Mercurial > repos > iuc > jbrowse
annotate jbrowse.xml @ 3:7342f467507b draft
Uploaded v0.4 of JBrowse
| author | iuc |
|---|---|
| date | Thu, 31 Dec 2015 13:58:43 -0500 |
| parents | 497c6bb3b717 |
| children | ae9382cfb6ac |
| rev | line source |
|---|---|
| 3 | 1 <tool id="jbrowse" name="JBrowse" version="0.4"> |
|
0
2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff
changeset
|
2 <description>genome browser</description> |
|
2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff
changeset
|
3 <macros> |
|
2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff
changeset
|
4 <import>macros.xml</import> |
|
2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff
changeset
|
5 </macros> |
|
2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff
changeset
|
6 <expand macro="requirements"/> |
|
2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff
changeset
|
7 <expand macro="stdio"/> |
|
2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff
changeset
|
8 <version_command>python jbrowse.py --version</version_command> |
| 3 | 9 <command><![CDATA[ |
| 10 mkdir -p $output.files_path && | |
| 11 ## Copy the XML file into the directory, mostly for debugging | |
| 12 ## but nice if users want to reproduce locally | |
| 13 cp $trackxml $output.files_path/galaxy.xml && | |
| 14 | |
| 15 ## Once that's done, we run the python script to handle the real work | |
| 16 python $__tool_directory__/jbrowse.py | |
| 17 $trackxml | |
|
0
2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff
changeset
|
18 |
|
2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff
changeset
|
19 --jbrowse \${JBROWSE_SOURCE_DIR} |
| 3 | 20 #if str($standalone) == "Complete": |
| 21 --standalone | |
| 22 #end if | |
| 23 --outdir $output.files_path; | |
| 24 | |
| 25 #if str($standalone) == "Complete": | |
| 26 mv $output.files_path/index.html $output; | |
| 27 #else: | |
| 28 mv $dummyIndex $output; | |
| 29 #end if | |
| 30 | |
| 31 | |
| 32 ## Ugly testing hack since I cannot get <extra_files> to test the files I want to test. Hmph. | |
| 33 #if str($uglyTestingHack) == "enabled": | |
| 34 mv $trackxml $output | |
| 35 #end if | |
| 36 ]]></command> | |
|
1
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
37 <configfiles> |
| 3 | 38 <configfile name="dummyIndex"> |
| 39 <![CDATA[ | |
| 40 <html> | |
| 41 <head> | |
| 42 </head> | |
| 43 <body> | |
| 44 <h1>JBrowse Data Directory</h1> | |
| 45 <p> | |
| 46 Hi! This is not a full JBrowse instance. JBrowse v0.4(+?) | |
| 47 started shipping with the ability to produce just the | |
| 48 "data" directory from a JBrowse instance, rather than a | |
| 49 complete, standalone instance. This was intended to be used | |
| 50 with the in-development Apollo integration, but may have other | |
| 51 uses as well. | |
| 52 </p> | |
| 53 <p> | |
| 54 <u>This is not usable on its own</u>. The output dataset may be | |
| 55 used with Apollo, or may be passed through the "JBrowse - | |
| 56 Convert to Standalone" tool in Galaxy to "upgrade" to a full | |
| 57 JBrowse instance. | |
| 58 </p> | |
| 59 </body> | |
| 60 </html> | |
| 61 ]]> | |
| 62 </configfile> | |
| 63 <configfile name="trackxml"><![CDATA[<?xml version="1.0"?> | |
| 64 <root> | |
| 65 <metadata> | |
| 66 <gencode>$gencode</gencode> | |
| 67 <genomes> | |
| 68 #for $genome in $genomes: | |
| 69 <genome>$genome</genome> | |
| 70 #end for | |
| 71 </genomes> | |
| 72 </metadata> | |
| 73 <tracks> | |
| 74 #for $tg in $track_groups: | |
| 75 #for $track in $tg.data_tracks: | |
| 76 <track cat="${tg.category}" format="${track.data_format.data_format_select}"> | |
| 77 <files> | |
| 78 #for $dataset in $track.data_format.annotation: | |
| 79 <trackFile path="${dataset}" ext="${dataset.ext}" label="${dataset.element_identifier}" /> | |
| 80 #end for | |
| 81 </files> | |
| 82 | |
| 83 <options> | |
| 84 #if str($track.data_format.data_format_select) == "gene_calls" or str($track.data_format.data_format_select) == "blast": | |
| 85 <style> | |
| 86 <className>${track.data_format.jbstyle.style_classname}</className> | |
| 87 <description>${track.data_format.jbstyle.style_description}</description> | |
| 88 <label>${track.data_format.jbstyle.style_label}</label> | |
| 89 <height>${track.data_format.jbstyle.style_height}</height> | |
| 90 </style> | |
| 91 <scaling> | |
| 92 #if str($track.data_format.jbcolor_scale.color_score.color_score_select) == "none": | |
| 93 <method>ignore</method> | |
| 94 <scheme> | |
| 95 #if str($track.data_format.jbcolor_scale.color_score.color.color_select) == "automatic": | |
| 96 <color>__auto__</color> | |
| 97 #else | |
| 98 <color>${track.data_format.jbcolor_scale.color_score.color.style_color}</color> | |
| 99 #end if | |
| 100 </scheme> | |
| 101 #else | |
| 102 <method>score</method> | |
| 103 <algo>${track.data_format.jbcolor_scale.color_score.score_scaling}</algo> | |
| 104 <scales> | |
| 105 <type>${track.data_format.jbcolor_scale.color_score.score_scales.scale_select}</type> | |
| 106 | |
| 107 #if str($track.data_format.jbcolor_scale.color_score.score_scales.scale_select) == "manual": | |
| 108 <min>${track.data_format.jbcolor_scale.color_score.score_scales.minimum}</min> | |
| 109 <max>${track.data_format.jbcolor_scale.color_score.score_scales.maximum}</max> | |
| 110 #end if | |
| 111 </scales> | |
| 112 <scheme> | |
| 113 <type>${track.data_format.jbcolor_scale.color_score.color_scheme.score_scheme}</type> | |
| 114 ## auto_color | |
| 115 #if str($track.data_format.jbcolor_scale.color_score.color_scheme.score_scheme) == "opacity": | |
| 116 #if str($track.data_format.jbcolor_scale.color_score.color_scheme.color.color_select) == "automatic": | |
| 117 <color>__auto__</color> | |
| 118 #else | |
| 119 <color>${track.data_format.jbcolor_scale.color_score.color_scheme.color.style_color}</color> | |
| 120 #end if | |
| 121 #end if | |
| 122 </scheme> | |
| 123 #end if | |
| 124 </scaling> | |
| 125 #end if | |
| 126 | |
| 127 #if str($track.data_format.data_format_select) == "wiggle": | |
| 128 <wiggle> | |
| 129 <type>${track.data_format.xyplot}</type> | |
| 130 <variance_band>${track.data_format.var_band}</variance_band> | |
| 131 #if str($track.data_format.scaling.scale_select) == "auto_local": | |
| 132 <autoscale>local</autoscale> | |
| 133 #else if str($track.data_format.scaling.scale_select) == "auto_global": | |
| 134 <autoscale>global</autoscale> | |
| 135 #else: | |
| 136 <min>${track.data_format.scaling.minimum}</min> | |
| 137 <max>${track.data_format.scaling.maximum}</max> | |
| 138 #end if | |
| 139 | |
| 140 ## Wiggle tracks need special color config | |
| 141 #if str($track.data_format.jbcolor.color.color_select) != "automatic": | |
| 142 <color_pos>${track.data_format.jbcolor.color.style_pos_color}</color_pos> | |
| 143 <color_neg>${track.data_format.jbcolor.color.style_neg_color}</color_neg> | |
| 144 #else: | |
| 145 <color_pos>__auto__</color_pos> | |
| 146 <color_neg>__auto__</color_neg> | |
| 147 #end if | |
| 148 | |
| 149 ## Bicolor pivot config | |
| 150 #if str($track.data_format.jbcolor.bicolor_pivot.bicolor_pivot_select) == "zero": | |
| 151 <bicolor_pivot>zero</bicolor_pivot> | |
| 152 #else if str($track.data_format.jbcolor.bicolor_pivot.bicolor_pivot_select) == "mean": | |
| 153 <bicolor_pivot>mean</bicolor_pivot> | |
| 154 #else: | |
| 155 <bicolor_pivot>${track.data_format.jbcolor.bicolor_pivot.pivot_point}</bicolor_pivot> | |
| 156 #end if | |
| 157 </wiggle> | |
| 158 #else if str($track.data_format.data_format_select) == "pileup": | |
| 159 <pileup> | |
| 160 <auto_snp>${track.data_format.auto_snp}</auto_snp> | |
| 161 <bam_indices> | |
| 162 #for $dataset in $track.data_format.annotation: | |
| 163 <bam_index>${dataset.metadata.bam_index}</bam_index> | |
| 164 #end for | |
| 165 </bam_indices> | |
| 166 </pileup> | |
| 167 #else if str($track.data_format.data_format_select) == "blast": | |
| 168 <blast> | |
| 169 #if str($track.data_format.blast_parent) != "": | |
| 170 <parent>${track.data_format.blast_parent}</parent> | |
| 171 #end if | |
| 172 <protein>${track.data_format.is_protein}</protein> | |
| 173 <min_gap>${track.data_format.min_gap}</min_gap> | |
| 174 </blast> | |
| 175 #else if str($track.data_format.data_format_select) == "gene_calls": | |
| 176 <gff> | |
| 177 #if $track.data_format.match_part.match_part_select: | |
| 178 <match>${track.data_format.match_part.name}</match> | |
| 179 #end if | |
| 180 </gff> | |
| 181 #end if | |
| 182 </options> | |
| 183 </track> | |
| 184 #end for | |
| 185 #end for | |
| 186 </tracks> | |
| 187 </root> | |
| 188 ]]> | |
|
1
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
189 </configfile> |
|
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
190 </configfiles> |
|
0
2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff
changeset
|
191 <inputs> |
| 3 | 192 <param label="Fasta Sequence(s)" |
| 193 name="genomes" | |
| 194 type="data" | |
| 195 format="fasta" | |
| 196 multiple="True"/> | |
| 197 <param name="standalone" label="Produce Standalone Instance" type="boolean" truevalue="Complete" falsevalue="Data Directory" help="Produce a full, working JBrowse instance or just the data directory. Data dir mode is experimental and intended to be used with Apollo" checked="True"/> | |
| 198 | |
| 199 <param label="Genetic Code" name="gencode" type="select"> | |
| 200 <option value="1">1. The Standard Code</option> | |
| 201 <option value="2">2. The Vertebrate Mitochondrial Code</option> | |
| 202 <option value="3">3. The Yeast Mitochondrial Code</option> | |
| 203 <option value="4">4. The Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option> | |
| 204 <option value="5">5. The Invertebrate Mitochondrial Code</option> | |
| 205 <option value="6">6. The Ciliate, Dasycladacean and Hexamita Nuclear Code</option> | |
| 206 <option value="9">9. The Echinoderm and Flatworm Mitochondrial Code</option> | |
| 207 <option value="10">10. The Euplotid Nuclear Code</option> | |
| 208 <option value="11">11. The Bacterial, Archaeal and Plant Plastid Code</option> | |
| 209 <option value="12">12. The Alternative Yeast Nuclear Code</option> | |
| 210 <option value="13">13. The Ascidian Mitochondrial Code</option> | |
| 211 <option value="14">14. The Alternative Flatworm Mitochondrial Code</option> | |
| 212 <option value="16">16. Chlorophycean Mitochondrial Code</option> | |
| 213 <option value="21">21. Trematode Mitochondrial Code</option> | |
| 214 <option value="22">22. Scenedesmus obliquus Mitochondrial Code</option> | |
| 215 <option value="23">23. Thraustochytrium Mitochondrial Code</option> | |
| 216 <option value="24">24. Pterobranchia Mitochondrial Code</option> | |
| 217 <option value="25">25. Candidate Division SR1 and Gracilibacteria Code</option> | |
| 218 </param> | |
| 219 | |
| 220 <repeat name="track_groups" title="Track Group"> | |
| 221 <param label="Track Category" | |
| 222 name="category" | |
| 223 type="text" | |
| 224 value="Default" | |
| 225 help="Organise your tracks into Categories for a nicer end-user experience" optional="False"/> | |
|
0
2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff
changeset
|
226 <repeat name="data_tracks" title="Annotation Track"> |
|
1
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
227 <conditional name="data_format" label="Track Options"> |
|
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
228 <param type="select" label="Track Type" name="data_format_select"> |
| 3 | 229 <option value="gene_calls">GFF/GFF3/BED/GBK Features</option> |
|
1
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
230 <option value="pileup">BAM Pileups</option> |
|
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
231 <option value="blast">Blast XML</option> |
|
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
232 <option value="wiggle">BigWig XY</option> |
|
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
233 <option value="vcf">VCF SNPs</option> |
|
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
234 </param> |
|
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
235 <when value="blast"> |
| 3 | 236 <expand macro="input_conditional" label="BlastXML Track Data" format="blastxml" /> |
|
1
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
237 |
| 3 | 238 <param label="Features used in Blast Search" |
| 239 help="in GFF3. This is used so we know where to map features. E.g. where results of which CDS Protein32 match up to. The query IDs in your blast results should MATCH some feature IDs in your GFF3 file. This is an optional field and is most useful if using JBrowse to display protein blast results on a DNA genome. blastn results don't need this, blastp results on a protein sequence don't need this." | |
| 240 format="gff3" | |
| 241 name="blast_parent" | |
| 242 optional="true" | |
| 243 type="data"/> | |
|
1
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
244 |
| 3 | 245 <param label="Minimum Gap Size" |
| 246 help="before a new match_part feature is created" | |
| 247 name="min_gap" | |
| 248 type="integer" | |
| 249 value="10" | |
| 250 min="2" /> | |
|
1
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
251 <param label="Is this a protein blast search?" |
| 3 | 252 type="boolean" |
| 253 name="is_protein" | |
| 254 truevalue="true" | |
| 255 falsevalue="false" /> | |
| 256 | |
| 257 <expand macro="track_styling" | |
| 258 classname="feature" | |
| 259 label="description" | |
| 260 description="Hit_titles" | |
| 261 height="600px"/> | |
| 262 <expand macro="color_selection" | |
| 263 token_scaling_lin_select="false" | |
| 264 token_scaling_log_select="true" /> | |
|
1
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
265 </when> |
|
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
266 <when value="vcf"> |
| 3 | 267 <expand macro="input_conditional" label="SNP Track Data" format="vcf" /> |
|
1
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
268 </when> |
|
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
269 <when value="gene_calls"> |
| 3 | 270 <expand macro="input_conditional" label="GFF/GFF3/BED Track Data" format="gff,gff3,bed" /> |
| 271 <conditional name="match_part" label="match/match_part data"> | |
| 272 <param label="This is match/match_part data" | |
| 273 type="boolean" | |
| 274 name="match_part_select" | |
| 275 truevalue="true" | |
| 276 falsevalue="false" /> | |
| 277 <when value="true"> | |
| 278 <param label="Match Part Feature Type" | |
| 279 name="name" | |
| 280 type="text" | |
| 281 value="match" | |
| 282 help="Match_parts have several options for the parent feature type, such as cDNA_match, match, translated_nucleotide_match, etc. Please select the appropriate one here" | |
| 283 optional="False"/> | |
| 284 </when> | |
| 285 <when value="false" /> | |
| 286 </conditional> | |
| 287 <expand macro="track_styling" /> | |
| 288 <expand macro="color_selection" /> | |
|
1
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
289 </when> |
|
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
290 <when value="pileup"> |
| 3 | 291 <expand macro="input_conditional" label="BAM Track Data" format="bam" /> |
| 292 <param label="Autogenerate SNP Track" | |
| 293 help="Not recommended for deep coverage BAM files" | |
| 294 type="boolean" | |
| 295 name="auto_snp" | |
| 296 truevalue="true" | |
| 297 falsevalue="false" /> | |
|
1
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
298 </when> |
|
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
299 <when value="wiggle"> |
| 3 | 300 <expand macro="input_conditional" label="BigWig Track Data" format="bigwig" /> |
| 301 | |
| 302 <param label="Use XYPlot" | |
| 303 help="instead of continuous colored band" | |
| 304 type="boolean" | |
| 305 name="xyplot" | |
| 306 truevalue="JBrowse/View/Track/Wiggle/XYPlot" | |
| 307 falsevalue="JBrowse/View/Track/Wiggle/Density" /> | |
| 308 <param label="Show variance band" | |
| 309 help="Only for XYPlots" | |
| 310 type="boolean" | |
| 311 name="var_band" | |
| 312 truevalue="true" | |
| 313 falsevalue="false" /> | |
|
1
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
314 |
|
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
315 <conditional name="scaling" label="Scaling"> |
|
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
316 <param type="select" label="Track Scaling" name="scale_select"> |
|
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
317 <option value="auto_local">Autoscale (local)</option> |
| 3 | 318 <option value="auto_global" selected="true">Autoscale (global)</option> |
| 319 <option value="fixed">Specify Min/Max</option> | |
|
1
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
320 </param> |
|
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
321 <when value="auto_local"></when> |
|
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
322 <when value="auto_global"></when> |
|
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
323 <when value="fixed"> |
|
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
324 <param label="Track minimum" name="minimum" |
|
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
325 type="integer" value="0" /> |
|
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
326 <param label="Track maximum" name="maximum" |
|
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
327 type="integer" value="100" /> |
|
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
328 </when> |
|
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
329 </conditional> |
| 3 | 330 <expand macro="color_selection_minmax" /> |
|
1
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
331 </when> |
|
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
332 </conditional> |
|
0
2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff
changeset
|
333 </repeat> |
| 3 | 334 </repeat> |
| 335 | |
| 336 <param type="hidden" name="uglyTestingHack" value="" /> | |
|
0
2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff
changeset
|
337 </inputs> |
|
2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff
changeset
|
338 <outputs> |
| 3 | 339 <data format="html" name="output" label="JBrowse on $on_string - $standalone"/> |
|
0
2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff
changeset
|
340 </outputs> |
| 3 | 341 <tests> |
| 342 <test> | |
| 343 <!-- gencode --> | |
| 344 <param name="genomes" value="merlin.fa"/> | |
| 345 <param name="gencode" value="1" /> | |
| 346 <param name="standalone" value="Data Directory" /> | |
| 347 <param name="uglyTestingHack" value="enabled" /> | |
| 348 <output name="output" file="gencode/test-1.xml" lines_diff="4" /> | |
| 349 </test> | |
| 350 <test> | |
| 351 <param name="genomes" value="merlin.fa"/> | |
| 352 <param name="gencode" value="11" /> | |
| 353 <param name="standalone" value="Data Directory" /> | |
| 354 <param name="uglyTestingHack" value="enabled" /> | |
| 355 <output name="output" file="gencode/test.xml" lines_diff="4"/> | |
| 356 </test> | |
| 357 <!-- | |
| 358 <test> | |
| 359 <param name="genomes" value="merlin.fa"/> | |
| 360 <param name="gencode" value="11" /> | |
| 361 <param name="standalone" value="Data Directory" /> | |
| 362 <param name="track_groups_0|category" value="Auto Coloured" /> | |
| 363 <param name="track_groups_0|data_tracks_0|data_format" value="gene_calls"/> | |
| 364 <param name="track_groups_0|data_tracks_0|annotation" value="gff3/A.gff,gff3/B.gff,gff3/C.gff,gff3/D.gff"/> | |
| 365 <param name="track_groups_0|data_tracks_0|match_part|match_part_select" value="false"/> | |
| 366 <param name="track_groups_0|data_tracks_0|jbcolor_scale|color_score|color_score_select" value="none"/> | |
| 367 <param name="track_groups_0|data_tracks_0|jbcolor_scale|color|color_select" value="automatic"/> | |
| 368 | |
| 369 | |
| 370 <param name="track_groups_1|category" value="Ignore Scale" /> | |
| 371 <param name="track_groups_1|data_tracks_0|data_format" value="gene_calls"/> | |
| 372 <param name="track_groups_1|data_tracks_0|annotation" value="gff3/1.gff"/> | |
| 373 <param name="track_groups_1|data_tracks_0|match_part|match_part_select" value="false"/> | |
| 374 <param name="track_groups_1|data_tracks_0|jbcolor_scale|color_score|color_score_select" value="none"/> | |
| 375 <param name="track_groups_1|data_tracks_0|jbcolor_scale|color_score|color|color_select" value="manual"/> | |
| 376 <param name="track_groups_1|data_tracks_0|jbcolor_scale|color_score|color|style_color" value="#ff00ff"/> | |
| 377 | |
| 378 <param name="track_groups_2|category" value="Scaled Colour" /> | |
| 379 <param name="track_groups_2|data_tracks_0|data_format" value="gene_calls"/> | |
| 380 <param name="track_groups_2|data_tracks_0|annotation" value="gff3/1.gff"/> | |
| 381 <param name="track_groups_2|data_tracks_0|match_part|match_part_select" value="false"/> | |
| 382 <param name="track_groups_2|data_tracks_0|jbcolor_scale|color_score|color_score_select" value="score"/> | |
| 383 <param name="track_groups_2|data_tracks_0|jbcolor_scale|color_score|score_scaling" value="linear"/> | |
| 384 <param name="track_groups_2|data_tracks_0|jbcolor_scale|color_score|score_scales|scale_select" value="automatic"/> | |
| 385 <param name="track_groups_2|data_tracks_0|jbcolor_scale|color_score|color_scheme|score_scheme" value="opacity"/> | |
| 386 <param name="track_groups_2|data_tracks_0|jbcolor_scale|color_score|color_scheme|color_select" value="automatic"/> | |
| 387 <param name="track_groups_2|data_tracks_1|data_format" value="gene_calls"/> | |
| 388 <param name="track_groups_2|data_tracks_1|annotation" value="gff3/1.gff"/> | |
| 389 <param name="track_groups_2|data_tracks_1|match_part|match_part_select" value="false"/> | |
| 390 <param name="track_groups_2|data_tracks_1|jbcolor_scale|color_score|color_score_select" value="score"/> | |
| 391 <param name="track_groups_2|data_tracks_1|jbcolor_scale|color_score|score_scaling" value="linear"/> | |
| 392 <param name="track_groups_2|data_tracks_1|jbcolor_scale|color_score|score_scales|scale_select" value="automatic"/> | |
| 393 <param name="track_groups_2|data_tracks_1|jbcolor_scale|color_score|color_scheme|score_scheme" value="opacity"/> | |
| 394 <param name="track_groups_2|data_tracks_1|jbcolor_scale|color_score|color_scheme|color_select" value="manual"/> | |
| 395 <param name="track_groups_2|data_tracks_1|jbcolor_scale|color_score|color_scheme|style_color" value="#0000ff"/> | |
| 396 <param name="track_groups_2|data_tracks_2|data_format" value="gene_calls"/> | |
| 397 <param name="track_groups_2|data_tracks_2|annotation" value="gff3/1.gff"/> | |
| 398 <param name="track_groups_2|data_tracks_2|match_part|match_part_select" value="false"/> | |
| 399 <param name="track_groups_2|data_tracks_2|jbcolor_scale|color_score|color_score_select" value="score"/> | |
| 400 <param name="track_groups_2|data_tracks_2|jbcolor_scale|color_score|score_scaling" value="linear"/> | |
| 401 <param name="track_groups_2|data_tracks_2|jbcolor_scale|color_score|score_scales|scale_select" value="automatic"/> | |
| 402 <param name="track_groups_2|data_tracks_2|jbcolor_scale|color_score|score_scales|minimum" value="0"/> | |
| 403 <param name="track_groups_2|data_tracks_2|jbcolor_scale|color_score|score_scales|maximum" value="1000"/> | |
| 404 <param name="track_groups_2|data_tracks_2|jbcolor_scale|color_score|color_scheme|score_scheme" value="opacity"/> | |
| 405 <param name="track_groups_2|data_tracks_2|jbcolor_scale|color_score|color_scheme|color_select" value="automatic"/> | |
| 406 <param name="track_groups_2|data_tracks_3|data_format" value="gene_calls"/> | |
| 407 <param name="track_groups_2|data_tracks_3|annotation" value="gff3/1.gff"/> | |
| 408 <param name="track_groups_2|data_tracks_3|match_part|match_part_select" value="false"/> | |
| 409 <param name="track_groups_2|data_tracks_3|jbcolor_scale|color_score|color_score_select" value="score"/> | |
| 410 <param name="track_groups_2|data_tracks_3|jbcolor_scale|color_score|score_scaling" value="linear"/> | |
| 411 <param name="track_groups_2|data_tracks_3|jbcolor_scale|color_score|score_scales|scale_select" value="automatic"/> | |
| 412 <param name="track_groups_2|data_tracks_3|jbcolor_scale|color_score|score_scales|minimum" value="0"/> | |
| 413 <param name="track_groups_2|data_tracks_3|jbcolor_scale|color_score|score_scales|maximum" value="1000"/> | |
| 414 <param name="track_groups_2|data_tracks_3|jbcolor_scale|color_score|color_scheme|score_scheme" value="opacity"/> | |
| 415 <param name="track_groups_2|data_tracks_3|jbcolor_scale|color_score|color_scheme|color_select" value="manual"/> | |
| 416 <param name="track_groups_2|data_tracks_3|jbcolor_scale|color_score|color_scheme|style_color" value="#ff0000"/> | |
| 417 | |
| 418 <param name="track_groups_3|category" value="Realistic" /> | |
| 419 <param name="track_groups_3|data_tracks_0|data_format" value="gene_calls"/> | |
| 420 <param name="track_groups_3|data_tracks_0|annotation" value="gff3/interpro.gff"/> | |
| 421 <param name="track_groups_3|data_tracks_0|match_part|match_part_select" value="false"/> | |
| 422 <param name="track_groups_3|data_tracks_0|jbcolor_scale|color_score|color_score_select" value="none"/> | |
| 423 <param name="track_groups_3|data_tracks_0|jbcolor_scale|color|color_select" value="automatic"/> | |
| 424 <param name="track_groups_3|data_tracks_1|data_format" value="gene_calls"/> | |
| 425 <param name="track_groups_3|data_tracks_1|annotation" value="gff3/2.gff"/> | |
| 426 <param name="track_groups_3|data_tracks_1|match_part|match_part_select" value="true"/> | |
| 427 <param name="track_groups_3|data_tracks_1|match_part|name" value="cDNA_match"/> | |
| 428 <param name="track_groups_3|data_tracks_1|jbcolor_scale|color_score|color_score_select" value="none"/> | |
| 429 <param name="track_groups_3|data_tracks_1|jbcolor_scale|color|color_select" value="automatic"/> | |
| 430 | |
| 431 <param name="uglyTestingHack" value="enabled" /> | |
| 432 <output name="output" file="gff3/test.xml" /> | |
| 433 </test> | |
| 434 --> | |
| 435 </tests> | |
|
0
2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff
changeset
|
436 <help><![CDATA[ |
| 3 | 437 JBrowse-in-Galaxy |
| 438 ================= | |
| 439 | |
| 440 JBrowse-in-Galaxy offers a highly configurable, workflow-compatible | |
| 441 alternative to Trackster. | |
| 442 | |
| 443 The JBrowse-in-Galaxy (JiG) tool was written to help build complex | |
| 444 JBrowse installations straight from Galaxy, taking advantage of the | |
| 445 latest Galaxy features such as dataset collections, sections, and colour | |
| 446 pickers. It allows you to build up a JBrowse instance without worrying | |
| 447 about how to run the command line tools to format your data, and which | |
| 448 options need to be supplied and where. Additionally it comes with many | |
| 449 javascript functions to handle colouring of features which would be | |
| 450 nearly impossible to write without the assistance of this tool. | |
| 451 | |
| 452 The JBrowse-in-Galaxy tool is maintained by `Eric | |
| 453 Rasche <mailto:esr+jig@tamu.edu>`__, who you can contact if you | |
| 454 encounter missing features or bugs. | |
| 455 | |
| 456 Options | |
| 457 ------- | |
| 458 | |
| 459 The first option you encounter is the **Fasta Sequence(s)**. This option | |
| 460 now accepts multiple fasta files, allowing you to build JBrowse | |
| 461 instances that contain data for multiple genomes or chrosomomes | |
| 462 (generally known as "landmark features" in gff3 terminology.) Up to 30 | |
| 463 will be shown from the dropdown selector within JBrowse, this is a known | |
| 464 issue. | |
| 465 | |
| 466 **Standalone Instances** are a somewhat in-development feature. | |
| 467 Currently Galaxy copies the entire JBrowse directory in order to have a | |
| 468 complete, downloadable file that contains a ready-to-go JBrowse | |
| 469 instance. This is obviously an anti-feature because users don't want a | |
| 470 complete copy of JBrowse (6-20Mb) that's duplicated for every JBrowse | |
| 471 dataset in their history, and admins don't want useless copies of | |
| 472 JBrowse on disk. Unfortunately we have not come up with the perfect | |
| 473 solution just yet, but we're working on it! In the meantime, users have | |
| 474 been given the option to produce just the ``data/`` directory. For those | |
| 475 unfamiliar with JBrowse, the ``data/`` directory contains processed data | |
| 476 files, but no way to view them. This feature is additionally implemented | |
| 477 for upcoming `Apollo <https://github.com/gmod/apollo>`__ integration. | |
| 478 | |
| 479 **Genetic Code** is a new feature in v0.4 of JiG / v1.12.0 of JBrowse, | |
| 480 which allows users to specify a non standard genetic code, and have | |
| 481 JBrowse highlight the correct start and stop codons. If you would like | |
| 482 to use a coding table not provided by this list, please let | |
| 483 `me <mailto:esr+jig@tamu.edu>`__ know so that I may add support for | |
| 484 this. | |
| 485 | |
| 486 **Track Groups** represent a set of tracks in a single category. These | |
| 487 can be used to let your users understand relationships between large | |
| 488 groups of tracks. | |
| 489 | |
| 490 .. image:: sections.png | |
| 491 | |
| 492 Annotation Tracks | |
| 493 ----------------- | |
| 494 | |
| 495 Within Track Groups, you have one or more **Annotation Tracks**. Each | |
| 496 Annotation Track is a groups of datasets which have similar styling. | |
| 497 This allows you to rapidly build up JBrowse instances without having to | |
| 498 configure tracks individually. A massive improvement over previous | |
| 499 versions. For example, if you have five different GFF3 files from | |
| 500 various gene callers that you wish to display, you can take advantage of | |
| 501 this feature to style all of them similarly. | |
| 502 | |
| 503 There are a few different types of tracks supported, each with their own | |
| 504 set of options: | |
| 505 | |
| 506 GFF3/BED/GBK | |
| 507 ~~~~~~~~~~~~ | |
| 508 | |
| 509 These are your standard feature tracks. They usually highlight genes, | |
| 510 mRNAs and other features of interest along a genomic region. The | |
| 511 underlying tool and this help documentation focus primarily on GFF3 | |
| 512 data, and have not been tested extensively with other formats. Automatic | |
| 513 min/max detection will likely fail under BED and GBK datasets. | |
| 514 | |
| 515 The data may be of a subclass we call **match/match part** data. This | |
| 516 consists of top level ``match`` features, with a child ``match_part`` | |
| 517 feature, and is often used in displaying alignments. (See "Alignments" | |
| 518 section on the `GFF3 | |
| 519 specification <http://www.sequenceontology.org/gff3.shtml>`__ for more | |
| 520 information). If the data is match/match part, you will need to specify | |
| 521 the top level match feature name, as it can be one of a few different SO | |
| 522 terms, and JiG does not yet have the ability to understand SO terms. | |
| 523 | |
| 524 Next up is the **Styling Options** section, which lets you control a few | |
| 525 properties on how the track is styled. Most of these you will not need | |
| 526 to configure and can safely leave on defaults. Occasionally you will | |
| 527 want to change what information is shown in the end product. | |
| 528 | |
| 529 .. image:: styling.png | |
| 530 | |
| 531 In the above image you can see some black text, and some blue text. The | |
| 532 source of the black text is configured with the **style.label** option, | |
| 533 and the source of the blue text is configured with the | |
| 534 **style.description** option. | |
| 535 | |
| 536 Feature Score Scaling & Colouring Options | |
| 537 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | |
| 538 | |
| 539 First, you need to choose between ignoring the score attribute of GFF3 | |
| 540 files, or using it. If you choose to ignore it, all features will be | |
| 541 coloured with a solid colour. If you choose to use it, features will | |
| 542 have slightly different colours based on their scores. | |
| 543 | |
| 544 .. image:: opacity.png | |
| 545 | |
| 546 If you choose **Ignore score**, you may choose between automatically | |
| 547 choosing a colour, or manually specifying one. The automatically chosen | |
| 548 colours vary along a brewer palette and generally look quite nice with | |
| 549 no human intervention required. The manual colour choice is somewhat | |
| 550 self explanatory. Clicking on the small coloured square will bring up a | |
| 551 colour palette. | |
| 552 | |
| 553 If you choose **Base on score**, you're faced with a dizzying array of | |
| 554 options. First is the function to map the colour choices to colour | |
| 555 values. JiG comes with a few functions built in such as linear scaling, | |
| 556 logarithmic scaling, and blast scaling. | |
| 557 | |
| 558 The **linear scaling** method says "take these values, and they map | |
| 559 directly to a range of output values". **Logarithmic scaling** says | |
| 560 "please take the log of the score before mapping", and **Blast scaling** | |
| 561 is further specialised to handle blast data more nicely. These are | |
| 562 convenience functions to help transform the wide array of possible | |
| 563 values in the GFF3 score attribute to more meaningful numbers. If you | |
| 564 need more comprehensive score scaling, it is recommended that you | |
| 565 pre-process your GFF3 files somehow. | |
| 566 | |
| 567 Once you've selected a scaling method, you can choose to manually | |
| 568 specify the minimum and maximum expected values, or you can let JiG | |
| 569 determine them for you automatically. | |
| 570 | |
| 571 Finally, opacity is the only mapping we currently provide. Future | |
| 572 iterations will attempt to improve upon this and provide more colour | |
| 573 scales. The Opacity option maps the highest scoring features to full | |
| 574 opacity, and everything else to lower ones. | |
| 575 | |
| 576 BAM Pileups | |
| 577 ~~~~~~~~~~~ | |
| 578 | |
| 579 We support BAM files and can automatically generate SNP tracks based on | |
| 580 that bam data. | |
| 581 | |
| 582 .. image:: bam.png | |
| 583 | |
| 584 This is *strongly discouraged* for high coverage density datasets. | |
| 585 Unfortunately there are no other configuration options exposed for bam | |
| 586 files. If you find JBrowse options you wish to see exposed, please let | |
| 587 `me <mailto:esr+jig@tamu.edu>`__ know. | |
| 588 | |
| 589 BlastXML | |
| 590 ~~~~~~~~ | |
| 591 | |
| 592 .. image:: blast.png | |
| 593 | |
| 594 JiG now supports both blastn and blastp datasets. JiG internally uses a | |
| 595 blastXML to gapped GFF3 tool to convert your blastxml datasets into a | |
| 596 format amenable to visualization in JBrowse. This tool is also | |
| 597 available separately from the IUC on the toolshed. | |
| 598 | |
| 599 **Minimum Gap Size** reflects how long a gap must be before it becomes a | |
| 600 real gap in the processed gff3 file. In the picture above, various sizes | |
| 601 of gaps can be seen. If the minimum gap size was set much higher, say | |
| 602 100nt, many of the smaller gaps would disappear, and the features on | |
| 603 both sides would be merged into one, longer feature. This setting is | |
| 604 inversely proportional to runtime and output file size. *Do not set this | |
| 605 to a low value for large datasets*. By setting this number lower, you | |
| 606 will have extremely large outputs and extremely long runtimes. The | |
| 607 default was configured based off of the author's experience, but the | |
| 608 author only works on small viruses. It is *strongly* recommended that | |
| 609 you filter your blast results before display, e.g. picking out the top | |
| 610 10 hits or so. | |
| 611 | |
| 612 **Protein blast search** option merely informs underlying tools that | |
| 613 they should adjust feature locations by 3x. | |
| 614 | |
| 615 Styling Options | |
| 616 ^^^^^^^^^^^^^^^ | |
| 617 | |
| 618 Please see the styling options for GFF3 datasets, they are identical. | |
| 619 | |
| 620 Feature Score Scaling & Coloring Options | |
| 621 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | |
| 622 | |
| 623 Please see the score scaling and colouring options for GFF3 datasets, | |
| 624 they are identical. Remember to set your score scaling to "blast" method | |
| 625 if you do use it. | |
| 626 | |
| 627 Bigwig XY | |
| 628 ~~~~~~~~~ | |
| 629 | |
| 630 .. image:: bigwig.png | |
| 631 | |
| 632 **XYPlot** | |
| 633 | |
| 634 BigWig tracks can be displayed as a "density" plot which is continuous | |
| 635 line which varies in colour, or as an "XYplot." XYplots are preferable | |
| 636 for users to visually identify specific features in a bigwig track, | |
| 637 however density tracks are more visually compact. | |
| 638 | |
| 639 **Variance Band** is an option available to XYPlots, and can be seen in | |
| 640 the third and fourth tracks in the above picture. This overlays a mean | |
| 641 line, and 1 and 2 standard deviation areas. | |
| 642 | |
| 643 **Track Scaling** is different from colour scaling, instead it | |
| 644 configures how the track behaves inside of JBrowse. **Autoscaling | |
| 645 globally** means that JBrowse will determine the minimum and maximum for | |
| 646 the track, and fix the bounds of the viewport to that. E.g. if your | |
| 647 track ranges from 1-1000, and the region you're currently zoomed to only | |
| 648 goes from 0-50, then the viewport range will still show 1-1000. This is | |
| 649 good for global genomic context. However you may wish to consider | |
| 650 **autoscaling locally** instead. In the example of a region which varies | |
| 651 from 0-50, autoscaling locally would cause the individual track's | |
| 652 viewport to re-adjust and show just the 0-50 region. If neither of these | |
| 653 options are palatable, you may manually hardcode the minimum and | |
| 654 maximums for the track to scale to. | |
| 655 | |
| 656 Colour Options | |
| 657 ^^^^^^^^^^^^^^ | |
| 658 | |
| 659 BigWig tracks have two colours in JBrowse, a positive and a negative | |
| 660 colour. | |
| 661 | |
| 662 As always you may manually choose a colour, or let JiG choose for you. | |
| 663 | |
| 664 One of the more interesting options is the **Bicolor pivot**. This | |
| 665 option allows you to control the point at which JBrowse switches from | |
| 666 the positive colour to the negative. In the above graphic, you can see | |
| 667 this has been configured to "mean" for the first two (orange and blue) | |
| 668 tracks. | |
| 669 | |
| 670 VCFs/SNPs | |
| 671 ~~~~~~~~~ | |
| 672 | |
| 673 These tracks do not support any special configuration. | |
| 674 | |
| 675 Known Issues | |
| 676 ------------ | |
| 677 | |
| 678 - More than 30 landmark features cannot be listed in the manual | |
| 679 selector. | |
| 680 - Non GFF3 likely has issue with automatically determined min/max | |
| 681 scores. Manually specify minimum and maximum score attributes, or do | |
| 682 not use varied colours based on scores to avoid this issue. | |
| 683 | |
|
0
2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff
changeset
|
684 |
|
2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff
changeset
|
685 @ATTRIBUTION@ |
|
2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff
changeset
|
686 ]]></help> |
|
2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff
changeset
|
687 <citations> |
|
2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff
changeset
|
688 <citation type="doi">10.1101/gr.094607.109</citation> |
|
2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff
changeset
|
689 </citations> |
|
2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff
changeset
|
690 </tool> |
|
2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff
changeset
|
691 |