# HG changeset patch
# User iuc
# Date 1529735315 14400
# Node ID 2074627b0f838293f5849e5e3640e023485a8ec3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
diff -r 000000000000 -r 2074627b0f83 macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Sat Jun 23 02:28:35 2018 -0400
@@ -0,0 +1,210 @@
+
+ \${GALAXY_SLOTS:-4}
+ 2.0
+
+
+ pygenometracks
+
+
+ @BINARY@ --version
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+ 10.5281/zenodo.1133705
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+.. class:: infomark
+
+For more information on the tools, please visit our `help site`_.
+
+If you would like to give us feedback or you run into any trouble, please send an email to deeptools@googlegroups.com
+
+This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for
+Immunobiology and Epigenetics`_.
+
+.. _Bioinformatics and Deep-Sequencing Unit: http://www3.ie-freiburg.mpg.de/facilities/research-facilities/bioinformatics-and-deep-sequencing-unit/
+.. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
+.. _help site: https://github.com/deeptools/pyGenomeTracks
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diff -r 000000000000 -r 2074627b0f83 pyGenomeTracks.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/pyGenomeTracks.xml Sat Jun 23 02:28:35 2018 -0400
@@ -0,0 +1,768 @@
+
+ plot genomic data tracks
+
+ pyGenomeTracks
+ macros.xml
+
+
+
+
+
+
+
+#if $x_axis.x_axis_select == "yes":
+[x-axis]
+#if $x_axis.fontsize:
+fontsize = $x_axis.fontsize
+#end if
+#if $x_axis.where:
+where = $x_axis.where
+#end if
+#end if
+#for $counter, $track in enumerate($tracks):
+#if $track.track_file_style_conditional.track_file_style_selector == "hic_matrix_option":
+
+#for $counter_matrix, $data_matrix in enumerate($track.track_file_style_conditional.matrix_h5_cooler_multiple):
+[hic_section_$counter]
+file = $data_matrix
+file_type = hic_matrix
+#if $track.track_file_style_conditional.title:
+title = $track.track_file_style_conditional.title
+#else:
+title = $data_matrix.name
+#end if
+#if $track.track_file_style_conditional.depth:
+depth = $track.track_file_style_conditional.depth
+#end if
+#if $track.track_file_style_conditional.colormap:
+colormap = $track.track_file_style_conditional.colormap
+#end if
+#if $track.track_file_style_conditional.min_value:
+min_value = $track.track_file_style_conditional.min_value
+#end if
+#if $track.track_file_style_conditional.max_value:
+max_value = $track.track_file_style_conditional.max_value
+#end if
+transform = $track.track_file_style_conditional.transform
+height = $track.track_file_style_conditional.height_matrix
+
+#if $track.track_file_style_conditional.boundaries_file is not None:
+#set boundary_file = $track.track_file_style_conditional.boundaries_file[$counter_matrix]
+boundaries_file = $boundary_file
+#end if
+
+#if $track.track_file_style_conditional.x_labels:
+x labels = $track.track_file_style_conditional.x_labels
+#end if
+#if $track.track_file_style_conditional.type:
+type = $track.track_file_style_conditional.type
+#end if
+#if $track.track_file_style_conditional.show_masked_bins:
+show_masked_bins = $track.track_file_style_conditional.show_masked_bins
+#end if
+#if $track.track_file_style_conditional.scale_factor:
+scale factor = $track.track_file_style_conditional.scale_factor
+#end if
+
+[spacer]
+#if $track.track_file_style_conditional.spacer_height:
+height = $track.track_file_style_conditional.spacer_height
+#end if
+#end for
+
+#end if
+
+
+
+#if $track.track_file_style_conditional.track_file_style_selector == "tad_score_track_option":
+
+#for $data_bedgraph in $track.track_file_style_conditional.track_input_bedgraph:
+[tad_score_$counter]
+file = $data_bedgraph
+#if $track.track_file_style_conditional.title:
+title = $track.track_file_style_conditional.title
+#else:
+title = $data_bedgraph.name
+#end if
+#if $track.track_file_style_conditional.color:
+color = $track.track_file_style_conditional.color
+#end if
+#if $track.track_file_style_conditional.height_tad:
+height = $track.track_file_style_conditional.height_tad
+#end if
+#if $track.track_file_style_conditional.type_lines:
+type = $track.track_file_style_conditional.type_lines
+#end if
+#if $track.track_file_style_conditional.show_data:
+show data range = $track.track_file_style_conditional.show_data
+#end if
+
+#set $columns = len(open(str($track.track_file_style_conditional.track_input_bedgraph)).readline().split('\t'))
+#if $columns > 5:
+file_type = bedgraph_matrix
+#else:
+file_type = bedgraph
+#end if
+type = lines
+[spacer]
+#if $track.track_file_style_conditional.spacer_height:
+height = $track.track_file_style_conditional.spacer_height
+#end if
+#end for
+#end if
+
+
+
+
+#if $track.track_file_style_conditional.track_file_style_selector == "chrom_states_option":
+#for $data_bed in $track.track_file_style_conditional.track_input_bed:
+
+[chrom states_$counter]
+file = $data_bed
+#if $track.track_file_style_conditional.title:
+title = $track.track_file_style_conditional.title
+#else:
+title = $data_bed.name
+#end if
+#if $track.track_file_style_conditional.color:
+color = $track.track_file_style_conditional.color
+#end if
+display = collapsed
+#if $track.track_file_style_conditional.height_chrom:
+height = $track.track_file_style_conditional.height_chrom
+#end if
+#if $track.track_file_style_conditional.border_color:
+border_color = $track.track_file_style_conditional.border_color
+#end if
+file_type = bed
+[spacer]
+#if $track.track_file_style_conditional.spacer_height:
+height = $track.track_file_style_conditional.spacer_height
+#end if
+#end for
+
+#end if
+
+
+
+
+#if $track.track_file_style_conditional.track_file_style_selector == "gene_track_option":
+#for $data_bed in $track.track_file_style_conditional.track_input_bed:
+
+[genes_$counter]
+file = $data_bed
+#if $track.track_file_style_conditional.title:
+title = $track.track_file_style_conditional.title
+#else:
+title = $data_bed.name
+#end if
+#if $track.track_file_style_conditional.color:
+color = $track.track_file_style_conditional.color
+#end if
+
+#if $track.track_file_style_conditional.height_bed:
+height = $track.track_file_style_conditional.height_bed
+#end if
+
+#if $track.track_file_style_conditional.labels:
+labels = $track.track_file_style_conditional.labels
+#end if
+
+#if $track.track_file_style_conditional.type:
+type = $track.track_file_style_conditional.type
+#end if
+
+file_type = bed
+#if $track.track_file_style_conditional.fontsize:
+fontsize = $track.track_file_style_conditional.fontsize
+#end if
+
+#if $track.track_file_style_conditional.gene_rows:
+gene rows = $track.track_file_style_conditional.gene_rows
+#end if
+
+#if $track.track_file_style_conditional.global_max_row:
+global max row = $track.track_file_style_conditional.global_max_row
+#end if
+[spacer]
+#if $track.track_file_style_conditional.spacer_height:
+height = $track.track_file_style_conditional.spacer_height
+#end if
+#end for
+#end if
+
+
+#if $track.track_file_style_conditional.track_file_style_selector == "bedgraph_track_option":
+#for $data_bedgraph in $track.track_file_style_conditional.track_input_bedgraph:
+
+[bedgraph_$counter]
+file = $data_bedgraph
+#if $track.track_file_style_conditional.title:
+title = $track.track_file_style_conditional.title
+#else:
+title = $data_bedgraph.name
+#end if
+#if $track.track_file_style_conditional.color:
+color = $track.track_file_style_conditional.color
+#end if
+#if $track.track_file_style_conditional.height_bedgraph:
+height = $track.track_file_style_conditional.height_bedgraph
+#end if
+#if $track.track_file_style_conditional.show_data:
+show data range = $track.track_file_style_conditional.show_data
+#end if
+
+#set $columns = len(open(str($track.track_file_style_conditional.track_input_bedgraph)).readline().split('\t'))
+#if $columns > 5:
+file_type = bedgraph_matrix
+#else:
+file_type = bedgraph
+#end if
+type = lines
+[spacer]
+#if $track.track_file_style_conditional.spacer_height:
+height = $track.track_file_style_conditional.spacer_height
+#end if
+#end for
+#end if
+
+#if $track.track_file_style_conditional.track_file_style_selector == "bigwig_track_option":
+#for $data_bigwig in $track.track_file_style_conditional.track_input_bigwig:
+[bigwig_$counter]
+file = $data_bigwig
+#if $track.track_file_style_conditional.title:
+title = $track.track_file_style_conditional.title
+#else:
+title = $data_bigwig.name
+#end if
+color = $track.track_file_style_conditional.color
+#if $track.track_file_style_conditional.min_value:
+min_value = $track.track_file_style_conditional.min_value
+#else:
+min_value = 0
+#end if
+#if $track.track_file_style_conditional.max_value:
+max_value = $track.track_file_style_conditional.max_value
+#else:
+max_value = auto
+#end if
+height = $track.track_file_style_conditional.height_bigwig
+#if $track.track_file_style_conditional.number_of_bins:
+number of bins = $track.track_file_style_conditional.number_of_bins
+#end if
+nans to zeros = $track.track_file_style_conditional.nans_to_zeros
+#if $track.track_file_style_conditional.type_conditional == 'fill_option':
+type = fill
+#elif $track.track_file_style_conditional.type_conditional == 'line_option':
+type = line:$track.track_file_style_conditional.type_conditional.height_line
+#elif $track.track_file_style_conditional.type_conditional == 'point_option':
+type = points:$track.track_file_style_conditional.type_conditional.width_point
+#end if
+#if $track.track_file_style_conditional.data_range:
+show data range = $track.track_file_style_conditional.data_range
+#end if
+file_type = bigwig
+[spacer]
+#if $track.track_file_style_conditional.spacer_height:
+height = $track.track_file_style_conditional.spacer_height
+#end if
+#end for
+#end if
+
+
+#if $track.track_file_style_conditional.track_file_style_selector == "bedgraph_matrix_track_option":
+#for $data_bedgraph_matrix in $track.track_file_style_conditional.track_input_bedgraph_matrix:
+
+[bedgraph_matrix_$counter]
+file = $data_bedgraph_matrix
+#if $track.track_file_style_conditional.title:
+title = $track.track_file_style_conditional.title
+#else:
+title = $data_bedgraph_matrix.name
+#end if
+#if $track.track_file_style_conditional.height_bedgraph:
+height = $track.track_file_style_conditional.height_bedgraph
+#end if
+orientation = inverted
+#if $track.track_file_style_conditional.min_value:
+min_value = $track.track_file_style_conditional.min_value
+#end if
+#if $track.track_file_style_conditional.max_value:
+max_value = $track.track_file_style_conditional.max_value
+#end if
+#if $track.track_file_style_conditional.type_lines:
+type = $track.track_file_style_conditional.type_lines
+#end if
+file_type = bedgraph_matrix
+plot horizontal lines=False
+[spacer]
+#if $track.track_file_style_conditional.spacer_height:
+height = $track.track_file_style_conditional.spacer_height
+#end if
+#end for
+#end if
+
+#if $track.track_file_style_conditional.track_file_style_selector == "vlines_track_option":
+
+[vlines_$counter]
+file = $track.track_file_style_conditional.track_input_bed_single
+type = vlines
+file_type = bed
+#end if
+#if $track.track_file_style_conditional.track_file_style_selector == "spacer_option":
+
+[spacer]
+#if $track.track_file_style_conditional.spacer_height:
+height = $track.track_file_style_conditional.spacer_height
+#end if
+#end if
+#end for
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diff -r 000000000000 -r 2074627b0f83 static/images/pyGenomeTracks.png
Binary file static/images/pyGenomeTracks.png has changed
diff -r 000000000000 -r 2074627b0f83 test-data/Li_et_al_2015.h5
Binary file test-data/Li_et_al_2015.h5 has changed
diff -r 000000000000 -r 2074627b0f83 test-data/bedgraph_chrx_2e6_5e6.bg
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bedgraph_chrx_2e6_5e6.bg Sat Jun 23 02:28:35 2018 -0400
@@ -0,0 +1,11308 @@
+chrX 2000700 2000750 1
+chrX 2000750 2000800 2
+chrX 2000800 2001000 0
+chrX 2001000 2001100 1
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+chrX 2001650 2001700 1
+chrX 2001700 2001750 2
+chrX 2001750 2001800 1
+chrX 2001800 2003300 0
+chrX 2003300 2003350 5
+chrX 2003350 2003400 6
+chrX 2003400 2003450 1
+chrX 2003450 2003500 0
+chrX 2003500 2003600 8
+chrX 2003600 2003650 2
+chrX 2003650 2003750 0
+chrX 2003750 2003800 5
+chrX 2003800 2003850 9
+chrX 2003850 2003900 8
+chrX 2003900 2003950 10
+chrX 2003950 2004000 8
+chrX 2004000 2004050 7
+chrX 2004050 2004100 5
+chrX 2004100 2004150 6
+chrX 2004150 2004200 7
+chrX 2004200 2004250 3
+chrX 2004250 2004300 4
+chrX 2004300 2004400 8
+chrX 2004400 2004450 4
+chrX 2004450 2004500 2
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+chrX 2008150 2008200 1
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+chrX 2008500 2008600 2
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+chrX 2010450 2010500 5
+chrX 2010500 2010550 3
+chrX 2010550 2010600 2
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+chrX 2010800 2010950 2
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+chrX 2011350 2011400 10
+chrX 2011400 2011450 12
+chrX 2011450 2011550 8
+chrX 2011550 2011600 2
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+chrX 2011650 2011700 0
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+chrX 2011750 2011800 5
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+chrX 2011850 2011900 0
+chrX 2011900 2011950 1
+chrX 2011950 2012050 3
+chrX 2012050 2012100 2
+chrX 2012100 2012200 1
+chrX 2012200 2012250 0
+chrX 2012250 2012350 2
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diff -r 000000000000 -r 2074627b0f83 test-data/dm3_genes.bed6.gz
Binary file test-data/dm3_genes.bed6.gz has changed
diff -r 000000000000 -r 2074627b0f83 test-data/domains.bed
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diff -r 000000000000 -r 2074627b0f83 test-data/master_TADs_plot.png
Binary file test-data/master_TADs_plot.png has changed
diff -r 000000000000 -r 2074627b0f83 test-data/tad_classification.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tad_classification.bed Sat Jun 23 02:28:35 2018 -0400
@@ -0,0 +1,2685 @@
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+chrX 20294608 20305771 active 4 . 20294608 20305771 255,255,153
+chrX 20305771 20339275 inactive 1 . 20305771 20339275 0,0,0
+chrX 20339275 20382809 active 2 . 20339275 20382809 255,255,153
+chrX 20382809 20395830 active 4 . 20382809 20395830 255,255,153
+chrX 20395830 20508892 inactive 1 . 20395830 20508892 0,0,0
+chrX 20508892 20526971 inactive 1 . 20508892 20526971 0,0,0
+chrX 20526971 20631727 inactive 1 . 20526971 20631727 0,0,0
+chrX 20631727 20894364 inactive 1 . 20631727 20894364 0,0,0
+chrX 20894364 20907117 active 4 . 20894364 20907117 255,255,153
+chrX 20907117 20916940 active 4 . 20907117 20916940 255,255,153
+chrX 20916940 20931445 active 2 . 20916940 20931445 255,255,153
+chrX 20931445 20944384 active 2 . 20931445 20944384 255,255,153
+chrX 20944384 20996348 inactive 1 . 20944384 20996348 0,0,0
+chrX 20996348 21012072 inactive 1 . 20996348 21012072 0,0,0
+chrX 21012072 21178100 inactive 1 . 21012072 21178100 0,0,0
+chrX 21178100 21186628 inactive 1 . 21178100 21186628 0,0,0
+chrX 21186628 21194946 active 4 . 21186628 21194946 255,255,153
+chrX 21194946 21220857 active 4 . 21194946 21220857 255,255,153
+chrX 21220857 21240098 active 4 . 21220857 21240098 255,255,153
+chrX 21240098 21271964 inactive 1 . 21240098 21271964 0,0,0
+chrX 21271964 21343699 inactive 1 . 21271964 21343699 0,0,0
+chrX 21343699 21656357 inactive 1 . 21343699 21656357 0,0,0
+chrX 21656357 21857607 HP1 3 . 21656357 21857607 51,160,44
+chrX 21857607 21873688 active 4 . 21857607 21873688 255,255,153
+chrX 21873688 21889804 active 2 . 21873688 21889804 255,255,153
+chrX 21889804 21907001 active 4 . 21889804 21907001 255,255,153
+chrX 21907001 21931844 inactive 1 . 21907001 21931844 0,0,0
+chrX 21931844 21954371 active 2 . 21931844 21954371 255,255,153
+chrX 21954371 22120033 inactive 1 . 21954371 22120033 0,0,0
+chrX 22120033 22274227 inactive 1 . 22120033 22274227 0,0,0
+chrX 22274227 22287785 inactive 1 . 22274227 22287785 0,0,0
+chrX 22287785 22349277 inactive 1 . 22287785 22349277 0,0,0
+chrX 22349277 22380885 inactive 1 . 22349277 22380885 0,0,0
+chrX 22380885 22421267 inactive 1 . 22380885 22421267 0,0,0
diff -r 000000000000 -r 2074627b0f83 test-data/tad_score.gz
Binary file test-data/tad_score.gz has changed