# HG changeset patch
# User iuc
# Date 1674660792 0
# Node ID 14e7c35f3d001ae74df0b05ff1b5e871ce3584af
# Parent  7dd841a322453d35f08cf9b9f986a3360de48d56
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 26f4478d873b339c5a1eccf18df68700a145a404

diff -r 7dd841a32245 -r 14e7c35f3d00 macros.xml
--- a/macros.xml	Sat Oct 01 08:43:22 2022 +0000
+++ b/macros.xml	Wed Jan 25 15:33:12 2023 +0000
@@ -1,5 +1,5 @@
 <macros>
-    <token name="@TOOL_VERSION@">3.7</token>
+    <token name="@TOOL_VERSION@">3.8</token>
     <token name="@VERSION_SUFFIX@">0</token>
     <xml name="requirements">
         <requirements>
diff -r 7dd841a32245 -r 14e7c35f3d00 pyGenomeTracks.xml
--- a/pyGenomeTracks.xml	Sat Oct 01 08:43:22 2022 +0000
+++ b/pyGenomeTracks.xml	Wed Jan 25 15:33:12 2023 +0000
@@ -581,6 +581,10 @@
 [vlines_$counter]
 file = $track.track_file_style_conditional.track_input_bed_single
 line_width = $track.track_file_style_conditional.line_width
+line_style = $track.track_file_style_conditional.line_style
+color = $track.track_file_style_conditional.color
+alpha = $track.track_file_style_conditional.alpha
+zorder = $track.track_file_style_conditional.zorder
 type = vlines
   #end if
 
@@ -588,8 +592,10 @@
   #if $track.track_file_style_conditional.track_file_style_selector == "vhighlight_track_option":
 [vhighlight_$counter]
 file = $track.track_file_style_conditional.track_input_bed_single
+line_width = $track.track_file_style_conditional.line_width
 color = $track.track_file_style_conditional.color
 alpha = $track.track_file_style_conditional.alpha
+border_color = $track.track_file_style_conditional.border_color
 type = vhighlight
   #end if
 
@@ -1185,11 +1191,29 @@
                 <when value="vlines_track_option">
                     <expand macro="track_input_bed_single_macro" />
                     <param name="line_width" type="float" value="0.5" label="width of lines"/>
+                    <param name="line_style" type="select" label="Line Style">
+                        <option value="dashed">Dashed</option>
+                        <option value="solid">Solid</option>
+                        <option value="dotted">Dotted</option>
+                        <option value="dashdot">Dashdot</option>
+                    </param>
+                    <param name="color" type="color" value="black" label="color of the vline"/>
+                    <param name="alpha" type="float" value="0.7" min="0" max="1" label="transparency (alpha) of the vline"/>
+                    <param name="zorder" type="select" label="Plot the vline above or behind other tracks">
+                        <option value="100">above</option>
+                        <option value="-100">behind</option>
+                    </param>
                 </when>
                 <when value="vhighlight_track_option">
                     <expand macro="track_input_bed_single_macro" />
                     <param name="color" type="color" value="yellow" label="color of the highlight"/>
                     <param name="alpha" type="float" value="0.5" min="0" max="1" label="transparency (alpha) of the highlight"/>
+                    <param name="line_width" type="float" min="0" value="0.5" label="width of the edge of the highlight" />
+                    <param name="border_color" type="color" value="yellow" label="color of the edge of the highlight"/>
+                    <param name="zorder" type="select" label="Plot the highlight above or behind other tracks">
+                        <option value="-100">behind</option>
+                        <option value="100">above</option>
+                    </param>
                 </when>
                 <when value="hlines_track_option">
                     <expand macro="plot_title" />
@@ -2169,6 +2193,19 @@
                 <conditional name="track_file_style_conditional">
                     <param name="track_file_style_selector" value="vlines_track_option" />
                     <param name="track_input_bed_single" value="dm3_subset_BDGP5.78_asbed4.bed.gz" ftype="bed" />
+                    <param name="line_width" value="2"/>
+                    <param name="zorder" value="100"/>
+                    <param name="color" value="red"/>
+                </conditional>
+            </repeat>
+            <repeat name="tracks">
+                <conditional name="track_file_style_conditional">
+                    <param name="track_file_style_selector" value="vlines_track_option" />
+                    <param name="track_input_bed_single" value="dm3_genes_end.bed" ftype="bed" />
+                    <param name="line_width" value="5"/>
+                    <param name="zorder" value="-100"/>
+                    <param name="color" value="blue"/>
+                    <param name="line_style" value="solid"/>
                 </conditional>
             </repeat>
             <param name="image_file_format" value="png" />
@@ -3336,16 +3373,13 @@
 Output
 ------
 
-**pyGenomeTracks** output is similar to a genome browser screen-shot that besides the usual genes, and score data (like bigwig or bedgraph files)
-may also contains Hi-C data. The plot is composed of tracks that need to be specified.
-Below is represented the 85 Mb to 110 Mb region from human chromosome 2 visualized using **pyGenomeTracks**.
-TADs were computed by HiCExplorer's ``hicFindTADs``. The additional tracks added correspond to:
-TAD-separation score (as reported by HiCExplorer's ``hicFindTADs``), chromatin states,
-principal component 1 (A/B compartment) computed using HiCExplorer's ``hicPCA``, ChIP-seq coverage for the H3K27ac mark, DNA methylation, and a gene track.
-Data are from mouse cardiac myocytes, published by `Nothjunge et al. (2017)`_.
+Here are two example plots with the different tracks you can use (on the right, you have the vlines and vhighlight which have been used):
 
-.. image:: $PATH_TO_IMAGES/pyGenomeTracks.png
-   :width: 70 %
+.. image:: static/images/demo.png
+   :width: 45 %
+.. image:: static/images/demo2.png
+   :width: 45 %
+
 
 _________________
 
diff -r 7dd841a32245 -r 14e7c35f3d00 static/images/demo.png
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diff -r 7dd841a32245 -r 14e7c35f3d00 static/images/demo2.png
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diff -r 7dd841a32245 -r 14e7c35f3d00 static/images/pyGenomeTracks.png
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diff -r 7dd841a32245 -r 14e7c35f3d00 test-data/bigwig_multiple.png
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diff -r 7dd841a32245 -r 14e7c35f3d00 test-data/dm3_genes_end.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/dm3_genes_end.bed	Wed Jan 25 15:33:12 2023 +0000
@@ -0,0 +1,7 @@
+chrX	3130718	3130719	CG14265_end
+chrX	3134603	3134604	ng2_end
+chrX	3136116	3136117	ng3_end
+chrX	3136966	3136967	ng1_end
+chrX	3138252	3138253	ng4_end
+chrX	3143321	3143322	Pig1_end
+chrX	3145072	3145073	Sgs4_end
diff -r 7dd841a32245 -r 14e7c35f3d00 test-data/master_TADs_BW_plot.png
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diff -r 7dd841a32245 -r 14e7c35f3d00 test-data/master_TADs_plot.png
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diff -r 7dd841a32245 -r 14e7c35f3d00 test-data/master_fasta.png
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diff -r 7dd841a32245 -r 14e7c35f3d00 test-data/master_scale_bar_startend.png
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diff -r 7dd841a32245 -r 14e7c35f3d00 test-data/test1.ini
--- a/test-data/test1.ini	Sat Oct 01 08:43:22 2022 +0000
+++ b/test-data/test1.ini	Wed Jan 25 15:33:12 2023 +0000
@@ -1,6 +1,6 @@
 [x-axis]
 where = top
-[hic_section_0_0]
+[hic_section_1_0]
 file = test-data/Li_et_al_2015.h5
 file_type = hic_matrix
 title = Kc DpnII (Li et al. 2015)
@@ -9,7 +9,7 @@
 transform = log1p
 scale_factor = 1.0
 rasterize = true
-[tads_0_0]
+[tads_1_0]
 file = test-data/domains.bed
 file_type = domains
 border_color = black
@@ -17,7 +17,7 @@
 overlay_previous = share-y
 [spacer]
 height = 0.05
-[chrom states_2]
+[chrom states_3]
 file = test-data/tad_classification.bed
 title = TAD state
 color = bed_rgb
@@ -26,17 +26,15 @@
 height = 0.5
 line_width = 0.5
 file_type = bed
-[bedgraph_matrix_3]
+[bedgraph_matrix_4]
 file = test-data/tad_score.gz
 title = TAD separation score (Ramirez et al.)
 height = 10.0
+type = matrix
 file_type = bedgraph_matrix
-show_data_range = false
-plot_horizontal_lines = false
-pos_score_in_bin = center
 [spacer]
 height = 1.0
-[bedgraph_5]
+[bedgraph_6]
 file = test-data/bedgraph_chrx_2e6_5e6.bg
 title = bedgraph
 color = blue
@@ -48,7 +46,7 @@
 file_type = bedgraph
 type = fill
 overlay_previous = no
-[bigwig_6]
+[bigwig_7]
 file = test-data/bigwig_chrx_2e6_5e6.bw
 title = rep 1 test fill
 color = blue
@@ -60,7 +58,7 @@
 show_data_range = false
 file_type = bigwig
 overlay_previous = no
-[bigwig_7]
+[bigwig_8]
 file = test-data/bigwig_chrx_2e6_5e6.bw
 title = rep 1 test line
 color = red
@@ -72,7 +70,7 @@
 show_data_range = false
 file_type = bigwig
 overlay_previous = no
-[bigwig_8]
+[bigwig_9]
 file = test-data/bigwig_chrx_2e6_5e6.bw
 title = rep 1 test lw=0.2
 color = red
@@ -84,7 +82,7 @@
 show_data_range = false
 file_type = bigwig
 overlay_previous = no
-[bigwig_9]
+[bigwig_10]
 file = test-data/bigwig_chrx_2e6_5e6.bw
 title = rep 1 test point:0.5
 color = black
@@ -98,7 +96,7 @@
 overlay_previous = no
 [spacer]
 height = 0.5
-[genes_11_0]
+[genes_12_0]
 file = test-data/dm3_genes.bed.gz
 title = genes
 color = #000000
@@ -109,8 +107,8 @@
 display = stacked
 height = 5.0
 labels = true
+fontsize = 10
 file_type = bed
-fontsize = 10
 global_max_row = false
 max_labels = 60
 line_width = 0.5
@@ -118,7 +116,7 @@
 overlay_previous = no
 [spacer]
 height = 1.0
-[genes_13_0]
+[genes_14_0]
 file = test-data/dm3_genes.bed.gz
 title = max num rows 3
 color = #000000
@@ -139,7 +137,7 @@
 overlay_previous = no
 [spacer]
 height = 1.0
-[genes_15_0]
+[genes_16_0]
 file = test-data/dm3_genes.bed6.gz
 title = bed6 global max row
 color = #000000
@@ -157,6 +155,6 @@
 line_width = 0.5
 arrowhead_included = false
 overlay_previous = no
-[vlines_16]
+[vlines_17]
 file = test-data/domains.bed
-type = vlines
\ No newline at end of file
+type = vlines
diff -r 7dd841a32245 -r 14e7c35f3d00 test-data/test9.ini
--- a/test-data/test9.ini	Sat Oct 01 08:43:22 2022 +0000
+++ b/test-data/test9.ini	Wed Jan 25 15:33:12 2023 +0000
@@ -97,5 +97,14 @@
 height = 1.0
 [vlines_5]
 file = dm3_subset_BDGP5.78_asbed4.bed.gz
-line_width = 0.5
-type = vlines
\ No newline at end of file
+line_width = 2
+zorder = 100
+color = red
+type = vlines
+[vlines_6]
+file = dm3_genes_end.bed
+line_width = 5
+zorder = -100
+color = blue
+line_style = solid
+type = vlines
diff -r 7dd841a32245 -r 14e7c35f3d00 test-data/test_TADs_bdgm.png
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diff -r 7dd841a32245 -r 14e7c35f3d00 test-data/test_alpha.png
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diff -r 7dd841a32245 -r 14e7c35f3d00 test-data/test_alpha_dec.png
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diff -r 7dd841a32245 -r 14e7c35f3d00 test-data/test_arcs_use_middle.png
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diff -r 7dd841a32245 -r 14e7c35f3d00 test-data/test_arrowhead_zoom.png
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diff -r 7dd841a32245 -r 14e7c35f3d00 test-data/test_gtf_bed4.png
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diff -r 7dd841a32245 -r 14e7c35f3d00 test-data/test_gtf_flybase_param.png
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diff -r 7dd841a32245 -r 14e7c35f3d00 test-data/test_link.png
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diff -r 7dd841a32245 -r 14e7c35f3d00 test-data/test_link2.png
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diff -r 7dd841a32245 -r 14e7c35f3d00 test-data/test_log.png
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diff -r 7dd841a32245 -r 14e7c35f3d00 test-data/test_ucsc_param.png
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diff -r 7dd841a32245 -r 14e7c35f3d00 test-data/test_vhighlight.png
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