| Previous changeset 9:2824d77cd8f8 (2020-11-18) Next changeset 11:7dd841a32245 (2022-10-01) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 5bd033a726b088eef3cf591da36ca1e9ba70d8c7" |
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modified:
macros.xml pyGenomeTracks.xml |
| b |
| diff -r 2824d77cd8f8 -r a1abfa420d9d macros.xml --- a/macros.xml Wed Nov 18 21:33:46 2020 +0000 +++ b/macros.xml Sun Feb 13 22:43:45 2022 +0000 |
| [ |
| @@ -1,9 +1,9 @@ <macros> - <token name="@THREADS@">\${GALAXY_SLOTS:-4}</token> - <token name="@WRAPPER_VERSION@">3.6</token> + <token name="@TOOL_VERSION@">3.6</token> + <token name="@VERSION_SUFFIX@">1</token> <xml name="requirements"> <requirements> - <requirement type="package" version="@WRAPPER_VERSION@">pygenometracks</requirement> + <requirement type="package" version="@TOOL_VERSION@">pygenometracks</requirement> <yield /> </requirements> <version_command><![CDATA[@BINARY@ --version | tail -n 1 ]]></version_command> @@ -204,7 +204,7 @@ <option value="dashdot">Dashdot</option> </param> </xml> - <xml name="colormap_macro"> + <xml name="colormap_macro_noRdYlBu_r_noViridis"> <option value="RdYlBu">RdYlBu</option> <option value="Accent">Accent</option> <option value="Spectral">Spectral</option> @@ -274,7 +274,6 @@ <option value="brg">brg</option> <option value="jet">jet</option> <option value="afmhot">afmhot</option> - <option value="viridis">viridis</option> <option value="plasma">plasma</option> <option value="inferno">inferno</option> <option value="magma">magma</option> @@ -328,7 +327,6 @@ <option value="RdPu_r">RdPu reversed</option> <option value="YlGn_r">YlGn reversed</option> <option value="PuBuGn_r">PuBuGn reversed</option> - <option value="RdYlBu_r">RdYlBu reversed</option> <option value="RdYlGn_r">RdYlGn reversed</option> <option value="YlGnBu_r">YlGnBu reversed</option> <option value="YlOrBr_r">YlOrBr reversed</option> |
| b |
| diff -r 2824d77cd8f8 -r a1abfa420d9d pyGenomeTracks.xml --- a/pyGenomeTracks.xml Wed Nov 18 21:33:46 2020 +0000 +++ b/pyGenomeTracks.xml Sun Feb 13 22:43:45 2022 +0000 |
| b |
| b'@@ -1,4 +1,4 @@\n-<tool id="pygenomeTracks" name="@BINARY@" version="@WRAPPER_VERSION@">\n+<tool id="pygenomeTracks" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">\n <description>plot genomic data tracks</description>\n <macros>\n <token name="@BINARY@">pyGenomeTracks</token>\n@@ -56,7 +56,7 @@\n #if $track.track_file_style_conditional.title:\n title = $track.track_file_style_conditional.title\n #else:\n-title = $data_matrix.name\n+title = $data_matrix.element_identifier\n #end if\n #if $track.track_file_style_conditional.depth:\n depth = $track.track_file_style_conditional.depth\n@@ -114,7 +114,7 @@\n #if $track.track_file_style_conditional.title:\n title = $track.track_file_style_conditional.title\n #else:\n-title = $data_bed.name\n+title = $data_bed.element_identifier\n #end if\n #if $track.track_file_style_conditional.color_bed.color_bed_select == "bed_rgb":\n color = bed_rgb\n@@ -153,7 +153,7 @@\n #if $track.track_file_style_conditional.title:\n title = $track.track_file_style_conditional.title\n #elif $track.track_file_style_conditional.overlay_select == \'no\':\n-title = $data_bed.name\n+title = $data_bed.element_identifier\n #end if\n #if $track.track_file_style_conditional.color_bed.color_bed_select == "bed_rgb":\n color = bed_rgb\n@@ -226,7 +226,7 @@\n #if $track.track_file_style_conditional.title:\n title = $track.track_file_style_conditional.title\n #elif $track.track_file_style_conditional.overlay_select == \'no\':\n-title = $track.track_file_style_conditional.track_input_link.name\n+title = $track.track_file_style_conditional.track_input_link.element_identifier\n #end if\n #if $track.track_file_style_conditional.height:\n height = $track.track_file_style_conditional.height\n@@ -267,7 +267,7 @@\n #if $track.track_file_style_conditional.title:\n title = $track.track_file_style_conditional.title\n #elif $track.track_file_style_conditional.overlay_select == \'no\':\n-title = $data_narrow_peak.name\n+title = $data_narrow_peak.element_identifier\n #end if\n color = $track.track_file_style_conditional.color\n type = $track.track_file_style_conditional.display.display_selector\n@@ -313,7 +313,7 @@\n #if $track.track_file_style_conditional.title:\n title = $track.track_file_style_conditional.title\n #elif $track.track_file_style_conditional.overlay_select == "no":\n-title = $data_bedgraph.name\n+title = $data_bedgraph.element_identifier\n #end if\n #if $track.track_file_style_conditional.color:\n color = $track.track_file_style_conditional.color\n@@ -388,7 +388,7 @@\n #if $track.track_file_style_conditional.title:\n title = $track.track_file_style_conditional.title\n #elif $track.track_file_style_conditional.overlay_select == "no":\n-title = $data_bigwig.name\n+title = $data_bigwig.element_identifier\n #end if\n #if $track.track_file_style_conditional.color:\n color = $track.track_file_style_conditional.color\n@@ -452,7 +452,7 @@\n #if $track.track_file_style_conditional.title:\n title = $track.track_file_style_conditional.title\n #else:\n-title = $data_bedgraph_matrix.name\n+title = $data_bedgraph_matrix.element_identifier\n #end if\n #if $track.track_file_style_conditional.height_bedgraph:\n height = $track.track_file_style_conditional.height_bedgraph\n@@ -623,13 +623,12 @@\n <param name="track_file_style_selector" type="select" label="Choose style of the track">\n <option value="hic_matrix_option">TAD visualization</option>\n <option value="chrom_states_option">Chromatine states</option>\n- <option value="bedgraph_matrix_track_option">TAD score</option>\n <option value="gene_track_option">Gene track / Bed track</option>\n <option value="link_track_option">Link track</option>\n <option value="narrow_peak_track_option">NarrowPeak track</option>\n <op'..b'edgraph matrix track</option>\n+ <option value="bedgraph_matrix_track_option">Bedgraph matrix track/TAD score</option>\n <option value="vlines_track_option">Vlines track</option>\n <option value="hlines_track_option">Hlines track</option>\n <option value="spacer_option">Spacer</option>\n@@ -642,7 +641,8 @@\n \n <param name="colormap" type="select" label="Color map to use for the heatmap" help="Available color map names can be found here: https://matplotlib.org/examples/color/colormaps_reference.html">\n <option value="RdYlBu_r">RdYlBu reversed</option>\n- <expand macro="colormap_macro"/>\n+ <option value="viridis">viridis</option>\n+ <expand macro="colormap_macro_noRdYlBu_r_noViridis"/>\n </param>\n <param name="depth" type="integer" value="8000000" optional="True" label="Depth" />\n <expand macro="minmax_macro" />\n@@ -679,7 +679,9 @@\n <when value="bed_rgb" />\n <when value="colormap">\n <param name="color" type="select" label="Color map to use for the scores" help=" Available color map names can be found here: https://matplotlib.org/examples/color/colormaps_reference.html">\n- <expand macro="colormap_macro" />\n+ <option value="RdYlBu_r">RdYlBu reversed</option>\n+ <option value="viridis">viridis</option>\n+ <expand macro="colormap_macro_noRdYlBu_r_noViridis" />\n </param>\n </when>\n </conditional>\n@@ -707,7 +709,9 @@\n <when value="bed_rgb" />\n <when value="colormap">\n <param name="color" type="select" label="Color map to use for the scores" help=" Available color map names can be found here: https://matplotlib.org/examples/color/colormaps_reference.html">\n- <expand macro="colormap_macro" />\n+ <option value="RdYlBu_r">RdYlBu reversed</option>\n+ <option value="viridis">viridis</option>\n+ <expand macro="colormap_macro_noRdYlBu_r_noViridis" />\n </param>\n </when>\n </conditional>\n@@ -782,7 +786,9 @@\n </when>\n <when value="colormap">\n <param name="color" type="select" label="Color map to use for the scores" help=" Available color map names can be found here: https://matplotlib.org/examples/color/colormaps_reference.html">\n- <expand macro="colormap_macro" />\n+ <option value="RdYlBu_r">RdYlBu reversed</option>\n+ <option value="viridis">viridis</option>\n+ <expand macro="colormap_macro_noRdYlBu_r_noViridis" />\n </param>\n </when>\n </conditional>\n@@ -936,8 +942,9 @@\n </when>\n <when value="matrix">\n <param name="colormap" type="select" label="colormap">\n- <option value="viridis">Viridis</option>\n- <expand macro="colormap_macro" />\n+ <option value="viridis">viridis</option>\n+ <option value="RdYlBu_r">RdYlBu reversed</option>\n+ <expand macro="colormap_macro_noRdYlBu_r_noViridis" />\n </param>\n </when>\n </conditional>\n' |