Mercurial > repos > fubar > jbrowse2
changeset 27:4ff1ed2065cc draft
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit d733fb18a02929c9e9959ad30bd0f1368118e924-dirty
| author | fubar |
|---|---|
| date | Wed, 07 Feb 2024 22:37:10 +0000 |
| parents | e578621acb13 |
| children | 9a5c409f33f4 |
| files | jbrowse2.py jbrowse2.xml macros.xml |
| diffstat | 3 files changed, 8 insertions(+), 13 deletions(-) [+] |
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--- a/jbrowse2.py Sat Feb 03 22:22:07 2024 +0000 +++ b/jbrowse2.py Wed Feb 07 22:37:10 2024 +0000 @@ -1224,7 +1224,7 @@ self.add_paf( dataset_path, outputTrackConfig, - track["conf"]["options"]["synteny"], + track["conf"]["options"]["paf"], ) else: log.warn("Do not know how to handle %s", dataset_ext) @@ -1279,6 +1279,7 @@ if data.get("defaultLocation", ""): ddl = data["defaultLocation"] loc_match = re.search(r"^([^:]+):([\d,]*)\.*([\d,]*)$", ddl) + # allow commas like 100,000 but ignore as integer if loc_match: refName = loc_match.group(1) drdict["refName"] = refName @@ -1291,12 +1292,6 @@ "@@@ regexp could not match contig:start..end in the supplied location %s - please fix" % ddl ) - elif self.genome_firstcontig is not None: - drdict["refName"] = self.genome_firstcontig - logging.info( - "@@@ no defaultlocation found for default session - using %s as first contig found" - % self.genome_firstcontig - ) if drdict.get("refName", None): # TODO displayedRegions is not just zooming to the region, it hides the rest of the chromosome
--- a/jbrowse2.xml Sat Feb 03 22:22:07 2024 +0000 +++ b/jbrowse2.xml Wed Feb 07 22:37:10 2024 +0000 @@ -165,11 +165,11 @@ <match>${track.data_format.match_part.name}</match> #end if </gff> - #else if str($track.data_format.data_format_select) == "synteny": - <synteny> + #else if str($track.data_format.data_format_select) == "paf": + <paf> <genome>${track.data_format.synteny_genome}</genome> <genome_label>${track.data_format.synteny_genome.name}</genome_label> - </synteny> + </paf> #else if str($track.data_format.data_format_select) == "hic": <hic> </hic> @@ -283,7 +283,7 @@ name="name" type="text" value="match" - 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. You can leave empty to try autodetection (only works with CanvasFeatures track type)." + 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)." optional="True"/> </when> <when value="false" /> @@ -316,7 +316,7 @@ </when> <when value="hic"> - <expand macro="input_conditional" label="HiC data" format="hic" /> + <expand macro="input_conditional" label="Binary Juicebox HiC data" format="hic,juicebox_hic" /> <expand macro="track_visibility" /> </when> <when value="cool">
--- a/macros.xml Sat Feb 03 22:22:07 2024 +0000 +++ b/macros.xml Wed Feb 07 22:37:10 2024 +0000 @@ -29,7 +29,7 @@ <token name="@ATTRIBUTION@"><![CDATA[ **Attribution** This Galaxy tool relies on the JBrowse2, maintained by the GMOD Community. The Galaxy wrapper is maintained by Ross Lazarus -until the IUC have their own. +until the IUC complete their own. ]]> </token> <xml name="genome_selector"