Mercurial > repos > bgruening > hicexplorer_hicplottads
comparison hicPlotTADs.xml @ 7:94fff1a6a899 draft
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 |
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| 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" /> |