Mercurial > repos > fubar > jbrowse2
comparison jbrowse2.xml @ 85:3b2ff9864995 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty
| author | fubar |
|---|---|
| date | Tue, 09 Apr 2024 00:26:49 +0000 |
| parents | c22c34695f1a |
| children | 0fae1d68347f |
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| 84:5c295cc220ed | 85:3b2ff9864995 |
|---|---|
| 1 <tool id="jbrowse2" name="JBrowse2" version="@TOOL_VERSION@+@WRAPPER_VERSION@_11" profile="22.05"> | 1 <tool id="jbrowse2" name="JBrowse2" version="@TOOL_VERSION@+@WRAPPER_VERSION@_12" profile="22.05"> |
| 2 <description>genome browser</description> | 2 <description>genome browser</description> |
| 3 <macros> | 3 <macros> |
| 4 <import>macros.xml</import> | 4 <import>macros.xml</import> |
| 5 </macros> | 5 </macros> |
| 6 <expand macro="edamInc"/> | 6 <expand macro="edamInc"/> |
| 202 #end if | 202 #end if |
| 203 #end if | 203 #end if |
| 204 #if $uglyTestingHack != "enabled": | 204 #if $uglyTestingHack != "enabled": |
| 205 <options> | 205 <options> |
| 206 <style> | 206 <style> |
| 207 #if str($track.data_format.data_format_select) in ["gff", "bed", "vcf", "maf", "blastxml"]: | 207 #if str($track.data_format.data_format_select) in ["gff", "bed", "maf", "blastxml"]: |
| 208 <type>${track.data_format.jbstyle.display}</type> | |
| 209 #if str($track.data_format.jbstyle.display) in ["LinearBasicDisplay", "LinearVariantDisplay"]: | |
| 210 <trackShowLabels>${track.data_format.jbstyle.show_labels}</trackShowLabels> | |
| 211 <trackShowDescriptions>${track.data_format.jbstyle.show_descriptions}</trackShowDescriptions> | |
| 212 #end if | |
| 213 #else if str($track.data_format.data_format_select) == "vcf": | |
| 208 <type>${track.data_format.jbstyle.track_style.display}</type> | 214 <type>${track.data_format.jbstyle.track_style.display}</type> |
| 209 #if str($track.data_format.jbstyle.track_style.display) in ["LinearBasicDisplay", "LinearVariantDisplay"]: | 215 #if str($track.data_format.jbstyle.track_style.display) in ["LinearBasicDisplay", "LinearVariantDisplay"]: |
| 210 <trackShowLabels>${track.data_format.jbstyle.track_style.show_labels}</trackShowLabels> | 216 <trackShowLabels>${track.data_format.jbstyle.track_style.show_labels}</trackShowLabels> |
| 211 <trackShowDescriptions>${track.data_format.jbstyle.track_style.show_descriptions}</trackShowDescriptions> | 217 <trackShowDescriptions>${track.data_format.jbstyle.track_style.show_descriptions}</trackShowDescriptions> |
| 212 #end if | 218 #end if |
| 219 | |
| 213 #end if | 220 #end if |
| 214 #if str($track.data_format.data_format_select) in ["bam", "cram"]: | 221 #if str($track.data_format.data_format_select) in ["bam", "cram"]: |
| 215 <type>LinearAlignmentsDisplay</type> | 222 <type>LinearAlignmentsDisplay</type> |
| 216 #end if | 223 #end if |
| 217 #if str($track.data_format.data_format_select) in ["paf"]: | 224 #if str($track.data_format.data_format_select) in ["hic", "cool", "mcool", "scool"]: |
| 218 <type>LinearBasicDisplay</type> | |
| 219 #end if | |
| 220 #if str($track.data_format.data_format_select) in ["hic"]: | |
| 221 <type>LinearHicDisplay</type> | 225 <type>LinearHicDisplay</type> |
| 222 #end if | 226 #end if |
| 223 </style> | 227 </style> |
| 224 #if str($track.data_format.data_format_select) == "bam": | 228 #if str($track.data_format.data_format_select) == "bam": |
| 225 <bam> | 229 <bam> |
| 230 <bam_index> | |
| 226 #for $dataset in $track.data_format.useuri.annotation: | 231 #for $dataset in $track.data_format.useuri.annotation: |
| 227 <bam_index>${dataset.metadata.bam_index}</bam_index> | 232 ${dataset.name},${dataset.metadata.bam_index} |
| 228 #end for | 233 #end for |
| 234 </bam_index> | |
| 229 </bam> | 235 </bam> |
| 230 #else if str($track.data_format.data_format_select) == "cram": | 236 #else if str($track.data_format.data_format_select) == "cram": |
| 231 <cram> | 237 <cram> |
| 238 <cram_index> | |
| 232 #for $dataset in $track.data_format.useuri.annotation: | 239 #for $dataset in $track.data_format.useuri.annotation: |
| 233 <cram_index>${dataset.metadata.cram_index}</cram_index> | 240 ${dataset.name},${dataset.metadata.cram_index} |
| 234 #end for | 241 #end for |
| 242 </cram_index> | |
| 235 </cram> | 243 </cram> |
| 236 #else if str($track.data_format.data_format_select) == "blastxml": | 244 #else if str($track.data_format.data_format_select) == "blastxml": |
| 237 <blast> | 245 <blast> |
| 238 #if str($track.data_format.blast_parent) != "": | 246 #if str($track.data_format.blast_parent) != "": |
| 239 <parent>${track.data_format.blast_parent}</parent> | 247 <parent>${track.data_format.blast_parent}</parent> |
| 247 <match>${track.data_format.match_part.name}</match> | 255 <match>${track.data_format.match_part.name}</match> |
| 248 #end if | 256 #end if |
| 249 </gff> | 257 </gff> |
| 250 #else if str($track.data_format.data_format_select) == "paf": | 258 #else if str($track.data_format.data_format_select) == "paf": |
| 251 <paf> | 259 <paf> |
| 260 #if $track.data_format.pafuseuri.insource == "history": | |
| 252 <genome> | 261 <genome> |
| 253 #for refgenome in $track.data_format.pafuseuri.refgenomes: | 262 #for $anno in $track.data_format.pafuseuri.annotation: |
| 254 $refgenome.annotation, | 263 ${anno}, |
| 255 #end for | 264 #end for |
| 256 </genome> | 265 </genome> |
| 257 <genome_label> | 266 <genome_label> |
| 258 #for refgenome in $track.data_format.pafuseuri.refgenomes: | 267 #for $anno in $track.data_format.pafuseuri.annotation: |
| 259 $refgenome.annoname, | 268 ${anno.name}, |
| 260 #end for | 269 #end for |
| 261 </genome_label> | 270 </genome_label> |
| 271 #else: | |
| 272 <genome> | |
| 273 #for $refgenome in $track.data_format.pafuseuri.refuri: | |
| 274 $refgenome.annotation, | |
| 275 #end for | |
| 276 </genome> | |
| 277 <genome_label> | |
| 278 #for $refgenome in $track.data_format.pafuseuri.refuri: | |
| 279 ${refgenome.annoname}, | |
| 280 #end for | |
| 281 </genome_label> | |
| 282 #end if | |
| 262 </paf> | 283 </paf> |
| 263 #else if str($track.data_format.data_format_select) == "hic": | 284 #else if str($track.data_format.data_format_select) == "hic": |
| 264 <hic> | 285 <hic> |
| 265 </hic> | 286 </hic> |
| 266 #else if str($track.data_format.data_format_select) == "cool": | 287 #else if str($track.data_format.data_format_select) == "cool": |
| 375 <param label="Is this a protein blast search?" | 396 <param label="Is this a protein blast search?" |
| 376 type="boolean" | 397 type="boolean" |
| 377 name="is_protein" | 398 name="is_protein" |
| 378 truevalue="true" | 399 truevalue="true" |
| 379 falsevalue="false" /> | 400 falsevalue="false" /> |
| 380 <expand macro="track_styling_feature" /> | 401 <expand macro="track_styling_vgp" /> |
| 381 <expand macro="track_visibility" /> | 402 <expand macro="track_visibility" /> |
| 382 </when> | 403 </when> |
| 383 <when value="vcf"> | 404 <when value="vcf"> |
| 384 <expand macro="input_conditional" label="SNP Track Data" format="vcf,vcf_bgzip" /> | 405 <expand macro="input_conditional" label="SNP Track Data" format="vcf,vcf_bgzip" /> |
| 385 <expand macro="track_styling_vcf"/> | 406 <expand macro="track_styling_vcf"/> |
| 400 help="Match_parts have options for the parent feature type, such as cDNA_match, match, translated_nucleotide_match, etc. Please select the appropriate one here. You can leave empty to try autodetection (only works with CanvasFeatures track type)." | 421 help="Match_parts have options for the parent feature type, such as cDNA_match, match, translated_nucleotide_match, etc. Please select the appropriate one here. You can leave empty to try autodetection (only works with CanvasFeatures track type)." |
| 401 optional="True"/> | 422 optional="True"/> |
| 402 </when> | 423 </when> |
| 403 <when value="false" /> | 424 <when value="false" /> |
| 404 </conditional> | 425 </conditional> |
| 405 <expand macro="track_styling_feature" /> | 426 <expand macro="track_styling_vgp" /> |
| 406 <expand macro="track_visibility" /> | 427 <expand macro="track_visibility" /> |
| 407 </when> | 428 </when> |
| 408 <when value="bam"> | 429 <when value="bam"> |
| 409 <expand macro="input_conditional" label="BAM Track Data" format="bam" /> | 430 <expand macro="input_conditional" label="BAM Track Data" format="bam" /> |
| 410 <expand macro="track_visibility" /> | 431 <expand macro="track_visibility" /> |
| 411 </when> | 432 </when> |
| 412 <when value="bed"> | 433 <when value="bed"> |
| 413 <expand macro="input_conditional" label="BED Track Data" format="bed" /> | 434 <expand macro="input_conditional" label="BED Track Data" format="bed" /> |
| 414 <expand macro="track_styling_feature" /> | 435 <expand macro="track_styling_vgp" /> |
| 415 <expand macro="track_visibility" /> | 436 <expand macro="track_visibility" /> |
| 416 </when> | 437 </when> |
| 417 <when value="cram"> | 438 <when value="cram"> |
| 418 <expand macro="input_conditional" label="CRAM Track Data" format="cram" /> | 439 <expand macro="input_conditional" label="CRAM Track Data" format="cram" /> |
| 419 <expand macro="track_visibility" /> | 440 <expand macro="track_visibility" /> |
| 420 </when> | 441 </when> |
| 421 <when value="maf"> | 442 <when value="maf"> |
| 422 <expand macro="input_conditional" label="MAF Track Data" format="maf" /> | 443 <expand macro="input_conditional" label="MAF Track Data" format="maf" /> |
| 423 <expand macro="track_styling_feature" /> | 444 <expand macro="track_styling_vgp" /> |
| 424 <expand macro="track_visibility" /> | 445 <expand macro="track_visibility" /> |
| 425 </when> | 446 </when> |
| 426 <when value="bigwig"> | 447 <when value="bigwig"> |
| 427 <expand macro="input_conditional" label="BigWig Track Data" format="bigwig" /> | 448 <expand macro="input_conditional" label="BigWig Track Data" format="bigwig" /> |
| 428 <expand macro="track_visibility" /> | 449 <expand macro="track_visibility" /> |