Mercurial > repos > iuc > pygenometracks
changeset 14:59fd173ac850 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit b0607963d6cf57fef81c5468e0af914430e7d35b
| author | iuc |
|---|---|
| date | Fri, 26 May 2023 07:54:55 +0000 |
| parents | 360df4999907 |
| children | 36b848d5f3ec |
| files | macros.xml pyGenomeTracks.xml test-data/master_TADs_BW_plot.png test-data/test13.ini test-data/test3.ini test-data/test_link2.png |
| diffstat | 6 files changed, 63 insertions(+), 27 deletions(-) [+] |
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--- a/macros.xml Tue Mar 28 10:48:50 2023 +0000 +++ b/macros.xml Fri May 26 07:54:55 2023 +0000 @@ -1,6 +1,6 @@ <macros> <token name="@TOOL_VERSION@">3.8</token> - <token name="@VERSION_SUFFIX@">1</token> + <token name="@VERSION_SUFFIX@">2</token> <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">pygenometracks</requirement> @@ -59,7 +59,7 @@ <param name="track_input_bedgraph_matrix" type="data" format="bedgraph" label="Track file(s) bedgraph format" multiple="True"/> </xml> <xml name="track_input_link_macro"> - <param name="track_input_link" type="data" format="bed,interval" label="Track file(s) for links" multiple="False"/> + <param name="track_input_link" type="data" format="bed,interval" label="Track file(s) for links" multiple="True"/> </xml> <xml name="track_input_fasta_macro"> <conditional name="fasta_source">
--- a/pyGenomeTracks.xml Tue Mar 28 10:48:50 2023 +0000 +++ b/pyGenomeTracks.xml Fri May 26 07:54:55 2023 +0000 @@ -188,6 +188,14 @@ color = bed_rgb #elif $track.track_file_style_conditional.color_bed.color: color = $track.track_file_style_conditional.color_bed.color + #if $track.track_file_style_conditional.color_bed.color_bed_select == "colormap": + #if str($track.track_file_style_conditional.color_bed.min_value) != '': +min_value = $track.track_file_style_conditional.color_bed.min_value + #end if + #if str($track.track_file_style_conditional.color_bed.max_value) != '': +max_value = $track.track_file_style_conditional.color_bed.max_value + #end if + #end if #end if #if $track.track_file_style_conditional.border_color_bed.border_color_bed_select == 'manually': border_color = $track.track_file_style_conditional.border_color_bed.color @@ -230,6 +238,14 @@ color = bed_rgb #elif $track.track_file_style_conditional.color_bed.color: color = $track.track_file_style_conditional.color_bed.color + #if $track.track_file_style_conditional.color_bed.color_bed_select == "colormap": + #if str($track.track_file_style_conditional.color_bed.min_value) != '': +min_value = $track.track_file_style_conditional.color_bed.min_value + #end if + #if str($track.track_file_style_conditional.color_bed.max_value) != '': +max_value = $track.track_file_style_conditional.color_bed.max_value + #end if + #end if #end if #if $track.track_file_style_conditional.border_color_bed.border_color_bed_select == 'manually': border_color = $track.track_file_style_conditional.border_color_bed.color @@ -305,47 +321,49 @@ ## Link #if $track.track_file_style_conditional.track_file_style_selector == "link_track_option": -[links_$counter] -file = $track.track_file_style_conditional.track_input_link - #if $track.track_file_style_conditional.title: + #for $counter_link, $data_link in enumerate($track.track_file_style_conditional.track_input_link): +[links_${counter}_${counter_link}] +file = $data_link + #if $track.track_file_style_conditional.title: title = $track.track_file_style_conditional.title - #elif $track.track_file_style_conditional.overlay_select == 'no': -title = $track.track_file_style_conditional.track_input_link.element_identifier - #end if - #if $track.track_file_style_conditional.height: + #elif $track.track_file_style_conditional.overlay_select == 'no': +title = $data_link.element_identifier + #end if + #if $track.track_file_style_conditional.height: height = $track.track_file_style_conditional.height - #end if - #if $track.track_file_style_conditional.min_value != "": + #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 != "": + #end if + #if $track.track_file_style_conditional.max_value != "": max_value = $track.track_file_style_conditional.max_value - #end if + #end if color = $track.track_file_style_conditional.color_link.color alpha = $track.track_file_style_conditional.alpha line_width = $track.track_file_style_conditional.line_width line_style = $track.track_file_style_conditional.line_style links_type = $track.track_file_style_conditional.display.links_type - #if $track.track_file_style_conditional.display.links_type in ['arcs', 'triangles']: + #if $track.track_file_style_conditional.display.links_type in ['arcs', 'triangles']: compact_arcs_level = $track.track_file_style_conditional.display.compact_arcs_level use_middle = $track.track_file_style_conditional.display.use_middle - #end if - #if $track.track_file_style_conditional.display.links_type != 'squares' and $track.track_file_style_conditional.display.ylim != "": + #end if + #if $track.track_file_style_conditional.display.links_type != 'squares' and $track.track_file_style_conditional.display.ylim != "": ylim = $track.track_file_style_conditional.display.ylim - #end if - #if $track.track_file_style_conditional.display.links_type == 'squares' and $track.track_file_style_conditional.display.region2 != "": + #end if + #if $track.track_file_style_conditional.display.links_type == 'squares' and $track.track_file_style_conditional.display.region2 != "": region2 = $track.track_file_style_conditional.display.region2 - #end if - #if $track.track_file_style_conditional.invert_orientation: + #end if + #if $track.track_file_style_conditional.invert_orientation: orientation = inverted - #end if + #end if overlay_previous = $track.track_file_style_conditional.overlay_select file_type = links - ## If spacer is asked a new section is created: - #if $track.track_file_style_conditional.spacer_height != "": + ## If spacer is asked a new section is created: + #if $track.track_file_style_conditional.spacer_height != "": [spacer] height = $track.track_file_style_conditional.spacer_height - #end if + #end if + #end for #end if ## Narrow peak @@ -889,6 +907,7 @@ <option value="viridis">viridis</option> <expand macro="colormap_macro_noRdYlBu_r_noViridis" /> </param> + <expand macro="minmax_macro" /> </when> </conditional> <expand macro="border_color_bed_macro" /> @@ -919,6 +938,7 @@ <option value="viridis">viridis</option> <expand macro="colormap_macro_noRdYlBu_r_noViridis" /> </param> + <expand macro="minmax_macro" /> </when> </conditional> <expand macro="border_color_bed_macro" /> @@ -1748,6 +1768,8 @@ <conditional name="color_bed"> <param name="color_bed_select" value="colormap" /> <param name="color" value="RdYlBu_r" /> + <param name="min_value" value="0" /> + <param name="max_value" value="2" /> </conditional> </conditional> </repeat> @@ -2428,7 +2450,7 @@ <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="link_track_option" /> - <param name="track_input_link" value="test.arcs" ftype="bed" /> + <param name="track_input_link" value="test.arcs,test.arcs" ftype="bed" /> <param name="title" value="highly compacted" /> <conditional name="color_link"> <param name="color_link_select" value="manually" />
--- a/test-data/test13.ini Tue Mar 28 10:48:50 2023 +0000 +++ b/test-data/test13.ini Fri May 26 07:54:55 2023 +0000 @@ -35,7 +35,7 @@ compact_arcs_level = 1 overlay_previous = no file_type = links -[links_4] +[links_4_0] file = test.arcs title = highly compacted height = 1.5 @@ -47,3 +47,15 @@ compact_arcs_level = 2 overlay_previous = no file_type = links +[links_4_1] +file = test.arcs +title = highly compacted +height = 1.5 +color = #000000 +alpha = 1.0 +line_width = 0.5 +line_style = solid +links_type = arcs +compact_arcs_level = 2 +overlay_previous = no +file_type = links
--- a/test-data/test3.ini Tue Mar 28 10:48:50 2023 +0000 +++ b/test-data/test3.ini Fri May 26 07:54:55 2023 +0000 @@ -147,6 +147,8 @@ line_width = 0.5 arrowhead_included = false overlay_previous = no +min_value = 0 +max_value = 2 [genes_12_0] file = test-data/domains.bed title = domains.bed using the 9th field for colors interleaved border=red