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comparison jbrowse2.xml @ 112:56f9a6e0fe80 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 566509061b742b73c8dd1a1db6813fbf6a7a3792
author bgruening
date Thu, 04 Jul 2024 08:40:21 +0000
parents 5d1259b88c27
children 878c27dfea9d
comparison
equal deleted inserted replaced
111:0a532764dcfa 112:56f9a6e0fe80
6 <expand macro="edamInc"/> 6 <expand macro="edamInc"/>
7 <xrefs> 7 <xrefs>
8 <xref type="bio.tools">jbrowse2</xref> 8 <xref type="bio.tools">jbrowse2</xref>
9 </xrefs> 9 </xrefs>
10 <expand macro="requirements"/> 10 <expand macro="requirements"/>
11 <expand macro="creators"/>
12 <required_files> 11 <required_files>
13 <include path="autogenJB2.py"/> 12 <include path="autogenJB2.py"/>
14 <include path="blastxml_to_gapped_gff3.py"/> 13 <include path="blastxml_to_gapped_gff3.py"/>
15 <include path="convertMAF.sh"/> 14 <include path="convertMAF.sh"/>
16 <include path="gff3_rebase.py"/> 15 <include path="gff3_rebase.py"/>
348 </when> 347 </when>
349 <when value="uri"> 348 <when value="uri">
350 <param name="uri" type="text" label="URI pointing to tabix compressed fasta - must always be on-line" 349 <param name="uri" type="text" label="URI pointing to tabix compressed fasta - must always be on-line"
351 help="Warning: Requires an internet connection to view. If this URI is not available for any reason, the track will show an error. Saves disk storage"> 350 help="Warning: Requires an internet connection to view. If this URI is not available for any reason, the track will show an error. Saves disk storage">
352 </param> 351 </param>
353 <param name="refname" type="text" label="Reference dbkey for tracks with this genome, such as hg38 or SacCer4"> 352 <param name="refname" type="text" label="Reference dbkey for tracks with this genome, such as hg38 or SacCer4"/>
354 </param>
355 </when> 353 </when>
356 </conditional> 354 </conditional>
357 <repeat name="track_groups" title="Track Group"> 355 <repeat name="track_groups" title="Track Group">
358 <param name="category" type="text" value="Default" optional="False" label="Track Category" help="Organise your tracks into Categories for a nicer end-user experience. You can use #date# and it will be replaced with the current date in 'yyyy-mm-dd' format, which is very useful for repeatedly updating a JBrowse instance when member databases / underlying tool versions are updated."/> 356 <param name="category" type="text" value="Default" optional="False" label="Track Category" help="Organise your tracks into Categories for a nicer end-user experience. You can use #date# and it will be replaced with the current date in 'yyyy-mm-dd' format, which is very useful for repeatedly updating a JBrowse instance when member databases / underlying tool versions are updated."/>
359 <repeat name="data_tracks" title="Annotation Track"> 357 <repeat name="data_tracks" title="Annotation Track">
1150 Use and local viewing 1148 Use and local viewing
1151 ===================== 1149 =====================
1152 1150
1153 Browser tracks need a coordinate system, based on the reference genome, so that must be chosen before adding groups of tracks. 1151 Browser tracks need a coordinate system, based on the reference genome, so that must be chosen before adding groups of tracks.
1154 1152
1155 At present, 10 Galaxy datatypes that can be turned into a track for display - in all cases, the selected reference genome must have been 1153 Many Galaxy datatypes can be turned into a track for display - in all cases, the selected reference genome must have been
1156 used to generate the data: 1154 used to generate the data:
1157 1155
1158 bam 1156 bam
1159 bed 1157 bed
1160 bigwig 1158 bigwig
1195 **Track Groups** represent a set of tracks in a single category. 1193 **Track Groups** represent a set of tracks in a single category.
1196 1194
1197 1195
1198 Annotation Tracks 1196 Annotation Tracks
1199 ----------------- 1197 -----------------
1198
1199
1200 BED
1201 ~~~
1202
1203 Bed feature annotation usually requires clicking on the feature.
1204
1205 Bed files created by the *Bigwig extremes to bed features* tool have the score in column 5
1206 set to *1* for regions above the quantile and *-1* for regions below. It is possible to set an advanced option for each bed track, to use the bed score in column 5
1207 for the feature colour, giving red and blue using a JBrowse2 plugin, so they are easy to distinguish in a combined track.
1208
1200 1209
1201 MAF 1210 MAF
1202 ~~~ 1211 ~~~
1203 1212
1204 For history references, the name of the reference genome dataset in your history is very important for MAF tracks, 1213 For history references, the name of the reference genome dataset in your history is very important for MAF tracks,