Mercurial > repos > iuc > pygenometracks

comparison pyGenomeTracks.xml @ 12:14e7c35f3d00 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 26f4478d873b339c5a1eccf18df68700a145a404
author iuc
date Wed, 25 Jan 2023 15:33:12 +0000
parents 7dd841a32245
children 360df4999907
comparison
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11:7dd841a32245 12:14e7c35f3d00
579 ## Vlines: 579 ## Vlines:
580 #if $track.track_file_style_conditional.track_file_style_selector == "vlines_track_option": 580 #if $track.track_file_style_conditional.track_file_style_selector == "vlines_track_option":
581 [vlines_$counter] 581 [vlines_$counter]
582 file = $track.track_file_style_conditional.track_input_bed_single 582 file = $track.track_file_style_conditional.track_input_bed_single
583 line_width = $track.track_file_style_conditional.line_width 583 line_width = $track.track_file_style_conditional.line_width
584 line_style = $track.track_file_style_conditional.line_style
585 color = $track.track_file_style_conditional.color
586 alpha = $track.track_file_style_conditional.alpha
587 zorder = $track.track_file_style_conditional.zorder
584 type = vlines 588 type = vlines
585 #end if 589 #end if
586 590
587 ## Vhighlight: 591 ## Vhighlight:
588 #if $track.track_file_style_conditional.track_file_style_selector == "vhighlight_track_option": 592 #if $track.track_file_style_conditional.track_file_style_selector == "vhighlight_track_option":
589 [vhighlight_$counter] 593 [vhighlight_$counter]
590 file = $track.track_file_style_conditional.track_input_bed_single 594 file = $track.track_file_style_conditional.track_input_bed_single
595 line_width = $track.track_file_style_conditional.line_width
591 color = $track.track_file_style_conditional.color 596 color = $track.track_file_style_conditional.color
592 alpha = $track.track_file_style_conditional.alpha 597 alpha = $track.track_file_style_conditional.alpha
598 border_color = $track.track_file_style_conditional.border_color
593 type = vhighlight 599 type = vhighlight
594 #end if 600 #end if
595 601
596 ## Hlines: 602 ## Hlines:
597 #if $track.track_file_style_conditional.track_file_style_selector == "hlines_track_option": 603 #if $track.track_file_style_conditional.track_file_style_selector == "hlines_track_option":
1183 1189
1184 </when> 1190 </when>
1185 <when value="vlines_track_option"> 1191 <when value="vlines_track_option">
1186 <expand macro="track_input_bed_single_macro" /> 1192 <expand macro="track_input_bed_single_macro" />
1187 <param name="line_width" type="float" value="0.5" label="width of lines"/> 1193 <param name="line_width" type="float" value="0.5" label="width of lines"/>
1194 <param name="line_style" type="select" label="Line Style">
1195 <option value="dashed">Dashed</option>
1196 <option value="solid">Solid</option>
1197 <option value="dotted">Dotted</option>
1198 <option value="dashdot">Dashdot</option>
1199 </param>
1200 <param name="color" type="color" value="black" label="color of the vline"/>
1201 <param name="alpha" type="float" value="0.7" min="0" max="1" label="transparency (alpha) of the vline"/>
1202 <param name="zorder" type="select" label="Plot the vline above or behind other tracks">
1203 <option value="100">above</option>
1204 <option value="-100">behind</option>
1205 </param>
1188 </when> 1206 </when>
1189 <when value="vhighlight_track_option"> 1207 <when value="vhighlight_track_option">
1190 <expand macro="track_input_bed_single_macro" /> 1208 <expand macro="track_input_bed_single_macro" />
1191 <param name="color" type="color" value="yellow" label="color of the highlight"/> 1209 <param name="color" type="color" value="yellow" label="color of the highlight"/>
1192 <param name="alpha" type="float" value="0.5" min="0" max="1" label="transparency (alpha) of the highlight"/> 1210 <param name="alpha" type="float" value="0.5" min="0" max="1" label="transparency (alpha) of the highlight"/>
1211 <param name="line_width" type="float" min="0" value="0.5" label="width of the edge of the highlight" />
1212 <param name="border_color" type="color" value="yellow" label="color of the edge of the highlight"/>
1213 <param name="zorder" type="select" label="Plot the highlight above or behind other tracks">
1214 <option value="-100">behind</option>
1215 <option value="100">above</option>
1216 </param>
1193 </when> 1217 </when>
1194 <when value="hlines_track_option"> 1218 <when value="hlines_track_option">
1195 <expand macro="plot_title" /> 1219 <expand macro="plot_title" />
1196 <param name="y_values" type="text" value="10, 200" label="Values where horizontal lines should be plotted separated by comma"/> 1220 <param name="y_values" type="text" value="10, 200" label="Values where horizontal lines should be plotted separated by comma"/>
1197 <param name="color" type="color" value="#000000" label="Color of line(s)" optional="True" /> 1221 <param name="color" type="color" value="#000000" label="Color of line(s)" optional="True" />
2167 </repeat> 2191 </repeat>
2168 <repeat name="tracks"> 2192 <repeat name="tracks">
2169 <conditional name="track_file_style_conditional"> 2193 <conditional name="track_file_style_conditional">
2170 <param name="track_file_style_selector" value="vlines_track_option" /> 2194 <param name="track_file_style_selector" value="vlines_track_option" />
2171 <param name="track_input_bed_single" value="dm3_subset_BDGP5.78_asbed4.bed.gz" ftype="bed" /> 2195 <param name="track_input_bed_single" value="dm3_subset_BDGP5.78_asbed4.bed.gz" ftype="bed" />
2196 <param name="line_width" value="2"/>
2197 <param name="zorder" value="100"/>
2198 <param name="color" value="red"/>
2199 </conditional>
2200 </repeat>
2201 <repeat name="tracks">
2202 <conditional name="track_file_style_conditional">
2203 <param name="track_file_style_selector" value="vlines_track_option" />
2204 <param name="track_input_bed_single" value="dm3_genes_end.bed" ftype="bed" />
2205 <param name="line_width" value="5"/>
2206 <param name="zorder" value="-100"/>
2207 <param name="color" value="blue"/>
2208 <param name="line_style" value="solid"/>
2172 </conditional> 2209 </conditional>
2173 </repeat> 2210 </repeat>
2174 <param name="image_file_format" value="png" /> 2211 <param name="image_file_format" value="png" />
2175 <output name="outFileName" file="test_arrowhead_zoom.png" ftype="png" compare="sim_size" delta="100" /> 2212 <output name="outFileName" file="test_arrowhead_zoom.png" ftype="png" compare="sim_size" delta="100" />
2176 </test> 2213 </test>
3334 _________________ 3371 _________________
3335 3372
3336 Output 3373 Output
3337 ------ 3374 ------
3338 3375
3339 **pyGenomeTracks** output is similar to a genome browser screen-shot that besides the usual genes, and score data (like bigwig or bedgraph files) 3376 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):
3340 may also contains Hi-C data. The plot is composed of tracks that need to be specified. 3377
3341 Below is represented the 85 Mb to 110 Mb region from human chromosome 2 visualized using **pyGenomeTracks**. 3378 .. image:: static/images/demo.png
3342 TADs were computed by HiCExplorer's ``hicFindTADs``. The additional tracks added correspond to: 3379 :width: 45 %
3343 TAD-separation score (as reported by HiCExplorer's ``hicFindTADs``), chromatin states, 3380 .. image:: static/images/demo2.png
3344 principal component 1 (A/B compartment) computed using HiCExplorer's ``hicPCA``, ChIP-seq coverage for the H3K27ac mark, DNA methylation, and a gene track. 3381 :width: 45 %
3345 Data are from mouse cardiac myocytes, published by `Nothjunge et al. (2017)`_. 3382
3346
3347 .. image:: $PATH_TO_IMAGES/pyGenomeTracks.png
3348 :width: 70 %
3349 3383
3350 _________________ 3384 _________________
3351 3385
3352 | For more information about pyGenomeTracks please consider our documentation on readthedocs_ or github_ 3386 | For more information about pyGenomeTracks please consider our documentation on readthedocs_ or github_
3353 3387