Mercurial > repos > iuc > jbrowse
comparison jbrowse.xml @ 33:0ae74c70b267 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
author | iuc |
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date | Fri, 30 Aug 2019 03:36:39 -0400 |
parents | 2bb2e07a7a21 |
children | 9de82b4963e6 |
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32:6b774e9d6387 | 33:0ae74c70b267 |
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399 value="Default" | 399 value="Default" |
400 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." optional="False"/> | 400 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." optional="False"/> |
401 <repeat name="data_tracks" title="Annotation Track"> | 401 <repeat name="data_tracks" title="Annotation Track"> |
402 <conditional name="data_format" label="Track Options"> | 402 <conditional name="data_format" label="Track Options"> |
403 <param type="select" label="Track Type" name="data_format_select"> | 403 <param type="select" label="Track Type" name="data_format_select"> |
404 <option value="gene_calls">GFF/GFF3/BED/GBK Features</option> | 404 <option value="gene_calls">GFF/GFF3/BED Features</option> |
405 <option value="pileup">BAM Pileups</option> | 405 <option value="pileup">BAM Pileups</option> |
406 <option value="blast">Blast XML</option> | 406 <option value="blast">Blast XML</option> |
407 <option value="wiggle">BigWig XY</option> | 407 <option value="wiggle">BigWig XY</option> |
408 <option value="vcf">VCF SNPs</option> | 408 <option value="vcf">VCF SNPs</option> |
409 <option value="rest">REST Endpoint</option> | 409 <option value="rest">REST Endpoint</option> |
1165 this feature to style all of them similarly. | 1165 this feature to style all of them similarly. |
1166 | 1166 |
1167 There are a few different types of tracks supported, each with their own | 1167 There are a few different types of tracks supported, each with their own |
1168 set of options: | 1168 set of options: |
1169 | 1169 |
1170 GFF3/BED/GBK | 1170 GFF3/BED |
1171 ~~~~~~~~~~~~ | 1171 ~~~~~~~~ |
1172 | 1172 |
1173 These are your standard feature tracks. They usually highlight genes, | 1173 These are your standard feature tracks. They usually highlight genes, |
1174 mRNAs and other features of interest along a genomic region. The | 1174 mRNAs and other features of interest along a genomic region. The |
1175 underlying tool and this help documentation focus primarily on GFF3 | 1175 underlying tool and this help documentation focus primarily on GFF3 |
1176 data, and have not been tested extensively with other formats. Automatic | 1176 data, and have not been tested extensively with other formats. Automatic |
1177 min/max detection will likely fail under BED and GBK datasets. | 1177 min/max detection will fail under BED datasets. |
1178 | 1178 |
1179 The data may be of a subclass we call **match/match part** data. This | 1179 The data may be of a subclass we call **match/match part** data. This |
1180 consists of top level ``match`` features, with a child ``match_part`` | 1180 consists of top level ``match`` features, with a child ``match_part`` |
1181 feature, and is often used in displaying alignments. (See "Alignments" | 1181 feature, and is often used in displaying alignments. (See "Alignments" |
1182 section on the `GFF3 | 1182 section on the `GFF3 |