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comparison pyGenomeTracks.xml @ 10:a1abfa420d9d draft

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"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
comparison
equal deleted inserted replaced
9:2824d77cd8f8 10:a1abfa420d9d
1 <tool id="pygenomeTracks" name="@BINARY@" version="@WRAPPER_VERSION@"> 1 <tool id="pygenomeTracks" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
2 <description>plot genomic data tracks</description> 2 <description>plot genomic data tracks</description>
3 <macros> 3 <macros>
4 <token name="@BINARY@">pyGenomeTracks</token> 4 <token name="@BINARY@">pyGenomeTracks</token>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
54 file = ${counter}_${counter_matrix}.$ext 54 file = ${counter}_${counter_matrix}.$ext
55 file_type = hic_matrix 55 file_type = hic_matrix
56 #if $track.track_file_style_conditional.title: 56 #if $track.track_file_style_conditional.title:
57 title = $track.track_file_style_conditional.title 57 title = $track.track_file_style_conditional.title
58 #else: 58 #else:
59 title = $data_matrix.name 59 title = $data_matrix.element_identifier
60 #end if 60 #end if
61 #if $track.track_file_style_conditional.depth: 61 #if $track.track_file_style_conditional.depth:
62 depth = $track.track_file_style_conditional.depth 62 depth = $track.track_file_style_conditional.depth
63 #end if 63 #end if
64 #if $track.track_file_style_conditional.colormap: 64 #if $track.track_file_style_conditional.colormap:
112 [chrom states_$counter] 112 [chrom states_$counter]
113 file = $data_bed 113 file = $data_bed
114 #if $track.track_file_style_conditional.title: 114 #if $track.track_file_style_conditional.title:
115 title = $track.track_file_style_conditional.title 115 title = $track.track_file_style_conditional.title
116 #else: 116 #else:
117 title = $data_bed.name 117 title = $data_bed.element_identifier
118 #end if 118 #end if
119 #if $track.track_file_style_conditional.color_bed.color_bed_select == "bed_rgb": 119 #if $track.track_file_style_conditional.color_bed.color_bed_select == "bed_rgb":
120 color = bed_rgb 120 color = bed_rgb
121 #elif $track.track_file_style_conditional.color_bed.color: 121 #elif $track.track_file_style_conditional.color_bed.color:
122 color = $track.track_file_style_conditional.color_bed.color 122 color = $track.track_file_style_conditional.color_bed.color
151 merge_transcripts = $track.track_file_style_conditional.bed_style.bed_advanced.gtf.merge_transcripts 151 merge_transcripts = $track.track_file_style_conditional.bed_style.bed_advanced.gtf.merge_transcripts
152 #end if 152 #end if
153 #if $track.track_file_style_conditional.title: 153 #if $track.track_file_style_conditional.title:
154 title = $track.track_file_style_conditional.title 154 title = $track.track_file_style_conditional.title
155 #elif $track.track_file_style_conditional.overlay_select == 'no': 155 #elif $track.track_file_style_conditional.overlay_select == 'no':
156 title = $data_bed.name 156 title = $data_bed.element_identifier
157 #end if 157 #end if
158 #if $track.track_file_style_conditional.color_bed.color_bed_select == "bed_rgb": 158 #if $track.track_file_style_conditional.color_bed.color_bed_select == "bed_rgb":
159 color = bed_rgb 159 color = bed_rgb
160 #elif $track.track_file_style_conditional.color_bed.color: 160 #elif $track.track_file_style_conditional.color_bed.color:
161 color = $track.track_file_style_conditional.color_bed.color 161 color = $track.track_file_style_conditional.color_bed.color
224 [links_$counter] 224 [links_$counter]
225 file = $track.track_file_style_conditional.track_input_link 225 file = $track.track_file_style_conditional.track_input_link
226 #if $track.track_file_style_conditional.title: 226 #if $track.track_file_style_conditional.title:
227 title = $track.track_file_style_conditional.title 227 title = $track.track_file_style_conditional.title
228 #elif $track.track_file_style_conditional.overlay_select == 'no': 228 #elif $track.track_file_style_conditional.overlay_select == 'no':
229 title = $track.track_file_style_conditional.track_input_link.name 229 title = $track.track_file_style_conditional.track_input_link.element_identifier
230 #end if 230 #end if
231 #if $track.track_file_style_conditional.height: 231 #if $track.track_file_style_conditional.height:
232 height = $track.track_file_style_conditional.height 232 height = $track.track_file_style_conditional.height
233 #end if 233 #end if
234 #if $track.track_file_style_conditional.min_value != "": 234 #if $track.track_file_style_conditional.min_value != "":
265 [narrow_peak_${counter}_${counter_narrow_peak}] 265 [narrow_peak_${counter}_${counter_narrow_peak}]
266 file = $data_narrow_peak 266 file = $data_narrow_peak
267 #if $track.track_file_style_conditional.title: 267 #if $track.track_file_style_conditional.title:
268 title = $track.track_file_style_conditional.title 268 title = $track.track_file_style_conditional.title
269 #elif $track.track_file_style_conditional.overlay_select == 'no': 269 #elif $track.track_file_style_conditional.overlay_select == 'no':
270 title = $data_narrow_peak.name 270 title = $data_narrow_peak.element_identifier
271 #end if 271 #end if
272 color = $track.track_file_style_conditional.color 272 color = $track.track_file_style_conditional.color
273 type = $track.track_file_style_conditional.display.display_selector 273 type = $track.track_file_style_conditional.display.display_selector
274 use_summit = $track.track_file_style_conditional.display.use_summit 274 use_summit = $track.track_file_style_conditional.display.use_summit
275 #if $track.track_file_style_conditional.display.display_selector == "peak": 275 #if $track.track_file_style_conditional.display.display_selector == "peak":
311 [bedgraph_$counter] 311 [bedgraph_$counter]
312 file = $data_bedgraph 312 file = $data_bedgraph
313 #if $track.track_file_style_conditional.title: 313 #if $track.track_file_style_conditional.title:
314 title = $track.track_file_style_conditional.title 314 title = $track.track_file_style_conditional.title
315 #elif $track.track_file_style_conditional.overlay_select == "no": 315 #elif $track.track_file_style_conditional.overlay_select == "no":
316 title = $data_bedgraph.name 316 title = $data_bedgraph.element_identifier
317 #end if 317 #end if
318 #if $track.track_file_style_conditional.color: 318 #if $track.track_file_style_conditional.color:
319 color = $track.track_file_style_conditional.color 319 color = $track.track_file_style_conditional.color
320 #end if 320 #end if
321 alpha = $track.track_file_style_conditional.alpha 321 alpha = $track.track_file_style_conditional.alpha
386 [bigwig_$counter] 386 [bigwig_$counter]
387 file = $data_bigwig 387 file = $data_bigwig
388 #if $track.track_file_style_conditional.title: 388 #if $track.track_file_style_conditional.title:
389 title = $track.track_file_style_conditional.title 389 title = $track.track_file_style_conditional.title
390 #elif $track.track_file_style_conditional.overlay_select == "no": 390 #elif $track.track_file_style_conditional.overlay_select == "no":
391 title = $data_bigwig.name 391 title = $data_bigwig.element_identifier
392 #end if 392 #end if
393 #if $track.track_file_style_conditional.color: 393 #if $track.track_file_style_conditional.color:
394 color = $track.track_file_style_conditional.color 394 color = $track.track_file_style_conditional.color
395 #end if 395 #end if
396 alpha = $track.track_file_style_conditional.alpha 396 alpha = $track.track_file_style_conditional.alpha
450 [bedgraph_matrix_$counter] 450 [bedgraph_matrix_$counter]
451 file = $data_bedgraph_matrix 451 file = $data_bedgraph_matrix
452 #if $track.track_file_style_conditional.title: 452 #if $track.track_file_style_conditional.title:
453 title = $track.track_file_style_conditional.title 453 title = $track.track_file_style_conditional.title
454 #else: 454 #else:
455 title = $data_bedgraph_matrix.name 455 title = $data_bedgraph_matrix.element_identifier
456 #end if 456 #end if
457 #if $track.track_file_style_conditional.height_bedgraph: 457 #if $track.track_file_style_conditional.height_bedgraph:
458 height = $track.track_file_style_conditional.height_bedgraph 458 height = $track.track_file_style_conditional.height_bedgraph
459 #end if 459 #end if
460 #if $track.track_file_style_conditional.min_value != "": 460 #if $track.track_file_style_conditional.min_value != "":
621 The order you add them represent the order they will be plotted from top to bottom."> 621 The order you add them represent the order they will be plotted from top to bottom.">
622 <conditional name="track_file_style_conditional"> 622 <conditional name="track_file_style_conditional">
623 <param name="track_file_style_selector" type="select" label="Choose style of the track"> 623 <param name="track_file_style_selector" type="select" label="Choose style of the track">
624 <option value="hic_matrix_option">TAD visualization</option> 624 <option value="hic_matrix_option">TAD visualization</option>
625 <option value="chrom_states_option">Chromatine states</option> 625 <option value="chrom_states_option">Chromatine states</option>
626 <option value="bedgraph_matrix_track_option">TAD score</option>
627 <option value="gene_track_option">Gene track / Bed track</option> 626 <option value="gene_track_option">Gene track / Bed track</option>
628 <option value="link_track_option">Link track</option> 627 <option value="link_track_option">Link track</option>
629 <option value="narrow_peak_track_option">NarrowPeak track</option> 628 <option value="narrow_peak_track_option">NarrowPeak track</option>
630 <option value="bigwig_track_option">Bigwig track</option> 629 <option value="bigwig_track_option">Bigwig track</option>
631 <option value="bedgraph_track_option">Bedgraph track </option> 630 <option value="bedgraph_track_option">Bedgraph track </option>
632 <option value="bedgraph_matrix_track_option">Bedgraph matrix track</option> 631 <option value="bedgraph_matrix_track_option">Bedgraph matrix track/TAD score</option>
633 <option value="vlines_track_option">Vlines track</option> 632 <option value="vlines_track_option">Vlines track</option>
634 <option value="hlines_track_option">Hlines track</option> 633 <option value="hlines_track_option">Hlines track</option>
635 <option value="spacer_option">Spacer</option> 634 <option value="spacer_option">Spacer</option>
636 <option value="xaxis_option">X-axis</option> 635 <option value="xaxis_option">X-axis</option>
637 <option value="scale_bar_option">Scale bar track</option> 636 <option value="scale_bar_option">Scale bar track</option>
640 <expand macro="plot_title" /> 639 <expand macro="plot_title" />
641 <expand macro="matrix_h5_cooler_multiple_macro" /> 640 <expand macro="matrix_h5_cooler_multiple_macro" />
642 641
643 <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"> 642 <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">
644 <option value="RdYlBu_r">RdYlBu reversed</option> 643 <option value="RdYlBu_r">RdYlBu reversed</option>
645 <expand macro="colormap_macro"/> 644 <option value="viridis">viridis</option>
645 <expand macro="colormap_macro_noRdYlBu_r_noViridis"/>
646 </param> 646 </param>
647 <param name="depth" type="integer" value="8000000" optional="True" label="Depth" /> 647 <param name="depth" type="integer" value="8000000" optional="True" label="Depth" />
648 <expand macro="minmax_macro" /> 648 <expand macro="minmax_macro" />
649 <param name="transform" type="select" label="Plot the transformed value"> 649 <param name="transform" type="select" label="Plot the transformed value">
650 <option value="log1p" selected="True" >log1p</option> 650 <option value="log1p" selected="True" >log1p</option>
677 <param name="color" type="color" value="#000000" label="Color of track" optional="True" /> 677 <param name="color" type="color" value="#000000" label="Color of track" optional="True" />
678 </when> 678 </when>
679 <when value="bed_rgb" /> 679 <when value="bed_rgb" />
680 <when value="colormap"> 680 <when value="colormap">
681 <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"> 681 <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">
682 <expand macro="colormap_macro" /> 682 <option value="RdYlBu_r">RdYlBu reversed</option>
683 <option value="viridis">viridis</option>
684 <expand macro="colormap_macro_noRdYlBu_r_noViridis" />
683 </param> 685 </param>
684 </when> 686 </when>
685 </conditional> 687 </conditional>
686 <expand macro="border_color_bed_macro" /> 688 <expand macro="border_color_bed_macro" />
687 <param name="line_width" type="float" value="0.5" label="width of lines" /> 689 <param name="line_width" type="float" value="0.5" label="width of lines" />
705 <param name="color" type="color" value="#000000" label="Color of track" optional="True" /> 707 <param name="color" type="color" value="#000000" label="Color of track" optional="True" />
706 </when> 708 </when>
707 <when value="bed_rgb" /> 709 <when value="bed_rgb" />
708 <when value="colormap"> 710 <when value="colormap">
709 <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"> 711 <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">
710 <expand macro="colormap_macro" /> 712 <option value="RdYlBu_r">RdYlBu reversed</option>
713 <option value="viridis">viridis</option>
714 <expand macro="colormap_macro_noRdYlBu_r_noViridis" />
711 </param> 715 </param>
712 </when> 716 </when>
713 </conditional> 717 </conditional>
714 <expand macro="border_color_bed_macro" /> 718 <expand macro="border_color_bed_macro" />
715 <param name="height_bed" type="float" value="1.5" optional="True" label="height"/> 719 <param name="height_bed" type="float" value="1.5" optional="True" label="height"/>
780 <when value="manually"> 784 <when value="manually">
781 <param name="color" type="color" value="#000000" label="Color of track" optional="True" /> 785 <param name="color" type="color" value="#000000" label="Color of track" optional="True" />
782 </when> 786 </when>
783 <when value="colormap"> 787 <when value="colormap">
784 <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"> 788 <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">
785 <expand macro="colormap_macro" /> 789 <option value="RdYlBu_r">RdYlBu reversed</option>
790 <option value="viridis">viridis</option>
791 <expand macro="colormap_macro_noRdYlBu_r_noViridis" />
786 </param> 792 </param>
787 </when> 793 </when>
788 </conditional> 794 </conditional>
789 <expand macro="lines_macro" /> 795 <expand macro="lines_macro" />
790 <param name="links_type" type="select" label="Representation of the link:"> 796 <param name="links_type" type="select" label="Representation of the link:">
934 <option value="block">Block (draw a horizontal line between start and end)</option> 940 <option value="block">Block (draw a horizontal line between start and end)</option>
935 </param> 941 </param>
936 </when> 942 </when>
937 <when value="matrix"> 943 <when value="matrix">
938 <param name="colormap" type="select" label="colormap"> 944 <param name="colormap" type="select" label="colormap">
939 <option value="viridis">Viridis</option> 945 <option value="viridis">viridis</option>
940 <expand macro="colormap_macro" /> 946 <option value="RdYlBu_r">RdYlBu reversed</option>
947 <expand macro="colormap_macro_noRdYlBu_r_noViridis" />
941 </param> 948 </param>
942 </when> 949 </when>
943 </conditional> 950 </conditional>
944 951
945 952