Mercurial > repos > iuc > pygenometracks
comparison pyGenomeTracks.xml @ 5:eca03db4f612 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
| author | iuc |
|---|---|
| date | Wed, 08 Jan 2020 09:15:19 -0500 |
| parents | c237ba772225 |
| children | 5cec5fb749f0 |
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| 4:c237ba772225 | 5:eca03db4f612 |
|---|---|
| 1 <tool id="pygenomeTracks" name="@BINARY@" version="@WRAPPER_VERSION@.1"> | 1 <tool id="pygenomeTracks" name="@BINARY@" version="@WRAPPER_VERSION@"> |
| 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> |
| 7 <expand macro="requirements" /> | 7 <expand macro="requirements" /> |
| 8 <command detect_errors="exit_code"> | 8 <command detect_errors="exit_code"> |
| 9 <![CDATA[ | 9 <![CDATA[ |
| 10 ## First symlink data of hic or bed/gtf to have the good extension | |
| 10 #for $counter, $track in enumerate($tracks): | 11 #for $counter, $track in enumerate($tracks): |
| 11 #if $track.track_file_style_conditional.track_file_style_selector == "hic_matrix_option": | 12 #if $track.track_file_style_conditional.track_file_style_selector == "hic_matrix_option": |
| 12 #for $counter_matrix, $data_matrix in enumerate($track.track_file_style_conditional.matrix_h5_cooler_multiple): | 13 #for $counter_matrix, $data_matrix in enumerate($track.track_file_style_conditional.matrix_h5_cooler_multiple): |
| 13 #set ext = $data_matrix.extension | 14 #set ext = $data_matrix.extension |
| 14 ln -s $data_matrix ${counter}_${counter_matrix}.$ext && | 15 ln -s $data_matrix ${counter}_${counter_matrix}.$ext && |
| 33 && mv plot.$image_file_format plot | 34 && mv plot.$image_file_format plot |
| 34 ]]> | 35 ]]> |
| 35 </command> | 36 </command> |
| 36 <configfiles> | 37 <configfiles> |
| 37 <configfile name="tracks_config"> | 38 <configfile name="tracks_config"> |
| 38 #if $x_axis.x_axis_select == "yes": | 39 ## First the xaxis if where = top |
| 39 #if $x_axis.where == 'top': | 40 #if $x_axis.x_axis_select == "true": |
| 41 #if $x_axis.where == 'top': | |
| 40 [x-axis] | 42 [x-axis] |
| 41 #if $x_axis.fontsize: | 43 #if $x_axis.fontsize: |
| 42 fontsize = $x_axis.fontsize | 44 fontsize = $x_axis.fontsize |
| 45 #end if | |
| 46 where = top | |
| 47 #end if | |
| 43 #end if | 48 #end if |
| 44 #if $x_axis.where: | 49 |
| 45 where = $x_axis.where | 50 ## Then each track: |
| 46 #end if | |
| 47 #end if | |
| 48 #end if | |
| 49 #for $counter, $track in enumerate($tracks): | 51 #for $counter, $track in enumerate($tracks): |
| 50 #if $track.track_file_style_conditional.track_file_style_selector == "hic_matrix_option": | 52 ## Hi-C Track |
| 51 | 53 #if $track.track_file_style_conditional.track_file_style_selector == "hic_matrix_option": |
| 52 #for $counter_matrix, $data_matrix in enumerate($track.track_file_style_conditional.matrix_h5_cooler_multiple): | 54 #for $counter_matrix, $data_matrix in enumerate($track.track_file_style_conditional.matrix_h5_cooler_multiple): |
| 53 [hic_section_${counter}_${counter_matrix}] | 55 [hic_section_${counter}_${counter_matrix}] |
| 54 #set ext = $data_matrix.extension | 56 #set ext = $data_matrix.extension |
| 55 file = ${counter}_${counter_matrix}.$ext | 57 file = ${counter}_${counter_matrix}.$ext |
| 56 file_type = hic_matrix | 58 file_type = hic_matrix |
| 57 #if $track.track_file_style_conditional.title: | 59 #if $track.track_file_style_conditional.title: |
| 58 title = $track.track_file_style_conditional.title | 60 title = $track.track_file_style_conditional.title |
| 59 #else: | 61 #else: |
| 60 title = $data_matrix.name | 62 title = $data_matrix.name |
| 61 #end if | 63 #end if |
| 62 #if $track.track_file_style_conditional.depth: | 64 #if $track.track_file_style_conditional.depth: |
| 63 depth = $track.track_file_style_conditional.depth | 65 depth = $track.track_file_style_conditional.depth |
| 64 #end if | 66 #end if |
| 65 #if $track.track_file_style_conditional.colormap: | 67 #if $track.track_file_style_conditional.colormap: |
| 66 colormap = $track.track_file_style_conditional.colormap | 68 colormap = $track.track_file_style_conditional.colormap |
| 67 #end if | 69 #end if |
| 68 #if $track.track_file_style_conditional.min_value: | 70 #if $track.track_file_style_conditional.min_value: |
| 69 min_value = $track.track_file_style_conditional.min_value | 71 min_value = $track.track_file_style_conditional.min_value |
| 70 #end if | 72 #end if |
| 71 #if $track.track_file_style_conditional.max_value: | 73 #if $track.track_file_style_conditional.max_value: |
| 72 max_value = $track.track_file_style_conditional.max_value | 74 max_value = $track.track_file_style_conditional.max_value |
| 73 #end if | 75 #end if |
| 74 #if $track.track_file_style_conditional.transform != "": | |
| 75 transform = $track.track_file_style_conditional.transform | 76 transform = $track.track_file_style_conditional.transform |
| 76 #end if | 77 #if $track.track_file_style_conditional.height_matrix != "": |
| 77 #if $track.track_file_style_conditional.height_matrix != "": | |
| 78 height = $track.track_file_style_conditional.height_matrix | 78 height = $track.track_file_style_conditional.height_matrix |
| 79 #end if | 79 #end if |
| 80 | 80 #if $track.track_file_style_conditional.show_masked_bins: |
| 81 #if $track.track_file_style_conditional.show_masked_bins: | |
| 82 show_masked_bins = $track.track_file_style_conditional.show_masked_bins | 81 show_masked_bins = $track.track_file_style_conditional.show_masked_bins |
| 83 #end if | 82 #end if |
| 84 #if $track.track_file_style_conditional.invert_orientation: | 83 #if $track.track_file_style_conditional.invert_orientation: |
| 85 orientation = inverted | 84 orientation = inverted |
| 86 #end if | 85 #end if |
| 87 #if $track.track_file_style_conditional.scale_factor: | 86 #if $track.track_file_style_conditional.scale_factor: |
| 88 scale factor = $track.track_file_style_conditional.scale_factor | 87 scale_factor = $track.track_file_style_conditional.scale_factor |
| 89 #end if | 88 #end if |
| 90 | 89 rasterize = $track.track_file_style_conditional.rasterize |
| 91 #if str($track.track_file_style_conditional.boundaries_file) != "None": | 90 ## If a boundary file is given a new section needs to be written: |
| 92 #if len($track.track_file_style_conditional.boundaries_file)>$counter_matrix: | 91 #if str($track.track_file_style_conditional.boundaries_file) != "None": |
| 93 #set boundary_file = $track.track_file_style_conditional.boundaries_file[$counter_matrix] | 92 #if len($track.track_file_style_conditional.boundaries_file)>$counter_matrix: |
| 94 #else: | 93 #set boundary_file = $track.track_file_style_conditional.boundaries_file[$counter_matrix] |
| 95 #set boundary_file = $track.track_file_style_conditional.boundaries_file[0] | 94 #else: |
| 96 #end if | 95 #set boundary_file = $track.track_file_style_conditional.boundaries_file[0] |
| 96 #end if | |
| 97 [tads_${counter}_${counter_matrix}] | 97 [tads_${counter}_${counter_matrix}] |
| 98 file = $boundary_file | 98 file = $boundary_file |
| 99 file_type = domains | 99 file_type = domains |
| 100 border color = black | 100 border_color = black |
| 101 color = none | 101 color = none |
| 102 overlay previous = share-y | 102 overlay_previous = share-y |
| 103 #end if | 103 #end if |
| 104 | 104 ## If spacer is asked a new section is created: |
| 105 | 105 #if $track.track_file_style_conditional.spacer_height != "": |
| 106 #if $track.track_file_style_conditional.spacer_height != "": | |
| 107 [spacer] | 106 [spacer] |
| 108 height = $track.track_file_style_conditional.spacer_height | 107 height = $track.track_file_style_conditional.spacer_height |
| 109 #end if | 108 #end if |
| 110 #end for | 109 #end for |
| 111 | 110 #end if |
| 112 #end if | 111 |
| 113 | 112 ## Chrom_state track |
| 114 | 113 #if $track.track_file_style_conditional.track_file_style_selector == "chrom_states_option": |
| 115 | 114 #for $data_bed in $track.track_file_style_conditional.track_input_bed: |
| 116 #if $track.track_file_style_conditional.track_file_style_selector == "tad_score_track_option": | 115 [chrom states_$counter] |
| 117 | 116 file = $data_bed |
| 118 #for $data_bedgraph in $track.track_file_style_conditional.track_input_bedgraph: | 117 #if $track.track_file_style_conditional.title: |
| 119 [tad_score_$counter] | |
| 120 file = $data_bedgraph | |
| 121 #if $track.track_file_style_conditional.title: | |
| 122 title = $track.track_file_style_conditional.title | 118 title = $track.track_file_style_conditional.title |
| 123 #else: | 119 #else: |
| 124 title = $data_bedgraph.name | 120 title = $data_bed.name |
| 125 #end if | 121 #end if |
| 126 #if $track.track_file_style_conditional.color: | 122 #if $track.track_file_style_conditional.color_bed.color_bed_select == "bed_rgb": |
| 127 color = $track.track_file_style_conditional.color | 123 color = bed_rgb |
| 128 #end if | 124 #elif $track.track_file_style_conditional.color_bed.color: |
| 129 #if $track.track_file_style_conditional.height_tad: | 125 color = $track.track_file_style_conditional.color_bed.color |
| 130 height = $track.track_file_style_conditional.height_tad | 126 #end if |
| 131 #end if | 127 #if $track.track_file_style_conditional.border_color: |
| 132 show data range = $track.track_file_style_conditional.show_data | 128 border_color = $track.track_file_style_conditional.border_color |
| 133 | 129 #end if |
| 134 #set $columns = len(open(str($track.track_file_style_conditional.track_input_bedgraph)).readline().split('\t')) | 130 display = collapsed |
| 135 #if $columns > 4: | 131 #if $track.track_file_style_conditional.height_chrom: |
| 136 file_type = bedgraph_matrix | 132 height = $track.track_file_style_conditional.height_chrom |
| 137 #if $track.track_file_style_conditional.type_lines: | 133 #end if |
| 138 type = $track.track_file_style_conditional.type_lines | 134 line_width = $track.track_file_style_conditional.line_width |
| 139 #end if | 135 file_type = bed |
| 140 #else: | 136 ## If spacer is asked a new section is created: |
| 141 file_type = bedgraph | 137 #if $track.track_file_style_conditional.spacer_height != "": |
| 142 #end if | |
| 143 #if $track.track_file_style_conditional.spacer_height != "": | |
| 144 [spacer] | 138 [spacer] |
| 145 height = $track.track_file_style_conditional.spacer_height | 139 height = $track.track_file_style_conditional.spacer_height |
| 146 #end if | 140 #end if |
| 147 #end for | 141 #end for |
| 148 #end if | 142 #end if |
| 149 | 143 |
| 150 | 144 ## Gene/gtf track |
| 151 | 145 #if $track.track_file_style_conditional.track_file_style_selector == "gene_track_option": |
| 152 | 146 #for $counter_bed, $data_bed in enumerate($track.track_file_style_conditional.track_input_bed): |
| 153 #if $track.track_file_style_conditional.track_file_style_selector == "chrom_states_option": | 147 [genes_${counter}_${counter_bed}] |
| 154 #for $data_bed in $track.track_file_style_conditional.track_input_bed: | 148 #set ext = $data_bed.extension |
| 155 | 149 file = ${counter}_${counter_bed}.$ext |
| 156 [chrom states_$counter] | 150 #if $ext == 'gtf': |
| 157 file = $data_bed | 151 prefered_name = $track.track_file_style_conditional.bed_advanced.gtf.prefered_name |
| 158 #if $track.track_file_style_conditional.title: | 152 merge_transcripts = $track.track_file_style_conditional.bed_advanced.gtf.merge_transcripts |
| 153 #end if | |
| 154 #if $track.track_file_style_conditional.title: | |
| 159 title = $track.track_file_style_conditional.title | 155 title = $track.track_file_style_conditional.title |
| 160 #else: | 156 #elif $track.track_file_style_conditional.overlay_select == 'no': |
| 161 title = $data_bed.name | 157 title = $data_bed.name |
| 162 #end if | 158 #end if |
| 163 #if $track.track_file_style_conditional.color_bed.color_bed_select == "bed_rgb": | 159 #if $track.track_file_style_conditional.color_bed.color_bed_select == "bed_rgb": |
| 164 color = bed_rgb | 160 color = bed_rgb |
| 165 #elif $track.track_file_style_conditional.color_bed.color: | 161 #elif $track.track_file_style_conditional.color_bed.color: |
| 166 color = $track.track_file_style_conditional.color_bed.color | 162 color = $track.track_file_style_conditional.color_bed.color |
| 167 #end if | 163 #end if |
| 168 #if $track.track_file_style_conditional.border_color: | 164 #if $track.track_file_style_conditional.border_color: |
| 169 border color = $track.track_file_style_conditional.border_color | 165 border_color = $track.track_file_style_conditional.border_color |
| 170 #end if | 166 #end if |
| 171 display = collapsed | 167 #if $track.track_file_style_conditional.flybase: |
| 172 #if $track.track_file_style_conditional.height_chrom: | 168 style = flybase |
| 173 height = $track.track_file_style_conditional.height_chrom | 169 height_utr = $track.track_file_style_conditional.bed_advanced.flybase.height_utr |
| 174 #end if | 170 color_utr = $track.track_file_style_conditional.bed_advanced.flybase.color_utr |
| 171 #else | |
| 172 style = UCSC | |
| 173 arrow_interval = $track.track_file_style_conditional.bed_advanced.ucsc.arrow_interval | |
| 174 #end if | |
| 175 display = $track.track_file_style_conditional.display | |
| 176 #if $track.track_file_style_conditional.height_bed: | |
| 177 height = $track.track_file_style_conditional.height_bed | |
| 178 #end if | |
| 179 labels = $track.track_file_style_conditional.labels | |
| 175 file_type = bed | 180 file_type = bed |
| 176 #if $track.track_file_style_conditional.spacer_height != "": | 181 #if $track.track_file_style_conditional.fontsize: |
| 182 fontsize = $track.track_file_style_conditional.fontsize | |
| 183 #end if | |
| 184 #if $track.track_file_style_conditional.bed_advanced.gene_rows: | |
| 185 gene_rows = $track.track_file_style_conditional.bed_advanced.gene_rows | |
| 186 #end if | |
| 187 global_max_row = $track.track_file_style_conditional.bed_advanced.global_max_row | |
| 188 max_labels = $track.track_file_style_conditional.bed_advanced.max_labels | |
| 189 line_width = $track.track_file_style_conditional.bed_advanced.line_width | |
| 190 arrowhead_included = $track.track_file_style_conditional.arrowhead_included | |
| 191 #if $track.track_file_style_conditional.invert_orientation: | |
| 192 orientation = inverted | |
| 193 #end if | |
| 194 overlay_previous = $track.track_file_style_conditional.overlay_select | |
| 195 ## If spacer is asked a new section is created: | |
| 196 #if $track.track_file_style_conditional.spacer_height != "": | |
| 177 [spacer] | 197 [spacer] |
| 178 height = $track.track_file_style_conditional.spacer_height | 198 height = $track.track_file_style_conditional.spacer_height |
| 179 #end if | 199 #end if |
| 180 #end for | 200 #end for |
| 181 | 201 #end if |
| 182 #end if | 202 |
| 183 | 203 ## Link |
| 184 | 204 #if $track.track_file_style_conditional.track_file_style_selector == "link_track_option": |
| 185 | 205 [links_$counter] |
| 186 | 206 file = $track.track_file_style_conditional.track_input_link |
| 187 #if $track.track_file_style_conditional.track_file_style_selector == "gene_track_option": | 207 #if $track.track_file_style_conditional.title: |
| 188 #for $counter_bed, $data_bed in enumerate($track.track_file_style_conditional.track_input_bed): | |
| 189 | |
| 190 [genes_${counter}_${counter_bed}] | |
| 191 #set ext = $data_bed.extension | |
| 192 file = ${counter}_${counter_bed}.$ext | |
| 193 #if $track.track_file_style_conditional.title: | |
| 194 title = $track.track_file_style_conditional.title | 208 title = $track.track_file_style_conditional.title |
| 195 #else: | 209 #elif $track.track_file_style_conditional.overlay_select == 'no': |
| 196 title = $data_bed.name | 210 title = $track.track_file_style_conditional.track_input_link.name |
| 197 #end if | 211 #end if |
| 198 #if $track.track_file_style_conditional.color_bed.color_bed_select == "bed_rgb": | 212 #if $track.track_file_style_conditional.height: |
| 199 color = bed_rgb | 213 height = $track.track_file_style_conditional.height |
| 200 #elif $track.track_file_style_conditional.color_bed.color: | 214 #end if |
| 201 color = $track.track_file_style_conditional.color_bed.color | 215 #if $track.track_file_style_conditional.min_value: |
| 202 #end if | 216 min_value = $track.track_file_style_conditional.min_value |
| 203 #if $track.track_file_style_conditional.border_color: | 217 #end if |
| 204 border color = $track.track_file_style_conditional.border_color | 218 #if $track.track_file_style_conditional.max_value: |
| 205 #end if | 219 max_value = $track.track_file_style_conditional.max_value |
| 206 | 220 #end if |
| 207 #if $track.track_file_style_conditional.flybase: | 221 color = $track.track_file_style_conditional.color_link.color |
| 208 style = flybase | 222 alpha = $track.track_file_style_conditional.alpha |
| 209 #else | 223 line_width = $track.track_file_style_conditional.line_width |
| 210 style = UCSC | 224 line_style = $track.track_file_style_conditional.line_style |
| 211 #end if | 225 links_type = $track.track_file_style_conditional.links_type |
| 212 | 226 #if $track.track_file_style_conditional.invert_orientation: |
| 213 display = $track.track_file_style_conditional.display | 227 orientation = inverted |
| 214 | 228 #end if |
| 215 #if $track.track_file_style_conditional.height_bed: | 229 overlay_previous = $track.track_file_style_conditional.overlay_select |
| 216 height = $track.track_file_style_conditional.height_bed | 230 file_type = links |
| 217 #end if | 231 ## If spacer is asked a new section is created: |
| 218 | 232 #if $track.track_file_style_conditional.spacer_height != "": |
| 219 labels = $track.track_file_style_conditional.labels | |
| 220 | |
| 221 file_type = bed | |
| 222 #if $track.track_file_style_conditional.fontsize: | |
| 223 fontsize = $track.track_file_style_conditional.fontsize | |
| 224 #end if | |
| 225 | |
| 226 #if $track.track_file_style_conditional.gene_rows: | |
| 227 gene rows = $track.track_file_style_conditional.gene_rows | |
| 228 #end if | |
| 229 | |
| 230 #if $track.track_file_style_conditional.global_max_row: | |
| 231 global max row = $track.track_file_style_conditional.global_max_row | |
| 232 #end if | |
| 233 #if $track.track_file_style_conditional.spacer_height != "": | |
| 234 [spacer] | 233 [spacer] |
| 235 height = $track.track_file_style_conditional.spacer_height | 234 height = $track.track_file_style_conditional.spacer_height |
| 236 #end if | 235 #end if |
| 237 #end for | 236 #end if |
| 238 #end if | 237 |
| 239 | 238 ## Narrow peak |
| 240 #if $track.track_file_style_conditional.track_file_style_selector == "narrow_peak_track_option": | 239 #if $track.track_file_style_conditional.track_file_style_selector == "narrow_peak_track_option": |
| 241 #for $counter_narrow_peak, $data_narrow_peak in enumerate($track.track_file_style_conditional.track_input_narrow_peak): | 240 #for $counter_narrow_peak, $data_narrow_peak in enumerate($track.track_file_style_conditional.track_input_narrow_peak): |
| 242 | |
| 243 [narrow_peak_${counter}_${counter_narrow_peak}] | 241 [narrow_peak_${counter}_${counter_narrow_peak}] |
| 244 file = $data_narrow_peak | 242 file = $data_narrow_peak |
| 245 #if $track.track_file_style_conditional.title: | 243 #if $track.track_file_style_conditional.title: |
| 246 title = $track.track_file_style_conditional.title | 244 title = $track.track_file_style_conditional.title |
| 247 #else: | 245 #elif $track.track_file_style_conditional.overlay_select == 'no': |
| 248 title = $data_narrow_peak.name | 246 title = $data_narrow_peak.name |
| 249 #end if | 247 #end if |
| 250 color = $track.track_file_style_conditional.color | 248 color = $track.track_file_style_conditional.color |
| 251 type = $track.track_file_style_conditional.display.display_selector | 249 type = $track.track_file_style_conditional.display.display_selector |
| 252 use summit = $track.track_file_style_conditional.display.use_summit | 250 use_summit = $track.track_file_style_conditional.display.use_summit |
| 253 #if $track.track_file_style_conditional.display.display_selector == "peak": | 251 #if $track.track_file_style_conditional.display.display_selector == "peak": |
| 254 show data range = $track.track_file_style_conditional.display.show_data | 252 show_data_range = $track.track_file_style_conditional.display.show_data |
| 255 #if $track.track_file_style_conditional.display.width_adjust: | 253 #if $track.track_file_style_conditional.display.width_adjust: |
| 256 width adjust = $track.track_file_style_conditional.display.width_adjust | 254 width_adjust = $track.track_file_style_conditional.display.width_adjust |
| 257 #end if | 255 #end if |
| 258 #if $track.track_file_style_conditional.display.min_value: | 256 #if $track.track_file_style_conditional.display.min_value: |
| 259 min_value = $track.track_file_style_conditional.display.min_value | 257 min_value = $track.track_file_style_conditional.display.min_value |
| 260 #end if | 258 #end if |
| 261 #if $track.track_file_style_conditional.display.max_value: | 259 #if $track.track_file_style_conditional.display.max_value: |
| 262 max_value = $track.track_file_style_conditional.display.max_value | 260 max_value = $track.track_file_style_conditional.display.max_value |
| 263 #end if | 261 #end if |
| 264 #end if | 262 #end if |
| 265 | 263 #if $track.track_file_style_conditional.height_narrow_peak: |
| 266 | |
| 267 #if $track.track_file_style_conditional.height_narrow_peak: | |
| 268 height = $track.track_file_style_conditional.height_narrow_peak | 264 height = $track.track_file_style_conditional.height_narrow_peak |
| 269 #end if | 265 #end if |
| 270 | 266 show_labels = $track.track_file_style_conditional.show_labels |
| 271 show labels = $track.track_file_style_conditional.show_labels | |
| 272 | |
| 273 file_type = narrow_peak | 267 file_type = narrow_peak |
| 274 #if $track.track_file_style_conditional.fontsize: | 268 #if $track.track_file_style_conditional.fontsize: |
| 275 fontsize = $track.track_file_style_conditional.fontsize | 269 fontsize = $track.track_file_style_conditional.fontsize |
| 276 #end if | 270 #end if |
| 277 | 271 #if $track.track_file_style_conditional.invert_orientation: |
| 278 #if $track.track_file_style_conditional.spacer_height != "": | 272 orientation = inverted |
| 273 #end if | |
| 274 overlay_previous = $track.track_file_style_conditional.overlay_select | |
| 275 ## If spacer is asked a new section is created: | |
| 276 #if $track.track_file_style_conditional.spacer_height != "": | |
| 279 [spacer] | 277 [spacer] |
| 280 height = $track.track_file_style_conditional.spacer_height | 278 height = $track.track_file_style_conditional.spacer_height |
| 281 #end if | 279 #end if |
| 282 #end for | 280 #end for |
| 283 #end if | 281 #end if |
| 284 | 282 |
| 285 | 283 ## Bedgraph track |
| 286 #if $track.track_file_style_conditional.track_file_style_selector == "bedgraph_track_option": | 284 #if $track.track_file_style_conditional.track_file_style_selector == "bedgraph_track_option": |
| 287 #for $data_bedgraph in $track.track_file_style_conditional.track_input_bedgraph: | 285 #for $data_bedgraph in $track.track_file_style_conditional.track_input_bedgraph: |
| 288 | |
| 289 [bedgraph_$counter] | 286 [bedgraph_$counter] |
| 290 file = $data_bedgraph | 287 file = $data_bedgraph |
| 291 #if $track.track_file_style_conditional.title: | 288 #if $track.track_file_style_conditional.title: |
| 292 title = $track.track_file_style_conditional.title | 289 title = $track.track_file_style_conditional.title |
| 293 #elif $track.track_file_style_conditional.overlay_select == "no": | 290 #elif $track.track_file_style_conditional.overlay_select == "no": |
| 294 title = $data_bedgraph.name | 291 title = $data_bedgraph.name |
| 295 #end if | 292 #end if |
| 296 #if $track.track_file_style_conditional.color: | 293 #if $track.track_file_style_conditional.color: |
| 297 color = $track.track_file_style_conditional.color | 294 color = $track.track_file_style_conditional.color |
| 298 #end if | 295 #end if |
| 299 alpha = $track.track_file_style_conditional.alpha | 296 alpha = $track.track_file_style_conditional.alpha |
| 300 #if $track.track_file_style_conditional.color_negative.color_negative_select == "yes": | 297 #if $track.track_file_style_conditional.color_negative.color_negative_select == "true": |
| 301 negative color = $track.track_file_style_conditional.color_negative.color | 298 negative_color = $track.track_file_style_conditional.color_negative.color |
| 302 #end if | 299 #end if |
| 303 #if $track.track_file_style_conditional.height_bedgraph: | 300 #if $track.track_file_style_conditional.height_bedgraph: |
| 304 height = $track.track_file_style_conditional.height_bedgraph | 301 height = $track.track_file_style_conditional.height_bedgraph |
| 305 #end if | 302 #end if |
| 306 #if $track.track_file_style_conditional.min_value: | 303 #if $track.track_file_style_conditional.min_value: |
| 307 min_value = $track.track_file_style_conditional.min_value | 304 min_value = $track.track_file_style_conditional.min_value |
| 308 #else: | 305 #end if |
| 309 min_value = auto | 306 #if $track.track_file_style_conditional.max_value: |
| 310 #end if | |
| 311 #if $track.track_file_style_conditional.max_value: | |
| 312 max_value = $track.track_file_style_conditional.max_value | 307 max_value = $track.track_file_style_conditional.max_value |
| 313 #else: | 308 #end if |
| 314 max_value = auto | 309 show_data_range = $track.track_file_style_conditional.show_data |
| 315 #end if | 310 nans_to_zeros = $track.track_file_style_conditional.nans_to_zeros |
| 316 | 311 use_middle = $track.track_file_style_conditional.use_middle |
| 317 show data range = $track.track_file_style_conditional.show_data | 312 #set $columns = len(open(str($track.track_file_style_conditional.track_input_bedgraph)).readline().split('\t')) |
| 318 | 313 #if $columns > 4: |
| 319 #set $columns = len(open(str($track.track_file_style_conditional.track_input_bedgraph)).readline().split('\t')) | |
| 320 #if $columns > 4: | |
| 321 file_type = bedgraph_matrix | 314 file_type = bedgraph_matrix |
| 322 type = lines | 315 type = lines |
| 323 #else: | 316 #else: |
| 324 file_type = bedgraph | 317 file_type = bedgraph |
| 325 #if $track.track_file_style_conditional.type_conditional.type_selector == 'fill_option': | 318 #if $track.track_file_style_conditional.type_conditional.type_selector == 'fill_option': |
| 326 type = fill | 319 type = fill |
| 327 #elif $track.track_file_style_conditional.type_conditional.type_selector == 'line_option': | 320 #elif $track.track_file_style_conditional.type_conditional.type_selector == 'line_option': |
| 328 type = line:$track.track_file_style_conditional.type_conditional.width_line | 321 type = line:$track.track_file_style_conditional.type_conditional.width_line |
| 329 #elif $track.track_file_style_conditional.type_conditional.type_selector == 'point_option': | 322 #elif $track.track_file_style_conditional.type_conditional.type_selector == 'point_option': |
| 330 type = points:$track.track_file_style_conditional.type_conditional.width_point | 323 type = points:$track.track_file_style_conditional.type_conditional.width_point |
| 331 #end if | 324 #end if |
| 332 #end if | 325 #end if |
| 333 #if $track.track_file_style_conditional.invert_orientation: | 326 #if $track.track_file_style_conditional.invert_orientation: |
| 334 orientation = inverted | 327 orientation = inverted |
| 335 #end if | 328 #end if |
| 336 overlay previous = $track.track_file_style_conditional.overlay_select | 329 overlay_previous = $track.track_file_style_conditional.overlay_select |
| 337 #if $track.track_file_style_conditional.spacer_height != "": | 330 ## If spacer is asked a new section is created: |
| 331 #if $track.track_file_style_conditional.spacer_height != "": | |
| 338 [spacer] | 332 [spacer] |
| 339 height = $track.track_file_style_conditional.spacer_height | 333 height = $track.track_file_style_conditional.spacer_height |
| 340 #end if | 334 #end if |
| 341 #end for | 335 #end for |
| 342 #end if | 336 #end if |
| 343 | 337 |
| 344 #if $track.track_file_style_conditional.track_file_style_selector == "bigwig_track_option": | 338 ## Bigwig tracks |
| 345 #for $data_bigwig in $track.track_file_style_conditional.track_input_bigwig: | 339 #if $track.track_file_style_conditional.track_file_style_selector == "bigwig_track_option": |
| 340 #for $data_bigwig in $track.track_file_style_conditional.track_input_bigwig: | |
| 346 [bigwig_$counter] | 341 [bigwig_$counter] |
| 347 file = $data_bigwig | 342 file = $data_bigwig |
| 348 #if $track.track_file_style_conditional.title: | 343 #if $track.track_file_style_conditional.title: |
| 349 title = $track.track_file_style_conditional.title | 344 title = $track.track_file_style_conditional.title |
| 350 #elif $track.track_file_style_conditional.overlay_select == "no": | 345 #elif $track.track_file_style_conditional.overlay_select == "no": |
| 351 title = $data_bigwig.name | 346 title = $data_bigwig.name |
| 352 #end if | 347 #end if |
| 353 #if $track.track_file_style_conditional.color: | 348 #if $track.track_file_style_conditional.color: |
| 354 color = $track.track_file_style_conditional.color | 349 color = $track.track_file_style_conditional.color |
| 355 #end if | 350 #end if |
| 356 alpha = $track.track_file_style_conditional.alpha | 351 alpha = $track.track_file_style_conditional.alpha |
| 357 #if $track.track_file_style_conditional.color_negative.color_negative_select == "yes": | 352 #if $track.track_file_style_conditional.color_negative.color_negative_select == "true": |
| 358 negative color = $track.track_file_style_conditional.color_negative.color | 353 negative_color = $track.track_file_style_conditional.color_negative.color |
| 359 #end if | 354 #end if |
| 360 #if $track.track_file_style_conditional.min_value: | 355 #if $track.track_file_style_conditional.min_value: |
| 361 min_value = $track.track_file_style_conditional.min_value | 356 min_value = $track.track_file_style_conditional.min_value |
| 362 #else: | 357 #end if |
| 363 min_value = 0 | 358 #if $track.track_file_style_conditional.max_value: |
| 364 #end if | |
| 365 #if $track.track_file_style_conditional.max_value: | |
| 366 max_value = $track.track_file_style_conditional.max_value | 359 max_value = $track.track_file_style_conditional.max_value |
| 367 #else: | 360 #end if |
| 368 max_value = auto | |
| 369 #end if | |
| 370 height = $track.track_file_style_conditional.height_bigwig | 361 height = $track.track_file_style_conditional.height_bigwig |
| 371 summary method = $track.track_file_style_conditional.reading_bw_conditional.summary | 362 summary_method = $track.track_file_style_conditional.reading_bw_conditional.summary |
| 372 nans to zeros = $track.track_file_style_conditional.reading_bw_conditional.nans_to_zeros | 363 nans_to_zeros = $track.track_file_style_conditional.reading_bw_conditional.nans_to_zeros |
| 373 #if $track.track_file_style_conditional.reading_bw_conditional.number_of_bins: | 364 #if $track.track_file_style_conditional.reading_bw_conditional.number_of_bins: |
| 374 number of bins = $track.track_file_style_conditional.reading_bw_conditional.number_of_bins | 365 number_of_bins = $track.track_file_style_conditional.reading_bw_conditional.number_of_bins |
| 375 #end if | 366 #end if |
| 376 #if $track.track_file_style_conditional.type_conditional.type_selector == 'fill_option': | 367 #if $track.track_file_style_conditional.type_conditional.type_selector == 'fill_option': |
| 377 type = fill | 368 type = fill |
| 378 #elif $track.track_file_style_conditional.type_conditional.type_selector == 'line_option': | 369 #elif $track.track_file_style_conditional.type_conditional.type_selector == 'line_option': |
| 379 type = line:$track.track_file_style_conditional.type_conditional.width_line | 370 type = line:$track.track_file_style_conditional.type_conditional.width_line |
| 380 #elif $track.track_file_style_conditional.type_conditional.type_selector == 'point_option': | 371 #elif $track.track_file_style_conditional.type_conditional.type_selector == 'point_option': |
| 381 type = points:$track.track_file_style_conditional.type_conditional.width_point | 372 type = points:$track.track_file_style_conditional.type_conditional.width_point |
| 382 #end if | 373 #end if |
| 383 show data range = $track.track_file_style_conditional.show_data | 374 show_data_range = $track.track_file_style_conditional.show_data |
| 384 file_type = bigwig | 375 file_type = bigwig |
| 385 #if $track.track_file_style_conditional.invert_orientation: | 376 #if $track.track_file_style_conditional.invert_orientation: |
| 386 orientation = inverted | 377 orientation = inverted |
| 387 #end if | 378 #end if |
| 388 overlay previous = $track.track_file_style_conditional.overlay_select | 379 overlay_previous = $track.track_file_style_conditional.overlay_select |
| 389 #if $track.track_file_style_conditional.spacer_height != "": | 380 ## If spacer is asked a new section is created: |
| 381 #if $track.track_file_style_conditional.spacer_height != "": | |
| 390 [spacer] | 382 [spacer] |
| 391 height = $track.track_file_style_conditional.spacer_height | 383 height = $track.track_file_style_conditional.spacer_height |
| 392 #end if | 384 #end if |
| 393 #end for | 385 #end for |
| 394 #end if | 386 #end if |
| 395 | 387 |
| 396 | 388 ## bedgraph_matrix |
| 397 #if $track.track_file_style_conditional.track_file_style_selector == "bedgraph_matrix_track_option": | 389 #if $track.track_file_style_conditional.track_file_style_selector == "bedgraph_matrix_track_option": |
| 398 #for $data_bedgraph_matrix in $track.track_file_style_conditional.track_input_bedgraph_matrix: | 390 #for $data_bedgraph_matrix in $track.track_file_style_conditional.track_input_bedgraph_matrix: |
| 399 | |
| 400 [bedgraph_matrix_$counter] | 391 [bedgraph_matrix_$counter] |
| 401 file = $data_bedgraph_matrix | 392 file = $data_bedgraph_matrix |
| 402 #if $track.track_file_style_conditional.title: | 393 #if $track.track_file_style_conditional.title: |
| 403 title = $track.track_file_style_conditional.title | 394 title = $track.track_file_style_conditional.title |
| 404 #else: | 395 #else: |
| 405 title = $data_bedgraph_matrix.name | 396 title = $data_bedgraph_matrix.name |
| 406 #end if | 397 #end if |
| 407 #if $track.track_file_style_conditional.height_bedgraph: | 398 #if $track.track_file_style_conditional.height_bedgraph: |
| 408 height = $track.track_file_style_conditional.height_bedgraph | 399 height = $track.track_file_style_conditional.height_bedgraph |
| 409 #end if | 400 #end if |
| 401 #if $track.track_file_style_conditional.min_value: | |
| 402 min_value = $track.track_file_style_conditional.min_value | |
| 403 #end if | |
| 404 #if $track.track_file_style_conditional.max_value: | |
| 405 max_value = $track.track_file_style_conditional.max_value | |
| 406 #end if | |
| 407 #if $track.track_file_style_conditional.type_lines: | |
| 408 type = $track.track_file_style_conditional.type_lines | |
| 409 #end if | |
| 410 file_type = bedgraph_matrix | |
| 411 show_data_range = $track.track_file_style_conditional.show_data | |
| 412 plot_horizontal_lines = $track.track_file_style_conditional.plot_horizontal_lines | |
| 413 pos_score_in_bin = $track.track_file_style_conditional.pos_score_in_bin | |
| 414 #if $track.track_file_style_conditional.invert_orientation: | |
| 410 orientation = inverted | 415 orientation = inverted |
| 411 #if $track.track_file_style_conditional.min_value: | 416 #end if |
| 412 min_value = $track.track_file_style_conditional.min_value | 417 ## If spacer is asked a new section is created: |
| 413 #end if | 418 #if $track.track_file_style_conditional.spacer_height != "": |
| 414 #if $track.track_file_style_conditional.max_value: | |
| 415 max_value = $track.track_file_style_conditional.max_value | |
| 416 #end if | |
| 417 #if $track.track_file_style_conditional.type_lines: | |
| 418 type = $track.track_file_style_conditional.type_lines | |
| 419 #end if | |
| 420 file_type = bedgraph_matrix | |
| 421 plot horizontal lines=False | |
| 422 #if $track.track_file_style_conditional.invert_orientation: | |
| 423 orientation = inverted | |
| 424 #end if | |
| 425 #if $track.track_file_style_conditional.spacer_height != "": | |
| 426 [spacer] | 419 [spacer] |
| 427 height = $track.track_file_style_conditional.spacer_height | 420 height = $track.track_file_style_conditional.spacer_height |
| 428 #end if | 421 #end if |
| 429 #end for | 422 #end for |
| 430 #end if | 423 #end if |
| 431 | 424 |
| 432 #if $track.track_file_style_conditional.track_file_style_selector == "vlines_track_option": | 425 ## Vlines: |
| 433 | 426 #if $track.track_file_style_conditional.track_file_style_selector == "vlines_track_option": |
| 434 [vlines_$counter] | 427 [vlines_$counter] |
| 435 file = $track.track_file_style_conditional.track_input_bed_single | 428 file = $track.track_file_style_conditional.track_input_bed_single |
| 436 type = vlines | 429 type = vlines |
| 437 file_type = bed | 430 #end if |
| 438 #end if | 431 |
| 439 #if $track.track_file_style_conditional.track_file_style_selector == "spacer_option": | 432 ## Hlines: |
| 440 | 433 #if $track.track_file_style_conditional.track_file_style_selector == "hlines_track_option": |
| 441 #if $track.track_file_style_conditional.spacer_height != "": | 434 [hlines_$counter] |
| 435 #if $track.track_file_style_conditional.title: | |
| 436 title = $track.track_file_style_conditional.title | |
| 437 #end if | |
| 438 #if $track.track_file_style_conditional.height: | |
| 439 height = $track.track_file_style_conditional.height | |
| 440 #end if | |
| 441 #if $track.track_file_style_conditional.min_value: | |
| 442 min_value = $track.track_file_style_conditional.min_value | |
| 443 #end if | |
| 444 #if $track.track_file_style_conditional.max_value: | |
| 445 max_value = $track.track_file_style_conditional.max_value | |
| 446 #end if | |
| 447 y_values = $track.track_file_style_conditional.y_values | |
| 448 show_data_range = $track.track_file_style_conditional.show_data | |
| 449 color = $track.track_file_style_conditional.color | |
| 450 alpha = $track.track_file_style_conditional.alpha | |
| 451 line_width = $track.track_file_style_conditional.line_width | |
| 452 line_style = $track.track_file_style_conditional.line_style | |
| 453 #if $track.track_file_style_conditional.invert_orientation: | |
| 454 orientation = inverted | |
| 455 #end if | |
| 456 overlay_previous = $track.track_file_style_conditional.overlay_select | |
| 457 file_type = hlines | |
| 458 ## If spacer is asked a new section is created: | |
| 459 #if $track.track_file_style_conditional.spacer_height != "": | |
| 442 [spacer] | 460 [spacer] |
| 443 height = $track.track_file_style_conditional.spacer_height | 461 height = $track.track_file_style_conditional.spacer_height |
| 444 #end if | 462 #end if |
| 445 #end if | 463 #end if |
| 464 | |
| 465 ## Spacer | |
| 466 #if $track.track_file_style_conditional.track_file_style_selector == "spacer_option": | |
| 467 [spacer] | |
| 468 #if $track.track_file_style_conditional.spacer_height != "": | |
| 469 height = $track.track_file_style_conditional.spacer_height | |
| 470 #end if | |
| 471 #end if | |
| 446 #end for | 472 #end for |
| 447 | 473 |
| 448 #if $x_axis.x_axis_select == "yes": | 474 #if $x_axis.x_axis_select == "true": |
| 449 #if $x_axis.where == 'bottom': | 475 #if $x_axis.where == 'bottom': |
| 450 [x-axis] | 476 [x-axis] |
| 451 #if $x_axis.fontsize: | 477 #if $x_axis.fontsize: |
| 452 fontsize = $x_axis.fontsize | 478 fontsize = $x_axis.fontsize |
| 453 #end if | 479 #end if |
| 454 #if $x_axis.where: | 480 where = bottom |
| 455 where = $x_axis.where | 481 #end if |
| 456 #end if | |
| 457 #end if | |
| 458 #end if | 482 #end if |
| 459 </configfile> | 483 </configfile> |
| 460 </configfiles> | 484 </configfiles> |
| 461 <inputs> | 485 <inputs> |
| 462 <expand macro="region" /> | 486 <expand macro="region" /> |
| 465 help="Tracks can be of different filetypes. E.g BED, HiC-Matrix, BigWig or BedGraph"> | 489 help="Tracks can be of different filetypes. E.g BED, HiC-Matrix, BigWig or BedGraph"> |
| 466 <conditional name="track_file_style_conditional"> | 490 <conditional name="track_file_style_conditional"> |
| 467 <param name="track_file_style_selector" type="select" label="Choose style of the track"> | 491 <param name="track_file_style_selector" type="select" label="Choose style of the track"> |
| 468 <option value="hic_matrix_option">TAD visualization</option> | 492 <option value="hic_matrix_option">TAD visualization</option> |
| 469 <option value="chrom_states_option">Chromatine states</option> | 493 <option value="chrom_states_option">Chromatine states</option> |
| 470 <option value="tad_score_track_option">TAD score</option> | 494 <option value="bedgraph_matrix_track_option">TAD score</option> |
| 471 <option value="gene_track_option">Gene track / Bed track</option> | 495 <option value="gene_track_option">Gene track / Bed track</option> |
| 496 <option value="link_track_option">Link track</option> | |
| 472 <option value="narrow_peak_track_option">NarrowPeak track</option> | 497 <option value="narrow_peak_track_option">NarrowPeak track</option> |
| 473 <option value="bigwig_track_option">Bigwig track</option> | 498 <option value="bigwig_track_option">Bigwig track</option> |
| 474 <option value="bedgraph_track_option">Bedgraph track </option> | 499 <option value="bedgraph_track_option">Bedgraph track </option> |
| 475 <option value="bedgraph_matrix_track_option">Bedgraph matrix track</option> | 500 <option value="bedgraph_matrix_track_option">Bedgraph matrix track</option> |
| 476 <option value="vlines_track_option">Vlines track</option> | 501 <option value="vlines_track_option">Vlines track</option> |
| 502 <option value="hlines_track_option">Hlines track</option> | |
| 477 <option value="spacer_option">Spacer</option> | 503 <option value="spacer_option">Spacer</option> |
| 478 </param> | 504 </param> |
| 479 <when value="hic_matrix_option"> | 505 <when value="hic_matrix_option"> |
| 480 <expand macro="plot_title" /> | 506 <expand macro="plot_title" /> |
| 481 <expand macro="matrix_h5_cooler_multiple_macro" /> | 507 <expand macro="matrix_h5_cooler_multiple_macro" /> |
| 485 <expand macro="minmax_macro" /> | 511 <expand macro="minmax_macro" /> |
| 486 <param name="transform" type="select" label="Plot the transformed value"> | 512 <param name="transform" type="select" label="Plot the transformed value"> |
| 487 <option value="log1p" selected="True" >log1p</option> | 513 <option value="log1p" selected="True" >log1p</option> |
| 488 <option value="log">log</option> | 514 <option value="log">log</option> |
| 489 <option value="-log">-log</option> | 515 <option value="-log">-log</option> |
| 490 <option value="">no transformation</option> | 516 <option value="no">no transformation</option> |
| 491 | 517 |
| 492 </param> | 518 </param> |
| 493 <param name="height_matrix" type="float" value="" optional="True" label="height"/> | 519 <param name="height_matrix" type="float" value="" optional="True" label="height"/> |
| 494 <param name="show_masked_bins" type="boolean" truevalue="yes" falsevalue="no" checked="false" | 520 <param name="show_masked_bins" type="boolean" truevalue="true" falsevalue="false" checked="false" |
| 495 label="Show masked bins" /> | 521 label="Show masked bins" /> |
| 496 <param name="boundaries_file" type="data" optional="True" format="bed" label="Boundaries file" multiple='True'/> <!-- multiple='True'--> | 522 <param name="boundaries_file" type="data" optional="True" format="bed" label="Boundaries file" multiple="True"/> |
| 497 <param name="scale_factor" type="float" value="1.0" optional="True" label="Scale factor" help="if the values in the matrix need to be scaled the following parameter can be used" /> | 523 <param name="scale_factor" type="float" value="1.0" optional="True" label="Scale factor" help="if the values in the matrix need to be scaled the following parameter can be used" /> |
| 524 <param name="rasterize" type="boolean" truevalue="true" falsevalue="false" checked="true" | |
| 525 label="Rasterize the heatmap" /> | |
| 498 <expand macro="inverted_macro" /> | 526 <expand macro="inverted_macro" /> |
| 499 <expand macro="spacer_macro" /> | |
| 500 | |
| 501 </when> | |
| 502 <when value="tad_score_track_option"> | |
| 503 <expand macro="plot_title" /> | |
| 504 <expand macro="track_input_bedgraph_macro" /> | |
| 505 <param name="color" type="color" value="#000000" label="Color of track" optional="True" /> | |
| 506 <param name="type_lines" type="boolean" truevalue="lines" falsevalue="" checked="false" | |
| 507 label="Set 'type' to 'lines'" help="if type is set as lines, then the TAD score lines are drawn instead | |
| 508 of the matrix set to lines if a heatmap representing the matrix is not wanted"/> | |
| 509 <param name="height_tad" type="float" value="0.2" optional="True" label="height"/> | |
| 510 <param name='show_data' type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Show visualization of data range" /> | |
| 511 <expand macro="spacer_macro" /> | 527 <expand macro="spacer_macro" /> |
| 512 | 528 |
| 513 </when> | 529 </when> |
| 514 <when value="chrom_states_option"> | 530 <when value="chrom_states_option"> |
| 515 <expand macro="plot_title" /> | 531 <expand macro="plot_title" /> |
| 516 | |
| 517 <expand macro="track_input_bed_macro" /> | 532 <expand macro="track_input_bed_macro" /> |
| 518 <expand macro="color_bed_macro" /> | 533 <expand macro="color_bed_macro" /> |
| 534 <param name="line_width" type="float" value="0.5" label="width of lines" /> | |
| 519 <param name="height_chrom" type="float" value="1.5" optional="True" label="height"/> | 535 <param name="height_chrom" type="float" value="1.5" optional="True" label="height"/> |
| 520 <param name="labels" type="boolean" truevalue="on" falsevalue="off" checked="true" | 536 <param name="labels" type="boolean" truevalue="true" falsevalue="false" checked="true" |
| 521 label="Plot labels" /> | 537 label="Plot labels" /> |
| 522 <expand macro="spacer_macro" /> | 538 <expand macro="spacer_macro" /> |
| 523 | 539 |
| 524 </when> | 540 </when> |
| 525 <when value="gene_track_option"> | 541 <when value="gene_track_option"> |
| 526 <expand macro="plot_title" /> | 542 <expand macro="plot_title" /> |
| 527 | 543 |
| 528 <expand macro="track_input_bed_gtf_macro" /> | 544 <expand macro="track_input_bed_gtf_macro" /> |
| 529 <expand macro="color_bed_macro" /> | 545 <expand macro="color_bed_macro" /> |
| 530 <param name="height_bed" type="float" value="1.5" optional="True" label="height"/> | 546 <param name="height_bed" type="float" value="1.5" optional="True" label="height"/> |
| 531 <param name="labels" type="boolean" truevalue="on" falsevalue="off" checked="true" | 547 <param name="labels" type="boolean" truevalue="true" falsevalue="false" checked="true" |
| 532 label="Plot labels" /> | 548 label="Plot labels" /> |
| 533 <param name="flybase" type="boolean" checked="true" label="Use flybase style" help="This will be only used for bed with 12 columns"/> | 549 <param name="flybase" type="boolean" checked="true" label="Use flybase style" help="This will be only used for bed with 12 columns"/> |
| 534 <param name="display" type="select" label="display to use"> | 550 <param name="display" type="select" label="display to use"> |
| 535 <option value="stacked" selected="True">stacked (no overlap even with the label)</option> | 551 <option value="stacked" selected="True">stacked (no overlap even with the label)</option> |
| 536 <option value="interlaced">interlaced (everything on 2 lines)</option> | 552 <option value="interleaved">interleaved (everything on 2 lines)</option> |
| 537 <option value="collapsed">collapsed (everything on 1 line)</option> | 553 <option value="collapsed">collapsed (everything on 1 line)</option> |
| 538 <option value="domain">domain (only the first line of stacked)</option> | 554 <option value="triangles">triangles (plot triangles between start and end)</option> |
| 539 </param> | 555 </param> |
| 540 <param name="global_max_row" type="boolean" truevalue="yes" falsevalue="no" checked="false" | 556 <param name="arrowhead_included" type="boolean" truevalue="true" falsevalue="false" checked="false" |
| 541 label="Global max rows" /> | 557 label="Include the arrowhead in the bed interval:" |
| 542 <param name="gene_rows" type="integer" value="" optional="True" label="Gene rows" /> | 558 help="When set to False, the arrow indicating the orientation of the interval is plotted outside of the interval."/> |
| 543 <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" /> | 559 <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" /> |
| 560 <expand macro="bed_advanced_macro" /> | |
| 561 <expand macro="overlay_macro" /> | |
| 562 <expand macro="inverted_macro" /> | |
| 544 <expand macro="spacer_macro" /> | 563 <expand macro="spacer_macro" /> |
| 545 | 564 |
| 546 </when> | 565 </when> |
| 566 <when value="link_track_option"> | |
| 567 <expand macro="plot_title" /> | |
| 568 <expand macro="track_input_link_macro" /> | |
| 569 <expand macro="links_color_macro" /> | |
| 570 <expand macro="lines_macro" /> | |
| 571 <param name="links_type" type="select" label="Representation of the link:"> | |
| 572 <option value="arcs" selected="True">arcs (a line between the centers of the 2 regions)</option> | |
| 573 <option value="triangles">triangles</option> | |
| 574 <option value="loops">loops (a rectangle highlighting the intersection)</option> | |
| 575 </param> | |
| 576 <param name="height" type="float" value="1.5" optional="True" label="height"/> | |
| 577 <expand macro="minmax_macro" /> | |
| 578 <expand macro="overlay_macro" /> | |
| 579 <expand macro="inverted_macro" /> | |
| 580 <expand macro="spacer_macro" /> | |
| 581 </when> | |
| 547 <when value="narrow_peak_track_option"> | 582 <when value="narrow_peak_track_option"> |
| 548 <expand macro="plot_title" /> | 583 <expand macro="plot_title" /> |
| 549 <expand macro="track_input_narrow_peak_macro" /> | 584 <expand macro="track_input_narrow_peak_macro" /> |
| 550 <param name="color" type="color" value="#000000" label="Color of track" optional="True" /> | 585 <param name="color" type="color" value="#000000" label="Color of track" optional="True" /> |
| 551 <param name="height_narrow_peak" type="float" value="1.5" optional="True" label="height"/> | 586 <param name="height_narrow_peak" type="float" value="1.5" optional="True" label="height"/> |
| 553 <param name="display_selector" type="select" label="display to use"> | 588 <param name="display_selector" type="select" label="display to use"> |
| 554 <option value="peak" selected="True">peak: Draw a peak shape from start, end, summit, height</option> | 589 <option value="peak" selected="True">peak: Draw a peak shape from start, end, summit, height</option> |
| 555 <option value="box">box: Draw a box</option> | 590 <option value="box">box: Draw a box</option> |
| 556 </param> | 591 </param> |
| 557 <when value="peak"> | 592 <when value="peak"> |
| 558 <param name='use_summit' type="boolean" truevalue="yes" falsevalue="no" checked="true" | 593 <param name="use_summit" type="boolean" truevalue="true" falsevalue="false" checked="true" |
| 559 optional="True" label="Use summit information to make the curve." /> | 594 optional="True" label="Use summit information to make the curve." /> |
| 560 <param name='show_data' type="boolean" truevalue="yes" falsevalue="no" checked="false" | 595 <param name="show_data" type="boolean" truevalue="true" falsevalue="false" checked="false" |
| 561 label="Show visualization of data range" /> | 596 label="Show visualization of data range" /> |
| 562 <param name='width_adjust' type="float" value="1.5" optional="True" | 597 <param name="width_adjust" type="float" value="1.5" optional="True" |
| 563 label="Factor to change the width of the curve."/> | 598 label="Factor to change the width of the curve."/> |
| 564 <expand macro="minmax_macro" /> | 599 <expand macro="minmax_macro" /> |
| 565 </when> | 600 </when> |
| 566 <when value="box"> | 601 <when value="box"> |
| 567 <param name='use_summit' type="boolean" truevalue="yes" falsevalue="no" checked="true" | 602 <param name="use_summit" type="boolean" truevalue="true" falsevalue="false" checked="true" |
| 568 optional="True" label="Plot a vertical bar at the summit position." /> | 603 optional="True" label="Plot a vertical bar at the summit position." /> |
| 569 </when> | 604 </when> |
| 570 </conditional> | 605 </conditional> |
| 571 <param name="show_labels" type="boolean" truevalue="yes" falsevalue="no" checked="true" | 606 <param name="show_labels" type="boolean" truevalue="true" falsevalue="false" checked="true" |
| 572 label="Plot labels (name, p-val, q-val)" /> | 607 label="Plot labels (name, p-val, q-val)" /> |
| 573 <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" /> | 608 <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" /> |
| 609 <expand macro="overlay_macro" /> | |
| 610 <expand macro="inverted_macro" /> | |
| 574 <expand macro="spacer_macro" /> | 611 <expand macro="spacer_macro" /> |
| 575 | 612 |
| 576 </when> | 613 </when> |
| 577 <when value="bedgraph_track_option"> | 614 <when value="bedgraph_track_option"> |
| 578 <expand macro="plot_title" /> | 615 <expand macro="plot_title" /> |
| 579 <expand macro="track_input_bedgraph_macro" /> | 616 <expand macro="track_input_bedgraph_macro" /> |
| 580 <expand macro="color_coverage_macro" /> | 617 <expand macro="color_coverage_macro" /> |
| 581 <expand macro="minmax_macro" /> | 618 <expand macro="minmax_macro" /> |
| 582 <param name="height_bedgraph" type="float" value="1.5" optional="True" label="height"/> | 619 <param name="height_bedgraph" type="float" value="1.5" optional="True" label="height"/> |
| 583 <expand macro="type_coverage_macro" /> | 620 <expand macro="type_coverage_macro" /> |
| 584 <param name='show_data' type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Show visualization of data range" /> | 621 <param name="nans_to_zeros" type="boolean" truevalue="true" falsevalue="false" checked="false" |
| 622 label="NAN's to zeros" /> | |
| 623 <param name="use_middle" type="boolean" truevalue="true" falsevalue="false" checked="false" | |
| 624 label="Use middle: Instead of using start and end, use the middle of intervals (useful for 4C-seq tracks)." /> | |
| 625 <param name="show_data" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Show visualization of data range" /> | |
| 585 <expand macro="inverted_macro" /> | 626 <expand macro="inverted_macro" /> |
| 586 <expand macro="overlay_macro" /> | 627 <expand macro="overlay_macro" /> |
| 587 <expand macro="spacer_macro" /> | 628 <expand macro="spacer_macro" /> |
| 588 | |
| 589 </when> | 629 </when> |
| 590 <when value="bigwig_track_option"> | 630 <when value="bigwig_track_option"> |
| 591 <expand macro="plot_title" /> | 631 <expand macro="plot_title" /> |
| 592 | 632 |
| 593 <expand macro="track_input_bigwig_macro" /> | 633 <expand macro="track_input_bigwig_macro" /> |
| 597 | 637 |
| 598 <param name="height_bigwig" type="float" value="1.5" optional="True" label="height"/> | 638 <param name="height_bigwig" type="float" value="1.5" optional="True" label="height"/> |
| 599 <expand macro="reading_bw_macro" /> | 639 <expand macro="reading_bw_macro" /> |
| 600 <expand macro="type_coverage_macro" /> | 640 <expand macro="type_coverage_macro" /> |
| 601 <expand macro="type_coverage_macro" /> | 641 <expand macro="type_coverage_macro" /> |
| 602 <param name="show_data" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Show visualization of data range"/> | 642 <param name="show_data" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Show visualization of data range"/> |
| 603 <expand macro="inverted_macro" /> | 643 <expand macro="inverted_macro" /> |
| 604 <expand macro="overlay_macro" /> | 644 <expand macro="overlay_macro" /> |
| 605 <expand macro="spacer_macro" /> | 645 <expand macro="spacer_macro" /> |
| 606 | 646 |
| 607 </when> | 647 </when> |
| 608 | 648 |
| 609 | |
| 610 <when value="bedgraph_matrix_track_option"> | 649 <when value="bedgraph_matrix_track_option"> |
| 611 <expand macro="plot_title" /> | 650 <expand macro="plot_title" /> |
| 612 | 651 |
| 613 <expand macro="track_input_bedgraph_matrix_macro" /> | 652 <expand macro="track_input_bedgraph_matrix_macro" /> |
| 614 <expand macro="minmax_macro" /> | 653 <expand macro="minmax_macro" /> |
| 615 | 654 |
| 616 <param name="height_bedgraph" type="float" value="1.5" optional="True" label="height"/> | 655 <param name="height_bedgraph" type="float" value="1.5" optional="True" label="height"/> |
| 617 | 656 |
| 618 <param name="type_lines" type="boolean" truevalue="lines" falsevalue="" checked="false" | 657 <param name="type_lines" type="boolean" truevalue="lines" falsevalue="" checked="false" |
| 619 label="Set 'type' to 'lines'" help="if type is set as lines, then the TAD score lines are drawn instead | 658 label="Set 'type' to 'lines'" help="if type is set as lines, then the TAD score lines are drawn instead |
| 620 of the matrix set to lines if a heatmap representing the matrix is not wanted"/> | 659 of the matrix."/> |
| 660 <param name="pos_score_in_bin" type="select" label="Position of the score with respect to bin start and end" help="Only used when type is lines"> | |
| 661 <option value="center" selected="True">Center</option> | |
| 662 <option value="block">Block (draw a horizontal line between start and end)</option> | |
| 663 </param> | |
| 664 <param name="plot_horizontal_lines" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Plot an horizontal line at 0 when type is lines" /> | |
| 665 <param name="show_data" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Show visualization of data range" /> | |
| 621 <expand macro="inverted_macro" /> | 666 <expand macro="inverted_macro" /> |
| 622 <expand macro="spacer_macro" /> | 667 <expand macro="spacer_macro" /> |
| 623 | 668 |
| 624 </when> | 669 </when> |
| 625 <when value="vlines_track_option"> | 670 <when value="vlines_track_option"> |
| 626 <expand macro="track_input_bed_single_macro" /> | 671 <expand macro="track_input_bed_single_macro" /> |
| 627 </when> | 672 </when> |
| 673 <when value="hlines_track_option"> | |
| 674 <expand macro="plot_title" /> | |
| 675 <param name="y_values" type="text" value="10, 200" label="Values where horizontal lines should be plotted separated by comma"/> | |
| 676 <param name="color" type="color" value="#000000" label="Color of line(s)" optional="True" /> | |
| 677 <expand macro="lines_macro" /> | |
| 678 <param name="height" type="float" value="1.5" optional="True" label="height"/> | |
| 679 <expand macro="minmax_macro" /> | |
| 680 <param name="show_data" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Show visualization of data range"/> | |
| 681 <expand macro="inverted_macro" /> | |
| 682 <expand macro="overlay_macro" /> | |
| 683 <expand macro="spacer_macro" /> | |
| 684 </when> | |
| 628 <when value="spacer_option"> | 685 <when value="spacer_option"> |
| 629 <expand macro="spacer_macro" /> | 686 <param name="spacer_height" type="float" value="" optional="True" |
| 687 label="Height of the spacer."/> | |
| 630 </when> | 688 </when> |
| 631 </conditional> | 689 </conditional> |
| 632 | 690 |
| 633 </repeat> | 691 </repeat> |
| 634 | 692 |
| 635 | 693 |
| 636 <conditional name="x_axis"> | 694 <conditional name="x_axis"> |
| 637 <param name="x_axis_select" type="select" label="Configure x-axis"> | 695 <param name="x_axis_select" type="select" label="Configure x-axis"> |
| 638 <option value="no" selected="True">No</option> | 696 <option value="false" selected="True">No</option> |
| 639 <option value="yes">Yes</option> | 697 <option value="true">Yes</option> |
| 640 </param> | 698 </param> |
| 641 <when value="yes"> | 699 <when value="true"> |
| 642 <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" /> | 700 <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" /> |
| 643 <param name="where" type="select" label="Where to place the x-axis"> | 701 <param name="where" type="select" label="Where to place the x-axis"> |
| 644 <option value="top" selected="True">Top</option> | 702 <option value="top" selected="True">Top</option> |
| 645 <option value="bottom">Bottom</option> | 703 <option value="bottom">Bottom</option> |
| 646 </param> | 704 </param> |
| 647 </when> | 705 </when> |
| 648 <when value="no" /> | 706 <when value="false" /> |
| 649 </conditional> | 707 </conditional> |
| 650 <param name="image_file_format" type="select" label="Image output format"> | 708 <param name="image_file_format" type="select" label="Image output format"> |
| 651 <option value="png">png</option> | 709 <option value="png">png</option> |
| 652 <option value="svg">svg</option> | 710 <option value="svg">svg</option> |
| 653 </param> | 711 </param> |
| 662 </outputs> | 720 </outputs> |
| 663 <tests> | 721 <tests> |
| 664 <test> | 722 <test> |
| 665 <param name="region" value="chrX:3000000-3500000"/> | 723 <param name="region" value="chrX:3000000-3500000"/> |
| 666 <conditional name="x_axis"> | 724 <conditional name="x_axis"> |
| 667 <param name="x_axis_select" value="yes" /> | 725 <param name="x_axis_select" value="true" /> |
| 668 </conditional> | 726 </conditional> |
| 669 <repeat name="tracks"> | 727 <repeat name="tracks"> |
| 670 <conditional name="track_file_style_conditional"> | 728 <conditional name="track_file_style_conditional"> |
| 671 <param name="track_file_style_selector" value="hic_matrix_option" /> | 729 <param name="track_file_style_selector" value="hic_matrix_option" /> |
| 672 <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.h5"/> | 730 <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.h5"/> |
| 673 <param name="title" value="Kc DpnII (Li et al. 2015)" /> | 731 <param name="title" value="Kc DpnII (Li et al. 2015)" /> |
| 674 <param name="colormap" value="RdYlBu_r" /> | 732 <param name="colormap" value="RdYlBu_r" /> |
| 675 <param name="depth" value="200000" /> | 733 <param name="depth" value="200000" /> |
| 676 <param name="transform" value="log1p" /> | 734 <param name="transform" value="log1p" /> |
| 677 <param name="boundaries_file" value="domains.bed" /> | 735 <param name="boundaries_file" value="domains.bed" /> |
| 678 <param name="x_labels" value="True" /> | |
| 679 </conditional> | 736 </conditional> |
| 680 </repeat> | 737 </repeat> |
| 681 <repeat name="tracks"> | 738 <repeat name="tracks"> |
| 682 <conditional name="track_file_style_conditional"> | 739 <conditional name="track_file_style_conditional"> |
| 683 <param name="track_file_style_selector" value="spacer_option" /> | 740 <param name="track_file_style_selector" value="spacer_option" /> |
| 688 <conditional name="track_file_style_conditional"> | 745 <conditional name="track_file_style_conditional"> |
| 689 <param name="track_file_style_selector" value="chrom_states_option" /> | 746 <param name="track_file_style_selector" value="chrom_states_option" /> |
| 690 <param name="track_input_bed" value="tad_classification.bed" ftype="bed" /> | 747 <param name="track_input_bed" value="tad_classification.bed" ftype="bed" /> |
| 691 <param name="title" value="TAD state" /> | 748 <param name="title" value="TAD state" /> |
| 692 <param name="height_chrom" value="0.5" /> | 749 <param name="height_chrom" value="0.5" /> |
| 693 <param name="labels" value="off" /> | 750 <param name="labels" value="false" /> |
| 694 <conditional name="color_bed"> | 751 <conditional name="color_bed"> |
| 695 <param name="color_bed_select" value="bed_rgb" /> | 752 <param name="color_bed_select" value="bed_rgb" /> |
| 696 </conditional> | 753 </conditional> |
| 697 </conditional> | 754 </conditional> |
| 698 </repeat> | 755 </repeat> |
| 699 <repeat name="tracks"> | 756 <repeat name="tracks"> |
| 700 <conditional name="track_file_style_conditional"> | 757 <conditional name="track_file_style_conditional"> |
| 701 <param name="track_file_style_selector" value="tad_score_track_option" /> | 758 <param name="track_file_style_selector" value="bedgraph_matrix_track_option" /> |
| 702 <param name="track_input_bedgraph" value="tad_score.gz" ftype="bedgraph" /> | 759 <param name="track_input_bedgraph_matrix" value="tad_score.gz" ftype="bedgraph" /> |
| 703 <param name="title" value="TAD separation score (Ramirez et al.)" /> | 760 <param name="title" value="TAD separation score (Ramirez et al.)" /> |
| 704 <param name="height_tad" value="10" /> | 761 <param name="height_bedgraph" value="10" /> |
| 705 </conditional> | 762 </conditional> |
| 706 </repeat> | 763 </repeat> |
| 707 <repeat name="tracks"> | 764 <repeat name="tracks"> |
| 708 <conditional name="track_file_style_conditional"> | 765 <conditional name="track_file_style_conditional"> |
| 709 <param name="track_file_style_selector" value="spacer_option" /> | 766 <param name="track_file_style_selector" value="spacer_option" /> |
| 798 <param name="track_file_style_selector" value="gene_track_option" /> | 855 <param name="track_file_style_selector" value="gene_track_option" /> |
| 799 <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" /> | 856 <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" /> |
| 800 <param name="title" value="max num rows 3" /> | 857 <param name="title" value="max num rows 3" /> |
| 801 <param name="height_bed" value="3" /> | 858 <param name="height_bed" value="3" /> |
| 802 <param name="fontsize" value="8" /> | 859 <param name="fontsize" value="8" /> |
| 803 <param name="gene_rows" value="3" /> | 860 <section name="bed_advanced"> |
| 861 <param name="gene_rows" value="3" /> | |
| 862 </section> | |
| 804 </conditional> | 863 </conditional> |
| 805 </repeat> | 864 </repeat> |
| 806 <repeat name="tracks"> | 865 <repeat name="tracks"> |
| 807 <conditional name="track_file_style_conditional"> | 866 <conditional name="track_file_style_conditional"> |
| 808 <param name="track_file_style_selector" value="spacer_option" /> | 867 <param name="track_file_style_selector" value="spacer_option" /> |
| 814 <param name="track_file_style_selector" value="gene_track_option" /> | 873 <param name="track_file_style_selector" value="gene_track_option" /> |
| 815 <param name="track_input_bed" value="dm3_genes.bed6.gz" ftype="bed" /> | 874 <param name="track_input_bed" value="dm3_genes.bed6.gz" ftype="bed" /> |
| 816 <param name="title" value="bed6 global max row" /> | 875 <param name="title" value="bed6 global max row" /> |
| 817 <param name="height_bed" value="20" /> | 876 <param name="height_bed" value="20" /> |
| 818 <param name="fontsize" value="10" /> | 877 <param name="fontsize" value="10" /> |
| 819 <param name="global_max_row" value="True" /> | 878 <section name="bed_advanced"> |
| 879 <param name="global_max_row" value="true" /> | |
| 880 </section> | |
| 820 </conditional> | 881 </conditional> |
| 821 </repeat> | 882 </repeat> |
| 822 <repeat name="tracks"> | 883 <repeat name="tracks"> |
| 823 <conditional name="track_file_style_conditional"> | 884 <conditional name="track_file_style_conditional"> |
| 824 <param name="track_file_style_selector" value="vlines_track_option" /> | 885 <param name="track_file_style_selector" value="vlines_track_option" /> |
| 825 <param name="track_input_bed_single" value="domains.bed" ftype="bed" /> | 886 <param name="track_input_bed_single" value="domains.bed" ftype="bed" /> |
| 826 <param name="type" value="vlines" /> | |
| 827 </conditional> | 887 </conditional> |
| 828 </repeat> | 888 </repeat> |
| 829 <param name="image_file_format" value="png" /> | 889 <param name="image_file_format" value="png" /> |
| 830 <output name="outFileName" file="master_TADs_plot.png" ftype="png" compare="sim_size" delta="35000" /> | 890 <output name="outFileName" file="master_TADs_plot.png" ftype="png" compare="sim_size" delta="35000" /> |
| 831 </test> | 891 </test> |
| 832 <test> | 892 <test> |
| 833 <param name="region" value="chrX:3000000-3500000"/> | 893 <param name="region" value="chrX:3000000-3500000"/> |
| 834 <conditional name="x_axis"> | 894 <conditional name="x_axis"> |
| 835 <param name="x_axis_select" value="yes" /> | 895 <param name="x_axis_select" value="true" /> |
| 836 </conditional> | 896 </conditional> |
| 837 <repeat name="tracks"> | 897 <repeat name="tracks"> |
| 838 <conditional name="track_file_style_conditional"> | 898 <conditional name="track_file_style_conditional"> |
| 839 <param name="track_file_style_selector" value="bigwig_track_option" /> | 899 <param name="track_file_style_selector" value="bigwig_track_option" /> |
| 840 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw,bigwig_chrx_2e6_5e6.bw" ftype="bigwig" /> | 900 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw,bigwig_chrx_2e6_5e6.bw" ftype="bigwig" /> |
| 845 <param name="type_selector" value="line_option" /> | 905 <param name="type_selector" value="line_option" /> |
| 846 <param name="width_line" value="1" /> | 906 <param name="width_line" value="1" /> |
| 847 </conditional> | 907 </conditional> |
| 848 </conditional> | 908 </conditional> |
| 849 </repeat> | 909 </repeat> |
| 910 <repeat name="tracks"> | |
| 911 <conditional name="track_file_style_conditional"> | |
| 912 <param name="track_file_style_selector" value="bigwig_track_option" /> | |
| 913 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" /> | |
| 914 <param name="title" value="nans_to_zeros" /> | |
| 915 <param name="height_bigwig" value="4" /> | |
| 916 <param name="color" value="blue" /> | |
| 917 <section name="reading_bw_conditional"> | |
| 918 <param name="nans_to_zeros" value="true" /> | |
| 919 </section> | |
| 920 <param name="show_data" value="true" /> | |
| 921 <conditional name="type_conditional"> | |
| 922 <param name="type_selector" value="line_option" /> | |
| 923 <param name="width_line" value="1" /> | |
| 924 </conditional> | |
| 925 </conditional> | |
| 926 </repeat> | |
| 927 <repeat name="tracks"> | |
| 928 <conditional name="track_file_style_conditional"> | |
| 929 <param name="track_file_style_selector" value="hlines_track_option" /> | |
| 930 <param name="title" value="" /> | |
| 931 <param name="color" value="orange" /> | |
| 932 <param name="y_values" value="50" /> | |
| 933 <param name="line_width" value="2" /> | |
| 934 <param name="line_style" value="dashed" /> | |
| 935 <param name="overlay_select" value="share-y" /> | |
| 936 </conditional> | |
| 937 </repeat> | |
| 938 <repeat name="tracks"> | |
| 939 <conditional name="track_file_style_conditional"> | |
| 940 <param name="track_file_style_selector" value="hlines_track_option" /> | |
| 941 <param name="title" value="hlines" /> | |
| 942 <param name="color" value="purple" /> | |
| 943 <param name="y_values" value="0, 10, 20, 100" /> | |
| 944 <param name="min_value" value="12" /> | |
| 945 <param name="show_data" value="true" /> | |
| 946 <param name="invert_orientation" value="true" /> | |
| 947 </conditional> | |
| 948 </repeat> | |
| 850 <param name="image_file_format" value="png" /> | 949 <param name="image_file_format" value="png" /> |
| 851 <output name="outFileName" file="bigwig_multiple.png" ftype="png" compare="sim_size" delta="35000" /> | 950 <output name="outFileName" file="bigwig_multiple.png" ftype="png" compare="sim_size" delta="35000" /> |
| 852 </test> | 951 </test> |
| 853 <test> | 952 <test> |
| 854 <param name="region" value="chrX:3000000-3500000"/> | 953 <param name="region" value="chrX:3000000-3500000"/> |
| 855 <conditional name="x_axis"> | 954 <conditional name="x_axis"> |
| 856 <param name="x_axis_select" value="yes" /> | 955 <param name="x_axis_select" value="true" /> |
| 857 </conditional> | 956 </conditional> |
| 858 <repeat name="tracks"> | 957 <repeat name="tracks"> |
| 859 <conditional name="track_file_style_conditional"> | 958 <conditional name="track_file_style_conditional"> |
| 860 <param name="track_file_style_selector" value="hic_matrix_option" /> | 959 <param name="track_file_style_selector" value="hic_matrix_option" /> |
| 861 <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.h5"/> | 960 <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.h5"/> |
| 870 <conditional name="track_file_style_conditional"> | 969 <conditional name="track_file_style_conditional"> |
| 871 <param name="track_file_style_selector" value="chrom_states_option" /> | 970 <param name="track_file_style_selector" value="chrom_states_option" /> |
| 872 <param name="track_input_bed" value="tad_classification.bed" ftype="bed" /> | 971 <param name="track_input_bed" value="tad_classification.bed" ftype="bed" /> |
| 873 <param name="title" value="TAD state" /> | 972 <param name="title" value="TAD state" /> |
| 874 <param name="height_chrom" value="0.5" /> | 973 <param name="height_chrom" value="0.5" /> |
| 875 <param name="labels" value="off" /> | 974 <param name="labels" value="false" /> |
| 876 <conditional name="color_bed"> | 975 <conditional name="color_bed"> |
| 877 <param name="color_bed_select" value="bed_rgb" /> | 976 <param name="color_bed_select" value="bed_rgb" /> |
| 878 </conditional> | 977 </conditional> |
| 879 </conditional> | 978 </conditional> |
| 880 </repeat> | 979 </repeat> |
| 883 <param name="track_file_style_selector" value="hic_matrix_option" /> | 982 <param name="track_file_style_selector" value="hic_matrix_option" /> |
| 884 <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.h5"/> | 983 <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.h5"/> |
| 885 <param name="title" value="Kc DpnII (Li et al. 2015) inverted no transform" /> | 984 <param name="title" value="Kc DpnII (Li et al. 2015) inverted no transform" /> |
| 886 <param name="colormap" value="Reds" /> | 985 <param name="colormap" value="Reds" /> |
| 887 <param name="depth" value="200000" /> | 986 <param name="depth" value="200000" /> |
| 888 <param name="transform" value="" /> | 987 <param name="transform" value="no" /> |
| 889 <param name="invert_orientation" value="yes" /> | 988 <param name="invert_orientation" value="true" /> |
| 890 <param name="min_value" value="5" /> | 989 <param name="min_value" value="5" /> |
| 891 <param name="max_value" value="70" /> | 990 <param name="max_value" value="70" /> |
| 892 </conditional> | 991 </conditional> |
| 893 </repeat> | 992 </repeat> |
| 894 <repeat name="tracks"> | 993 <repeat name="tracks"> |
| 903 <param name="track_input_bedgraph" value="test_with_neg_values.bg.gz" ftype="bedgraph" /> | 1002 <param name="track_input_bedgraph" value="test_with_neg_values.bg.gz" ftype="bedgraph" /> |
| 904 <param name="title" value="bedgraph with negative values" /> | 1003 <param name="title" value="bedgraph with negative values" /> |
| 905 <param name="height_bedgraph" value="4" /> | 1004 <param name="height_bedgraph" value="4" /> |
| 906 <param name="color" value="black" /> | 1005 <param name="color" value="black" /> |
| 907 <conditional name="color_negative"> | 1006 <conditional name="color_negative"> |
| 908 <param name="color_negative_select" value="yes" /> | 1007 <param name="color_negative_select" value="true" /> |
| 909 <param name="color" value="red" /> | 1008 <param name="color" value="red" /> |
| 910 </conditional> | 1009 </conditional> |
| 911 <conditional name="type_conditional"> | 1010 <conditional name="type_conditional"> |
| 912 <param name="type_selector" value="fill_option" /> | 1011 <param name="type_selector" value="fill_option" /> |
| 913 </conditional> | 1012 </conditional> |
| 1001 <param name="track_file_style_selector" value="gene_track_option" /> | 1100 <param name="track_file_style_selector" value="gene_track_option" /> |
| 1002 <param name="track_input_bed" value="dm3_genes.bed6.gz" ftype="bed" /> | 1101 <param name="track_input_bed" value="dm3_genes.bed6.gz" ftype="bed" /> |
| 1003 <param name="title" value="bed6 global max row color from score" /> | 1102 <param name="title" value="bed6 global max row color from score" /> |
| 1004 <param name="height_bed" value="20" /> | 1103 <param name="height_bed" value="20" /> |
| 1005 <param name="fontsize" value="10" /> | 1104 <param name="fontsize" value="10" /> |
| 1006 <param name="global_max_row" value="True" /> | 1105 <section name="bed_advanced"> |
| 1106 <param name="global_max_row" value="true" /> | |
| 1107 </section> | |
| 1007 <conditional name="color_bed"> | 1108 <conditional name="color_bed"> |
| 1008 <param name="color_bed_select" value="colormap" /> | 1109 <param name="color_bed_select" value="colormap" /> |
| 1009 <param name="color" value="RdYlBu_r" /> | 1110 <param name="color" value="RdYlBu_r" /> |
| 1010 </conditional> | 1111 </conditional> |
| 1011 </conditional> | 1112 </conditional> |
| 1012 </repeat> | 1113 </repeat> |
| 1013 <repeat name="tracks"> | 1114 <repeat name="tracks"> |
| 1014 <conditional name="track_file_style_conditional"> | 1115 <conditional name="track_file_style_conditional"> |
| 1015 <param name="track_file_style_selector" value="gene_track_option" /> | 1116 <param name="track_file_style_selector" value="gene_track_option" /> |
| 1016 <param name="track_input_bed" value="domains.bed" ftype="bed" /> | 1117 <param name="track_input_bed" value="domains.bed" ftype="bed" /> |
| 1017 <param name="title" value="domains.bed using the 9th field for colors interlaced" /> | 1118 <param name="title" value="domains.bed using the 9th field for colors interleaved" /> |
| 1018 <param name="height_bed" value="2" /> | 1119 <param name="height_bed" value="2" /> |
| 1019 <param name="fontsize" value="10" /> | 1120 <param name="fontsize" value="10" /> |
| 1020 <conditional name="color_bed"> | 1121 <conditional name="color_bed"> |
| 1021 <param name="color_bed_select" value="bed_rgb" /> | 1122 <param name="color_bed_select" value="bed_rgb" /> |
| 1022 </conditional> | 1123 </conditional> |
| 1023 <param name="display" value="interlaced" /> | 1124 <param name="border_color" value="red" /> |
| 1125 <param name="labels" value="false" /> | |
| 1126 <param name="display" value="interleaved" /> | |
| 1024 </conditional> | 1127 </conditional> |
| 1025 </repeat> | 1128 </repeat> |
| 1026 <param name="image_file_format" value="png" /> | 1129 <param name="image_file_format" value="png" /> |
| 1027 <output name="outFileName" file="master_TADs_BW_plot.png" ftype="png" compare="sim_size" delta="35000" /> | 1130 <output name="outFileName" file="master_TADs_BW_plot.png" ftype="png" compare="sim_size" delta="35000" /> |
| 1028 </test> | 1131 </test> |
| 1029 <test> | 1132 <test> |
| 1030 <param name="region" value="X:2700000-3100000"/> | 1133 <param name="region" value="X:2700000-3100000"/> |
| 1031 <conditional name="x_axis"> | 1134 <conditional name="x_axis"> |
| 1032 <param name="x_axis_select" value="yes" /> | 1135 <param name="x_axis_select" value="true" /> |
| 1033 <param name="where" value="bottom" /> | 1136 <param name="where" value="bottom" /> |
| 1034 </conditional> | 1137 </conditional> |
| 1035 <repeat name="tracks"> | 1138 <repeat name="tracks"> |
| 1036 <conditional name="track_file_style_conditional"> | 1139 <conditional name="track_file_style_conditional"> |
| 1037 <param name="track_file_style_selector" value="bigwig_track_option" /> | 1140 <param name="track_file_style_selector" value="bigwig_track_option" /> |
| 1062 <output name="outFileName" file="test_alpha.png" ftype="png" compare="sim_size" delta="35000" /> | 1165 <output name="outFileName" file="test_alpha.png" ftype="png" compare="sim_size" delta="35000" /> |
| 1063 </test> | 1166 </test> |
| 1064 <test> | 1167 <test> |
| 1065 <param name="region" value="X:3000000-3300000"/> | 1168 <param name="region" value="X:3000000-3300000"/> |
| 1066 <conditional name="x_axis"> | 1169 <conditional name="x_axis"> |
| 1067 <param name="x_axis_select" value="yes" /> | 1170 <param name="x_axis_select" value="true" /> |
| 1068 </conditional> | 1171 </conditional> |
| 1069 <repeat name="tracks"> | 1172 <repeat name="tracks"> |
| 1070 <conditional name="track_file_style_conditional"> | 1173 <conditional name="track_file_style_conditional"> |
| 1071 <param name="track_file_style_selector" value="gene_track_option" /> | 1174 <param name="track_file_style_selector" value="gene_track_option" /> |
| 1072 <param name="track_input_bed" value="dm3_subset_BDGP5.78.gtf.gz" ftype="gtf" /> | 1175 <param name="track_input_bed" value="dm3_subset_BDGP5.78.gtf.gz" ftype="gtf" /> |
| 1092 <output name="outFileName" file="test_gtf_bed4.png" ftype="png" compare="sim_size" delta="35000" /> | 1195 <output name="outFileName" file="test_gtf_bed4.png" ftype="png" compare="sim_size" delta="35000" /> |
| 1093 </test> | 1196 </test> |
| 1094 <test> | 1197 <test> |
| 1095 <param name="region" value="X:2760000-2802000"/> | 1198 <param name="region" value="X:2760000-2802000"/> |
| 1096 <conditional name="x_axis"> | 1199 <conditional name="x_axis"> |
| 1097 <param name="x_axis_select" value="yes" /> | 1200 <param name="x_axis_select" value="true" /> |
| 1098 <param name="where" value="bottom" /> | 1201 <param name="where" value="bottom" /> |
| 1099 </conditional> | 1202 </conditional> |
| 1100 <repeat name="tracks"> | 1203 <repeat name="tracks"> |
| 1101 <conditional name="track_file_style_conditional"> | 1204 <conditional name="track_file_style_conditional"> |
| 1102 <param name="track_file_style_selector" value="narrow_peak_track_option" /> | 1205 <param name="track_file_style_selector" value="narrow_peak_track_option" /> |
| 1104 <param name="track_input_narrow_peak" value="test2.narrowPeak" ftype="encodepeak" /> | 1207 <param name="track_input_narrow_peak" value="test2.narrowPeak" ftype="encodepeak" /> |
| 1105 <param name="color" value="#9bbb59" /> | 1208 <param name="color" value="#9bbb59" /> |
| 1106 <param name="height_narrow_peak" value="4" /> | 1209 <param name="height_narrow_peak" value="4" /> |
| 1107 <conditional name="display"> | 1210 <conditional name="display"> |
| 1108 <param name="display_selector" value="box" /> | 1211 <param name="display_selector" value="box" /> |
| 1109 <param name="use_summit" value="yes" /> | 1212 <param name="use_summit" value="true" /> |
| 1110 </conditional> | 1213 </conditional> |
| 1111 <param name="show_labels" value="yes" /> | 1214 <param name="show_labels" value="true" /> |
| 1112 </conditional> | 1215 </conditional> |
| 1113 </repeat> | 1216 </repeat> |
| 1114 <repeat name="tracks"> | 1217 <repeat name="tracks"> |
| 1115 <conditional name="track_file_style_conditional"> | 1218 <conditional name="track_file_style_conditional"> |
| 1116 <param name="track_file_style_selector" value="narrow_peak_track_option" /> | 1219 <param name="track_file_style_selector" value="narrow_peak_track_option" /> |
| 1118 <param name="track_input_narrow_peak" value="test2.narrowPeak" ftype="encodepeak" /> | 1221 <param name="track_input_narrow_peak" value="test2.narrowPeak" ftype="encodepeak" /> |
| 1119 <param name="color" value="#c0504d" /> | 1222 <param name="color" value="#c0504d" /> |
| 1120 <param name="height_narrow_peak" value="4" /> | 1223 <param name="height_narrow_peak" value="4" /> |
| 1121 <conditional name="display"> | 1224 <conditional name="display"> |
| 1122 <param name="display_selector" value="peak" /> | 1225 <param name="display_selector" value="peak" /> |
| 1123 <param name="use_summit" value="yes" /> | 1226 <param name="use_summit" value="true" /> |
| 1124 <param name="show_data" value="yes" /> | 1227 <param name="show_data" value="true" /> |
| 1125 <param name="width_adjust" value="3" /> | 1228 <param name="width_adjust" value="3" /> |
| 1126 <param name="max_value" value="50" /> | 1229 <param name="max_value" value="50" /> |
| 1127 </conditional> | 1230 </conditional> |
| 1128 <param name="show_labels" value="no" /> | 1231 <param name="show_labels" value="false" /> |
| 1129 <param name="spacer_height" value="0.5"/> | 1232 <param name="spacer_height" value="0.5"/> |
| 1130 </conditional> | 1233 </conditional> |
| 1131 </repeat> | 1234 </repeat> |
| 1132 <repeat name="tracks"> | 1235 <repeat name="tracks"> |
| 1133 <conditional name="track_file_style_conditional"> | 1236 <conditional name="track_file_style_conditional"> |
| 1136 <param name="track_input_narrow_peak" value="test2.narrowPeak" ftype="encodepeak" /> | 1239 <param name="track_input_narrow_peak" value="test2.narrowPeak" ftype="encodepeak" /> |
| 1137 <param name="color" value="#000000" /> | 1240 <param name="color" value="#000000" /> |
| 1138 <param name="height_narrow_peak" value="4" /> | 1241 <param name="height_narrow_peak" value="4" /> |
| 1139 <conditional name="display"> | 1242 <conditional name="display"> |
| 1140 <param name="display_selector" value="peak" /> | 1243 <param name="display_selector" value="peak" /> |
| 1141 <param name="use_summit" value="no" /> | 1244 <param name="use_summit" value="false" /> |
| 1142 <param name="show_data" value="no" /> | 1245 <param name="show_data" value="false" /> |
| 1143 </conditional> | 1246 </conditional> |
| 1144 <param name="show_labels" value="yes" /> | 1247 <param name="show_labels" value="true" /> |
| 1145 </conditional> | 1248 </conditional> |
| 1146 </repeat> | 1249 </repeat> |
| 1147 <param name="image_file_format" value="png" /> | 1250 <param name="image_file_format" value="png" /> |
| 1148 <output name="outFileName" file="test_narrowPeak.png" ftype="png" compare="sim_size" delta="35000" /> | 1251 <output name="outFileName" file="test_narrowPeak.png" ftype="png" compare="sim_size" delta="35000" /> |
| 1252 </test> | |
| 1253 <test> | |
| 1254 <param name="region" value="chrX:3300000-3500000"/> | |
| 1255 <conditional name="x_axis"> | |
| 1256 <param name="x_axis_select" value="true" /> | |
| 1257 </conditional> | |
| 1258 <repeat name="tracks"> | |
| 1259 <conditional name="track_file_style_conditional"> | |
| 1260 <param name="track_file_style_selector" value="gene_track_option" /> | |
| 1261 <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" /> | |
| 1262 <param name="title" value="genes" /> | |
| 1263 <param name="height_bed" value="10" /> | |
| 1264 </conditional> | |
| 1265 </repeat> | |
| 1266 <repeat name="tracks"> | |
| 1267 <conditional name="track_file_style_conditional"> | |
| 1268 <param name="track_file_style_selector" value="gene_track_option" /> | |
| 1269 <param name="track_input_bed" value="dm3_subset_BDGP5.78.gtf.gz" ftype="gtf" /> | |
| 1270 <param name="title" value="gtf" /> | |
| 1271 <param name="height_bed" value="10" /> | |
| 1272 <section name="bed_advanced"> | |
| 1273 <section name ="flybase"> | |
| 1274 <param name="height_utr" value="0.75"/> | |
| 1275 <param name="color_utr" value="#ff0000"/> | |
| 1276 </section> | |
| 1277 <section name ="gtf"> | |
| 1278 <param name="prefered_name" value="gene_name"/> | |
| 1279 <param name="merge_transcripts" value="true"/> | |
| 1280 </section> | |
| 1281 </section> | |
| 1282 </conditional> | |
| 1283 </repeat> | |
| 1284 <param name="image_file_format" value="png" /> | |
| 1285 <output name="outFileName" file="test_gtf_flybase_param.png" ftype="png" compare="sim_size" delta="35000" /> | |
| 1286 </test> | |
| 1287 <test> | |
| 1288 <param name="region" value="chrX:3300000-3500000"/> | |
| 1289 <conditional name="x_axis"> | |
| 1290 <param name="x_axis_select" value="true" /> | |
| 1291 </conditional> | |
| 1292 <repeat name="tracks"> | |
| 1293 <conditional name="track_file_style_conditional"> | |
| 1294 <param name="track_file_style_selector" value="gene_track_option" /> | |
| 1295 <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" /> | |
| 1296 <param name="title" value="dm3_genes.bed" /> | |
| 1297 <param name="height_bed" value="10" /> | |
| 1298 <param name="flybase" value="false" /> | |
| 1299 <section name="bed_advanced"> | |
| 1300 <param name="global_max_row" value="true" /> | |
| 1301 <param name="max_labels" value="15" /> | |
| 1302 </section> | |
| 1303 </conditional> | |
| 1304 </repeat> | |
| 1305 <repeat name="tracks"> | |
| 1306 <conditional name="track_file_style_conditional"> | |
| 1307 <param name="track_file_style_selector" value="gene_track_option" /> | |
| 1308 <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" /> | |
| 1309 <param name="title" value="genes.bed.gz" /> | |
| 1310 <param name="height_bed" value="10" /> | |
| 1311 <param name="flybase" value="false" /> | |
| 1312 <section name="bed_advanced"> | |
| 1313 <param name="line_width" value="2"/> | |
| 1314 <section name ="ucsc"> | |
| 1315 <param name="arrow_interval" value="10"/> | |
| 1316 </section> | |
| 1317 </section> | |
| 1318 </conditional> | |
| 1319 </repeat> | |
| 1320 <param name="image_file_format" value="png" /> | |
| 1321 <output name="outFileName" file="test_ucsc_param.png" ftype="png" compare="sim_size" delta="35000" /> | |
| 1322 </test> | |
| 1323 <test> | |
| 1324 <param name="region" value="X:3133000-3138000"/> | |
| 1325 <conditional name="x_axis"> | |
| 1326 <param name="x_axis_select" value="true" /> | |
| 1327 </conditional> | |
| 1328 <repeat name="tracks"> | |
| 1329 <conditional name="track_file_style_conditional"> | |
| 1330 <param name="track_file_style_selector" value="gene_track_option" /> | |
| 1331 <param name="track_input_bed" value="dm3_subset_BDGP5.78.gtf.gz" ftype="gtf" /> | |
| 1332 <param name="title" value="test" /> | |
| 1333 <param name="height_bed" value="10" /> | |
| 1334 <param name="flybase" value="true" /> | |
| 1335 <param name="spacer_height" value="1"/> | |
| 1336 </conditional> | |
| 1337 </repeat> | |
| 1338 <repeat name="tracks"> | |
| 1339 <conditional name="track_file_style_conditional"> | |
| 1340 <param name="track_file_style_selector" value="gene_track_option" /> | |
| 1341 <param name="track_input_bed" value="dm3_subset_BDGP5.78_asbed4.bed.gz" ftype="bed" /> | |
| 1342 <param name="title" value="test" /> | |
| 1343 <param name="height_bed" value="10" /> | |
| 1344 <conditional name="color_bed"> | |
| 1345 <param name="color_bed_select" value="manually" /> | |
| 1346 <param name="color" value="red" /> | |
| 1347 </conditional> | |
| 1348 <param name="flybase" value="false" /> | |
| 1349 <param name="spacer_height" value="1"/> | |
| 1350 </conditional> | |
| 1351 </repeat> | |
| 1352 <repeat name="tracks"> | |
| 1353 <conditional name="track_file_style_conditional"> | |
| 1354 <param name="track_file_style_selector" value="gene_track_option" /> | |
| 1355 <param name="track_input_bed" value="dm3_subset_BDGP5.78.gtf.gz" ftype="gtf" /> | |
| 1356 <param name="title" value="test" /> | |
| 1357 <param name="height_bed" value="10" /> | |
| 1358 <conditional name="color_bed"> | |
| 1359 <param name="color_bed_select" value="manually" /> | |
| 1360 <param name="color" value="red" /> | |
| 1361 </conditional> | |
| 1362 <param name="flybase" value="true" /> | |
| 1363 <param name="spacer_height" value="1"/> | |
| 1364 <param name="arrowhead_included" value="true"/> | |
| 1365 </conditional> | |
| 1366 </repeat> | |
| 1367 <repeat name="tracks"> | |
| 1368 <conditional name="track_file_style_conditional"> | |
| 1369 <param name="track_file_style_selector" value="vlines_track_option" /> | |
| 1370 <param name="track_input_bed_single" value="dm3_subset_BDGP5.78_asbed4.bed.gz" ftype="bed" /> | |
| 1371 </conditional> | |
| 1372 </repeat> | |
| 1373 <param name="image_file_format" value="png" /> | |
| 1374 <output name="outFileName" file="test_arrowhead_zoom.png" ftype="png" compare="sim_size" delta="35000" /> | |
| 1375 </test> | |
| 1376 <test> | |
| 1377 <param name="region" value="X:3340000-3380000"/> | |
| 1378 <conditional name="x_axis"> | |
| 1379 <param name="x_axis_select" value="true" /> | |
| 1380 </conditional> | |
| 1381 <repeat name="tracks"> | |
| 1382 <conditional name="track_file_style_conditional"> | |
| 1383 <param name="track_file_style_selector" value="gene_track_option" /> | |
| 1384 <param name="track_input_bed" value="domains.bed" ftype="bed" /> | |
| 1385 <param name="height_bed" value="6" /> | |
| 1386 <conditional name="color_bed"> | |
| 1387 <param name="color_bed_select" value="manually" /> | |
| 1388 <param name="color" value="yellow" /> | |
| 1389 </conditional> | |
| 1390 <param name="display" value="triangles" /> | |
| 1391 <param name="spacer_height" value="1"/> | |
| 1392 </conditional> | |
| 1393 </repeat> | |
| 1394 <repeat name="tracks"> | |
| 1395 <conditional name="track_file_style_conditional"> | |
| 1396 <param name="track_file_style_selector" value="bedgraph_track_option" /> | |
| 1397 <param name="track_input_bedgraph" value="bedgraph_chrx_2e6_5e6.bg" ftype="bedgraph" /> | |
| 1398 <param name="title" value="bedgraph" /> | |
| 1399 <param name="height_bedgraph" value="4" /> | |
| 1400 <param name="color" value="blue" /> | |
| 1401 <conditional name="type_conditional"> | |
| 1402 <param name="type_selector" value="line_option" /> | |
| 1403 </conditional> | |
| 1404 </conditional> | |
| 1405 </repeat> | |
| 1406 <repeat name="tracks"> | |
| 1407 <conditional name="track_file_style_conditional"> | |
| 1408 <param name="track_file_style_selector" value="bedgraph_track_option" /> | |
| 1409 <param name="track_input_bedgraph" value="bedgraph_chrx_2e6_5e6.bg" ftype="bedgraph" /> | |
| 1410 <param name="title" value="bedgraph" /> | |
| 1411 <param name="height_bedgraph" value="4" /> | |
| 1412 <param name="color" value="blue" /> | |
| 1413 <param name="use_middle" value="true" /> | |
| 1414 <conditional name="type_conditional"> | |
| 1415 <param name="type_selector" value="line_option" /> | |
| 1416 </conditional> | |
| 1417 </conditional> | |
| 1418 </repeat> | |
| 1419 <param name="image_file_format" value="png" /> | |
| 1420 <output name="outFileName" file="test_middle_triangle.png" ftype="png" compare="sim_size" delta="35000" /> | |
| 1421 </test> | |
| 1422 <test> | |
| 1423 <param name="region" value="chrX:3250000-3400000"/> | |
| 1424 <conditional name="x_axis"> | |
| 1425 <param name="x_axis_select" value="true" /> | |
| 1426 </conditional> | |
| 1427 <repeat name="tracks"> | |
| 1428 <conditional name="track_file_style_conditional"> | |
| 1429 <param name="track_file_style_selector" value="hic_matrix_option" /> | |
| 1430 <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.h5"/> | |
| 1431 <param name="title" value="Kc DpnII (Li et al. 2015)" /> | |
| 1432 <param name="colormap" value="RdYlBu_r" /> | |
| 1433 <param name="depth" value="100000" /> | |
| 1434 <param name="transform" value="log1p" /> | |
| 1435 <param name="show_masked_bins" value="true" /> | |
| 1436 <param name="scale_factor" value="2.0" /> | |
| 1437 </conditional> | |
| 1438 </repeat> | |
| 1439 <repeat name="tracks"> | |
| 1440 <conditional name="track_file_style_conditional"> | |
| 1441 <param name="track_file_style_selector" value="spacer_option" /> | |
| 1442 <param name="spacer_height" value="0.05" /> | |
| 1443 </conditional> | |
| 1444 </repeat> | |
| 1445 <repeat name="tracks"> | |
| 1446 <conditional name="track_file_style_conditional"> | |
| 1447 <param name="track_file_style_selector" value="bedgraph_matrix_track_option" /> | |
| 1448 <param name="track_input_bedgraph_matrix" value="tad_score.gz" ftype="bedgraph" /> | |
| 1449 <param name="title" value="TAD separation score (Ramirez et al.)" /> | |
| 1450 <param name="height_bedgraph" value="10" /> | |
| 1451 <param name="type_lines" value="lines" /> | |
| 1452 <param name="pos_score_in_bin" value="block" /> | |
| 1453 <param name="plot_horizontal_lines" value="true" /> | |
| 1454 <param name="show_data" value="true" /> | |
| 1455 </conditional> | |
| 1456 </repeat> | |
| 1457 <repeat name="tracks"> | |
| 1458 <conditional name="track_file_style_conditional"> | |
| 1459 <param name="track_file_style_selector" value="bedgraph_matrix_track_option" /> | |
| 1460 <param name="track_input_bedgraph_matrix" value="tad_score.gz" ftype="bedgraph" /> | |
| 1461 <param name="title" value="TAD separation score (Ramirez et al.)" /> | |
| 1462 <param name="height_bedgraph" value="10" /> | |
| 1463 <param name="type_lines" value="lines" /> | |
| 1464 <param name="pos_score_in_bin" value="center" /> | |
| 1465 <param name="plot_horizontal_lines" value="false" /> | |
| 1466 </conditional> | |
| 1467 </repeat> | |
| 1468 <param name="image_file_format" value="png" /> | |
| 1469 <output name="outFileName" file="test_TADs_bdgm.png" ftype="png" compare="sim_size" delta="35000" /> | |
| 1470 </test> | |
| 1471 <test> | |
| 1472 <param name="region" value="chrX:3000000-3300000"/> | |
| 1473 <conditional name="x_axis"> | |
| 1474 <param name="x_axis_select" value="true" /> | |
| 1475 </conditional> | |
| 1476 <repeat name="tracks"> | |
| 1477 <conditional name="track_file_style_conditional"> | |
| 1478 <param name="track_file_style_selector" value="hic_matrix_option" /> | |
| 1479 <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.h5"/> | |
| 1480 <param name="title" value="Kc DpnII (Li et al. 2015)" /> | |
| 1481 <param name="colormap" value="Purples" /> | |
| 1482 <param name="depth" value="190000" /> | |
| 1483 <param name="transform" value="no" /> | |
| 1484 </conditional> | |
| 1485 </repeat> | |
| 1486 <repeat name="tracks"> | |
| 1487 <conditional name="track_file_style_conditional"> | |
| 1488 <param name="track_file_style_selector" value="link_track_option" /> | |
| 1489 <param name="track_input_link" value="test.arcs" ftype="bed" /> | |
| 1490 <param name="title" value="" /> | |
| 1491 <param name="line_width" value="10" /> | |
| 1492 <param name="links_type" value="loops" /> | |
| 1493 <conditional name="color_link"> | |
| 1494 <param name="color_link_select" value="manually" /> | |
| 1495 <param name="color" value="red" /> | |
| 1496 </conditional> | |
| 1497 <param name="overlay_select" value="share-y" /> | |
| 1498 </conditional> | |
| 1499 </repeat> | |
| 1500 <repeat name="tracks"> | |
| 1501 <conditional name="track_file_style_conditional"> | |
| 1502 <param name="track_file_style_selector" value="link_track_option" /> | |
| 1503 <param name="track_input_link" value="test.arcs" ftype="bed" /> | |
| 1504 <param name="title" value="" /> | |
| 1505 <param name="height" value="5" /> | |
| 1506 <conditional name="color_link"> | |
| 1507 <param name="color_link_select" value="colormap" /> | |
| 1508 <param name="color" value="hot" /> | |
| 1509 </conditional> | |
| 1510 <param name="max_value" value="5"/> | |
| 1511 <param name="invert_orientation" value="true" /> | |
| 1512 </conditional> | |
| 1513 </repeat> | |
| 1514 <param name="image_file_format" value="png" /> | |
| 1515 <output name="outFileName" file="test_link.png" ftype="png" compare="sim_size" delta="35000" /> | |
| 1149 </test> | 1516 </test> |
| 1150 </tests> | 1517 </tests> |
| 1151 <help><![CDATA[ | 1518 <help><![CDATA[ |
| 1152 | 1519 |
| 1153 pyGenomeTracks | 1520 pyGenomeTracks |