Mercurial > repos > bgruening > hicexplorer_hicplottads

comparison hicPlotTADs.xml @ 7:94fff1a6a899 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
author bgruening
date Wed, 07 Mar 2018 03:46:02 -0500
parents 144bf28956a7
children 7e535e3b71f3
comparison
equal deleted inserted replaced
6:36ef3cb8ae2e 7:94fff1a6a899
46 #end if 46 #end if
47 #if $track.track_file_style_conditional.max_value: 47 #if $track.track_file_style_conditional.max_value:
48 max_value = $track.track_file_style_conditional.max_value 48 max_value = $track.track_file_style_conditional.max_value
49 #end if 49 #end if
50 transform = $track.track_file_style_conditional.transform 50 transform = $track.track_file_style_conditional.transform
51 width = $track.track_file_style_conditional.width_matrix
51 #if $track.track_file_style_conditional.boundaries_file: 52 #if $track.track_file_style_conditional.boundaries_file:
52 boundaries_file = $track.track_file_style_conditional.boundaries_file 53 boundaries_file = $track.track_file_style_conditional.boundaries_file
53 #end if 54 #end if
54 #if $track.track_file_style_conditional.x_labels: 55 #if $track.track_file_style_conditional.x_labels:
55 x labels = $track.track_file_style_conditional.x_labels 56 x labels = $track.track_file_style_conditional.x_labels
73 #if $track.track_file_style_conditional.color: 74 #if $track.track_file_style_conditional.color:
74 color = $track.track_file_style_conditional.color 75 color = $track.track_file_style_conditional.color
75 #end if 76 #end if
76 #if $track.track_file_style_conditional.width_tad: 77 #if $track.track_file_style_conditional.width_tad:
77 width = $track.track_file_style_conditional.width_tad 78 width = $track.track_file_style_conditional.width_tad
79 #end if
80 #if $track.track_file_style_conditional.type_lines:
81 type = $track.track_file_style_conditional.type_lines
78 #end if 82 #end if
79 #if $track.track_file_style_conditional.show_data: 83 #if $track.track_file_style_conditional.show_data:
80 show data range = $track.track_file_style_conditional.show_data 84 show data range = $track.track_file_style_conditional.show_data
81 #end if 85 #end if
82 86
244 <conditional name="track_file_style_conditional"> 248 <conditional name="track_file_style_conditional">
245 <param name="track_file_style_selector" type="select" label="Choose style of the track"> 249 <param name="track_file_style_selector" type="select" label="Choose style of the track">
246 <option value="hic_matrix_option">TAD visualization</option> 250 <option value="hic_matrix_option">TAD visualization</option>
247 <option value="chrom_states_option">Chromatine states</option> 251 <option value="chrom_states_option">Chromatine states</option>
248 <option value="tad_score_track_option">TAD score</option> 252 <option value="tad_score_track_option">TAD score</option>
249 <option value="gene_track_option">Gene track</option> 253 <option value="gene_track_option">Gene track / Bed track</option>
250 <option value="bigwig_track_option">Bigwig track</option> 254 <option value="bigwig_track_option">Bigwig track</option>
251 <option value="bedgraph_track_option">Bedgraph track </option> 255 <option value="bedgraph_track_option">Bedgraph track </option>
252 <option value="bedgraph_matrix_track_option">Bedgraph matrix track</option> 256 <option value="bedgraph_matrix_track_option">Bedgraph matrix track</option>
253 <option value="vlines_track_option">Vlines track</option> 257 <option value="vlines_track_option">Vlines track</option>
254 <option value="spacer_option">Spacer</option> 258 <option value="spacer_option">Spacer</option>
265 <option value="log1p" selected="True" >log1p</option> 269 <option value="log1p" selected="True" >log1p</option>
266 <option value="log">log</option> 270 <option value="log">log</option>
267 <option value="-log">-log</option> 271 <option value="-log">-log</option>
268 272
269 </param> 273 </param>
274 <param name="width_matrix" type="float" value="1.5" optional="True" label="Width"/>
275
270 <param name="type" type="select" optional="True" label="Plotting type"> 276 <param name="type" type="select" optional="True" label="Plotting type">
271 <option value="arcplot">arcplot</option> 277 <option value="arcplot">arcplot</option>
272 <option value="interaction">interaction</option> 278 <option value="interaction">interaction</option>
273 </param> 279 </param>
274 <param name="show_masked_bins" type="boolean" truevalue="yes" falsevalue="no" checked="false" 280 <param name="show_masked_bins" type="boolean" truevalue="yes" falsevalue="no" checked="false"
280 </when> 286 </when>
281 <when value="tad_score_track_option"> 287 <when value="tad_score_track_option">
282 <expand macro="plot_title" /> 288 <expand macro="plot_title" />
283 <expand macro="track_input_bedgraph_macro" /> 289 <expand macro="track_input_bedgraph_macro" />
284 <param name="color" type="color" value="#000000" label="Color of track" optional="True" /> 290 <param name="color" type="color" value="#000000" label="Color of track" optional="True" />
285 291 <param name="type_lines" type="boolean" truevalue="lines" falsevalue="" checked="false"
292 label="Set 'type' to 'lines'" help="if type is set as lines, then the TAD score lines are drawn instead
293 of the matrix set to lines if a heatmap representing the matrix is not wanted"/>
286 <param name="width_tad" type="float" value="0.2" optional="True" label="Width"/> 294 <param name="width_tad" type="float" value="0.2" optional="True" label="Width"/>
287 <param name='show_data' type="boolean" truevalue="yes" falsevalue="no" checked="false" optional="True" label="Show visualization of data range" /> 295 <param name='show_data' type="boolean" truevalue="yes" falsevalue="no" checked="false" optional="True" label="Show visualization of data range" />
288 </when> 296 </when>
289 <when value="chrom_states_option"> 297 <when value="chrom_states_option">
290 <expand macro="plot_title" /> 298 <expand macro="plot_title" />