Mercurial > repos > iuc > pygenometracks
changeset 10:a1abfa420d9d draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 5bd033a726b088eef3cf591da36ca1e9ba70d8c7"
| author | iuc |
|---|---|
| date | Sun, 13 Feb 2022 22:43:45 +0000 |
| parents | 2824d77cd8f8 |
| children | 7dd841a32245 |
| files | macros.xml pyGenomeTracks.xml |
| diffstat | 2 files changed, 28 insertions(+), 23 deletions(-) [+] |
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--- 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>
--- a/pyGenomeTracks.xml Wed Nov 18 21:33:46 2020 +0000 +++ b/pyGenomeTracks.xml Sun Feb 13 22:43:45 2022 +0000 @@ -1,4 +1,4 @@ -<tool id="pygenomeTracks" name="@BINARY@" version="@WRAPPER_VERSION@"> +<tool id="pygenomeTracks" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> <description>plot genomic data tracks</description> <macros> <token name="@BINARY@">pyGenomeTracks</token> @@ -56,7 +56,7 @@ #if $track.track_file_style_conditional.title: title = $track.track_file_style_conditional.title #else: -title = $data_matrix.name +title = $data_matrix.element_identifier #end if #if $track.track_file_style_conditional.depth: depth = $track.track_file_style_conditional.depth @@ -114,7 +114,7 @@ #if $track.track_file_style_conditional.title: title = $track.track_file_style_conditional.title #else: -title = $data_bed.name +title = $data_bed.element_identifier #end if #if $track.track_file_style_conditional.color_bed.color_bed_select == "bed_rgb": color = bed_rgb @@ -153,7 +153,7 @@ #if $track.track_file_style_conditional.title: title = $track.track_file_style_conditional.title #elif $track.track_file_style_conditional.overlay_select == 'no': -title = $data_bed.name +title = $data_bed.element_identifier #end if #if $track.track_file_style_conditional.color_bed.color_bed_select == "bed_rgb": color = bed_rgb @@ -226,7 +226,7 @@ #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.name +title = $track.track_file_style_conditional.track_input_link.element_identifier #end if #if $track.track_file_style_conditional.height: height = $track.track_file_style_conditional.height @@ -267,7 +267,7 @@ #if $track.track_file_style_conditional.title: title = $track.track_file_style_conditional.title #elif $track.track_file_style_conditional.overlay_select == 'no': -title = $data_narrow_peak.name +title = $data_narrow_peak.element_identifier #end if color = $track.track_file_style_conditional.color type = $track.track_file_style_conditional.display.display_selector @@ -313,7 +313,7 @@ #if $track.track_file_style_conditional.title: title = $track.track_file_style_conditional.title #elif $track.track_file_style_conditional.overlay_select == "no": -title = $data_bedgraph.name +title = $data_bedgraph.element_identifier #end if #if $track.track_file_style_conditional.color: color = $track.track_file_style_conditional.color @@ -388,7 +388,7 @@ #if $track.track_file_style_conditional.title: title = $track.track_file_style_conditional.title #elif $track.track_file_style_conditional.overlay_select == "no": -title = $data_bigwig.name +title = $data_bigwig.element_identifier #end if #if $track.track_file_style_conditional.color: color = $track.track_file_style_conditional.color @@ -452,7 +452,7 @@ #if $track.track_file_style_conditional.title: title = $track.track_file_style_conditional.title #else: -title = $data_bedgraph_matrix.name +title = $data_bedgraph_matrix.element_identifier #end if #if $track.track_file_style_conditional.height_bedgraph: height = $track.track_file_style_conditional.height_bedgraph @@ -623,13 +623,12 @@ <param name="track_file_style_selector" type="select" label="Choose style of the track"> <option value="hic_matrix_option">TAD visualization</option> <option value="chrom_states_option">Chromatine states</option> - <option value="bedgraph_matrix_track_option">TAD score</option> <option value="gene_track_option">Gene track / Bed track</option> <option value="link_track_option">Link track</option> <option value="narrow_peak_track_option">NarrowPeak track</option> <option value="bigwig_track_option">Bigwig track</option> <option value="bedgraph_track_option">Bedgraph track </option> - <option value="bedgraph_matrix_track_option">Bedgraph matrix track</option> + <option value="bedgraph_matrix_track_option">Bedgraph matrix track/TAD score</option> <option value="vlines_track_option">Vlines track</option> <option value="hlines_track_option">Hlines track</option> <option value="spacer_option">Spacer</option> @@ -642,7 +641,8 @@ <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"> <option value="RdYlBu_r">RdYlBu reversed</option> - <expand macro="colormap_macro"/> + <option value="viridis">viridis</option> + <expand macro="colormap_macro_noRdYlBu_r_noViridis"/> </param> <param name="depth" type="integer" value="8000000" optional="True" label="Depth" /> <expand macro="minmax_macro" /> @@ -679,7 +679,9 @@ <when value="bed_rgb" /> <when value="colormap"> <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"> - <expand macro="colormap_macro" /> + <option value="RdYlBu_r">RdYlBu reversed</option> + <option value="viridis">viridis</option> + <expand macro="colormap_macro_noRdYlBu_r_noViridis" /> </param> </when> </conditional> @@ -707,7 +709,9 @@ <when value="bed_rgb" /> <when value="colormap"> <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"> - <expand macro="colormap_macro" /> + <option value="RdYlBu_r">RdYlBu reversed</option> + <option value="viridis">viridis</option> + <expand macro="colormap_macro_noRdYlBu_r_noViridis" /> </param> </when> </conditional> @@ -782,7 +786,9 @@ </when> <when value="colormap"> <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"> - <expand macro="colormap_macro" /> + <option value="RdYlBu_r">RdYlBu reversed</option> + <option value="viridis">viridis</option> + <expand macro="colormap_macro_noRdYlBu_r_noViridis" /> </param> </when> </conditional> @@ -936,8 +942,9 @@ </when> <when value="matrix"> <param name="colormap" type="select" label="colormap"> - <option value="viridis">Viridis</option> - <expand macro="colormap_macro" /> + <option value="viridis">viridis</option> + <option value="RdYlBu_r">RdYlBu reversed</option> + <expand macro="colormap_macro_noRdYlBu_r_noViridis" /> </param> </when> </conditional>