsize = 10 +global_max_row = true +max_labels = 60 +line_width = 0.5 +arrowhead_included = false +overlay_previous = no +[vlines_16] +file = test-data/domains.bed +type = vlines \ No newline at end of file |
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| diff -r c237ba772225 -r eca03db4f612 test-data/test10.ini --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test10.ini Wed Jan 08 09:15:19 2020 -0500 |
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| @@ -0,0 +1,45 @@ +[x-axis] +where = top +[genes_0_0] +file = test-data/domains.bed +title = domains.bed +color = yellow +border_color = #000000 +style = flybase +height_utr = 1.0 +color_utr = grey +display = triangles +height = 6.0 +labels = true +file_type = bed +global_max_row = false +max_labels = 60 +line_width = 0.5 +arrowhead_included = false +overlay_previous = no +[spacer] +height = 1.0 +[bedgraph_1] +file = test-data/bedgraph_chrx_2e6_5e6.bg +title = bedgraph +color = blue +alpha = 1.0 +height = 4.0 +show_data_range = false +nans_to_zeros = false +use_middle = false +file_type = bedgraph +type = line:0.5 +overlay_previous = no +[bedgraph_2] +file = test-data/bedgraph_chrx_2e6_5e6.bg +title = bedgraph +color = blue +alpha = 1.0 +height = 4.0 +show_data_range = false +nans_to_zeros = false +use_middle = true +file_type = bedgraph +type = line:0.5 +overlay_previous = no \ No newline at end of file |
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| diff -r c237ba772225 -r eca03db4f612 test-data/test11.ini --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test11.ini Wed Jan 08 09:15:19 2020 -0500 |
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| @@ -0,0 +1,32 @@ +[x-axis] +where = top +[hic_section_0_0] +file = test-data/Li_et_al_2015.h5 +file_type = hic_matrix +title = Kc DpnII (Li et al. 2015) +depth = 100000 +colormap = RdYlBu_r +transform = log1p +show_masked_bins = true +scale_factor = 2.0 +rasterize = true +[spacer] +height = 0.05 +[bedgraph_matrix_2] +file = test-data/tad_score.gz +title = TAD separation score (Ramirez et al.) +height = 10.0 +type = lines +file_type = bedgraph_matrix +show_data_range = true +plot_horizontal_lines = true +pos_score_in_bin = block +[bedgraph_matrix_3] +file = test-data/tad_score.gz +title = TAD separation score (Ramirez et al.) +height = 10.0 +type = lines +file_type = bedgraph_matrix +show_data_range = false +plot_horizontal_lines = false +pos_score_in_bin = center \ No newline at end of file |
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| diff -r c237ba772225 -r eca03db4f612 test-data/test12.ini --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test12.ini Wed Jan 08 09:15:19 2020 -0500 |
| [ |
| @@ -0,0 +1,34 @@ +[x-axis] +where = top +[hic_section_0_0] +file = Li_et_al_2015.h5 +file_type = hic_matrix +title = Kc DpnII (Li et al. 2015) +depth = 190000 +colormap = Purples +transform = no +scale_factor = 1.0 +rasterize = true +[links_1] +file = test.arcs +height = 1.5 +color = red +alpha = 1.0 +line_width = 10.0 +line_style = solid +links_type = loops +overlay_previous = share-y +file_type = links +[links_2] +file = test.arcs +title = test.arcs +height = 5.0 +max_value = 5.0 +color = hot +alpha = 1.0 +line_width = 0.5 +line_style = solid +links_type = arcs +orientation = inverted +overlay_previous = no +file_type = links \ No newline at end of file |
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| diff -r c237ba772225 -r eca03db4f612 test-data/test2.ini --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test2.ini Wed Jan 08 09:15:19 2020 -0500 |
| [ |
| @@ -0,0 +1,61 @@ +[x-axis] +where = top +[bigwig_0] +file = test-data/bigwig_chrx_2e6_5e6.bw +title = rep 1 test line +color = red +alpha = 1.0 +height = 4.0 +summary_method = mean +nans_to_zeros = false +type = line:1.0 +show_data_range = false +file_type = bigwig +overlay_previous = no +[bigwig_0] +file = test-data/bigwig_chrx_2e6_5e6.bw +title = rep 1 test line +color = red +alpha = 1.0 +height = 4.0 +summary_method = mean +nans_to_zeros = false +type = line:1.0 +show_data_range = false +file_type = bigwig +overlay_previous = no +[bigwig_1] +file = test-data/bigwig_chrx_2e6_5e6.bw +title = nans_to_zeros +color = blue +alpha = 1.0 +height = 4.0 +summary_method = mean +nans_to_zeros = true +type = line:1.0 +show_data_range = true +file_type = bigwig +overlay_previous = no +[hlines_2] +height = 1.5 +y_values = 50 +show_data_range = false +color = orange +alpha = 1.0 +line_width = 2.0 +line_style = dashed +overlay_previous = share-y +file_type = hlines +[hlines_3] +title = hlines +height = 1.5 +min_value = 12.0 +y_values = 0, 10, 20, 100 +show_data_range = true +color = purple +alpha = 1.0 +line_width = 0.5 +line_style = solid +orientation = inverted +overlay_previous = no +file_type = hlines \ No newline at end of file |
| b |
| diff -r c237ba772225 -r eca03db4f612 test-data/test3.ini --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test3.ini Wed Jan 08 09:15:19 2020 -0500 |
| [ |
| @@ -0,0 +1,167 @@ +[x-axis] +where = top +[hic_section_0_0] +file = test-data/Li_et_al_2015.h5 +file_type = hic_matrix +title = Kc DpnII (Li et al. 2015) log1p +depth = 200000 +colormap = RdYlBu_r +transform = log1p +scale_factor = 1.0 +rasterize = true +[tads_0_0] +file = test-data/domains.bed +file_type = domains +border_color = black +color = none +overlay_previous = share-y +[chrom states_1] +file = test-data/tad_classification.bed +title = TAD state +color = bed_rgb +border_color = #000000 +display = collapsed +height = 0.5 +line_width = 0.5 +file_type = bed +[hic_section_2_0] +file = test-data/Li_et_al_2015.h5 +file_type = hic_matrix +title = Kc DpnII (Li et al. 2015) inverted no transform +depth = 200000 +colormap = Reds +min_value = 5.0 +max_value = 70.0 +orientation = inverted +scale_factor = 1.0 +rasterize = true +[spacer] +height = 1.0 +[bedgraph_4] +file = test-data/test_with_neg_values.bg.gz +title = bedgraph with negative values +color = black +alpha = 1.0 +negative_color = red +height = 4.0 +show_data_range = false +nans_to_zeros = false +use_middle = false +file_type = bedgraph +type = fill +overlay_previous = no +[bedgraph_5] +file = test-data/bedgraph_chrx_2e6_5e6.bg +title = bedgraph +color = blue +alpha = 1.0 +height = 4.0 +show_data_range = false +nans_to_zeros = false +use_middle = false +file_type = bedgraph +type = fill +overlay_previous = no +[bigwig_6] +file = test-data/bigwig_chrx_2e6_5e6.bw +title = rep 1 test fill +color = blue +alpha = 1.0 +height = 4.0 +summary_method = mean +nans_to_zeros = false +type = fill +show_data_range = false +file_type = bigwig +overlay_previous = no +[bigwig_7] +file = test-data/bigwig_chrx_2e6_5e6.bw +title = (red points/width=5/max value/100 bins) overlayed with (dark red line/min value/30000 bins) overlayed with (black line/min value) +color = red +alpha = 1.0 +height = 10.0 +summary_method = max +nans_to_zeros = false +number_of_bins = 100 +type = points:5.0 +show_data_range = false +file_type = bigwig +overlay_previous = no +[bigwig_8] +file = test-data/bigwig_chrx_2e6_5e6.bw +color = #c00000 +alpha = 1.0 +height = 10.0 +summary_method = min +nans_to_zeros = false +type = line:0.5 +show_data_range = false +file_type = bigwig +overlay_previous = share-y +[bigwig_9] +file = test-data/bigwig_chrx_2e6_5e6.bw +color = black +alpha = 1.0 +height = 10.0 +summary_method = min +nans_to_zeros = false +number_of_bins = 30000 +type = line:0.5 +show_data_range = false +file_type = bigwig +overlay_previous = share-y +[spacer] +height = 1.0 +[genes_10_0] +file = test-data/dm3_genes.bed.gz +title = genes in ucsc +color = #000000 +border_color = #000000 +style = UCSC +arrow_interval = 2 +display = stacked +height = 5.0 +labels = true +file_type = bed +fontsize = 10 +global_max_row = false +max_labels = 60 +line_width = 0.5 +arrowhead_included = false +overlay_previous = no +[genes_11_0] +file = test-data/dm3_genes.bed6.gz +title = bed6 global max row color from score +color = RdYlBu_r +border_color = #000000 +style = flybase +height_utr = 1.0 +color_utr = grey +display = stacked +height = 20.0 +labels = true +file_type = bed +fontsize = 10 +global_max_row = true +max_labels = 60 +line_width = 0.5 +arrowhead_included = false +overlay_previous = no +[genes_12_0] +file = test-data/domains.bed +title = domains.bed using the 9th field for colors interleaved +color = bed_rgb +border_color = red +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 c237ba772225 -r eca03db4f612 test-data/test4.ini --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test4.ini Wed Jan 08 09:15:19 2020 -0500 |
| [ |
| @@ -0,0 +1,27 @@ +[bigwig_0] +file = test-data/bigwig_chrx_2e6_5e6.bw +title = (bigwig color=blue 2000 bins) overlayed with (bigwig mean color=red alpha = 0.5 max over 300 bins) +color = #00b0f0 +alpha = 1.0 +height = 7.0 +summary_method = mean +nans_to_zeros = false +number_of_bins = 2000 +type = fill +show_data_range = false +file_type = bigwig +overlay_previous = no +[bigwig_1] +file = test-data/bigwig_chrx_2e6_5e6.bw +color = #ff0000 +alpha = 0.5 +height = 1.5 +summary_method = mean +nans_to_zeros = false +number_of_bins = 300 +type = fill +show_data_range = false +file_type = bigwig +overlay_previous = share-y +[x-axis] +where = bottom \ No newline at end of file |
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| diff -r c237ba772225 -r eca03db4f612 test-data/test5.ini --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test5.ini Wed Jan 08 09:15:19 2020 -0500 |
| [ |
| @@ -0,0 +1,40 @@ +[x-axis] +where = top +[genes_0_0] +file = dm3_subset_BDGP5.78.gtf.gz +prefered_name = transcript_name +merge_transcripts = false +title = test +color = #000000 +border_color = #000000 +style = UCSC +arrow_interval = 2 +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 +[spacer] +height = 1.0 +[genes_1_0] +file = dm3_subset_BDGP5.78_asbed4.bed.gz +title = test +color = #000000 +border_color = #000000 +style = UCSC +arrow_interval = 2 +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 +[spacer] +height = 1.0 \ No newline at end of file |
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| diff -r c237ba772225 -r eca03db4f612 test-data/test6.ini --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test6.ini Wed Jan 08 09:15:19 2020 -0500 |
| [ |
| @@ -0,0 +1,39 @@ +[narrow_peak_0_0] +file = test-data/test2.narrowPeak +title = box +color = #9bbb59 +type = box +use_summit = true +height = 4.0 +show_labels = true +file_type = narrow_peak +overlay_previous = no +[narrow_peak_1_0] +file = test-data/test2.narrowPeak +title = peak width 3 +color = #c0504d +type = peak +use_summit = true +show_data_range = true +width_adjust = 3.0 +max_value = 50.0 +height = 4.0 +show_labels = false +file_type = narrow_peak +overlay_previous = no +[spacer] +height = 0.5 +[narrow_peak_2_0] +file = test-data/test2.narrowPeak +title = peak no data range +color = #000000 +type = peak +use_summit = false +show_data_range = false +width_adjust = 1.5 +height = 4.0 +show_labels = true +file_type = narrow_peak +overlay_previous = no +[x-axis] +where = bottom \ No newline at end of file |
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| diff -r c237ba772225 -r eca03db4f612 test-data/test7.ini --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test7.ini Wed Jan 08 09:15:19 2020 -0500 |
| [ |
| @@ -0,0 +1,38 @@ +[x-axis] +where = top +[genes_0_0] +file = test-data/dm3_genes.bed.gz +title = genes +color = #000000 +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_1_0] +file = test-data/dm3_subset_BDGP5.78.gtf.gz +prefered_name = gene_name +merge_transcripts = true +title = gtf +color = #000000 +border_color = #000000 +style = flybase +height_utr = 0.75 +color_utr = #ff0000 +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 \ No newline at end of file |
| b |
| diff -r c237ba772225 -r eca03db4f612 test-data/test8.ini --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test8.ini Wed Jan 08 09:15:19 2020 -0500 |
| [ |
| @@ -0,0 +1,34 @@ +[x-axis] +where = top +[genes_0_0] +file = test-data/dm3_genes.bed.gz +title = dm3_genes.bed +color = #000000 +border_color = #000000 +style = UCSC +arrow_interval = 2 +display = stacked +height = 10.0 +labels = true +file_type = bed +global_max_row = true +max_labels = 15 +line_width = 0.5 +arrowhead_included = false +overlay_previous = no +[genes_1_0] +file = test-data/dm3_genes.bed.gz +title = genes.bed.gz +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 = 2.0 +arrowhead_included = false +overlay_previous = no \ No newline at end of file |
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| diff -r c237ba772225 -r eca03db4f612 test-data/test9.ini --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test9.ini Wed Jan 08 09:15:19 2020 -0500 |
| [ |
| @@ -0,0 +1,65 @@ +[x-axis] +where = top +[genes_0_0] +file = dm3_subset_BDGP5.78.gtf.gz +prefered_name = transcript_name +merge_transcripts = false +title = test +color = #000000 +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 +[spacer] +height = 1.0 +[genes_1_0] +file = dm3_subset_BDGP5.78_asbed4.bed.gz +title = test +color = red +border_color = #000000 +style = UCSC +arrow_interval = 2 +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 +[spacer] +height = 1.0 +[genes_2_0] +file = dm3_subset_BDGP5.78.gtf.gz +prefered_name = transcript_name +merge_transcripts = false +title = test +color = red +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 = true +overlay_previous = no +[spacer] +height = 1.0 +[vlines_3] +file = dm3_subset_BDGP5.78_asbed4.bed.gz +type = vlines \ No newline at end of file |
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| diff -r c237ba772225 -r eca03db4f612 test-data/test_TADs_bdgm.png |
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| diff -r c237ba772225 -r eca03db4f612 test-data/test_alpha.png |
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| diff -r c237ba772225 -r eca03db4f612 test-data/test_arrowhead_zoom.png |
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| diff -r c237ba772225 -r eca03db4f612 test-data/test_link.png |
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| diff -r c237ba772225 -r eca03db4f612 test-data/test_middle_triangle.png |
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| diff -r c237ba772225 -r eca03db4f612 test-data/test_narrowPeak.png |
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| diff -r c237ba772225 -r eca03db4f612 test-data/test_ucsc_param.png |
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| diff -r c237ba772225 -r eca03db4f612 test-data/testpyGT.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/testpyGT.sh Wed Jan 08 09:15:19 2020 -0500 |
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| @@ -0,0 +1,15 @@ +. <(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 + +conda_env_deactivate |
