Mercurial > repos > fubar > jbrowse2
diff jbrowse2.xml @ 60:81d535970196 draft
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 403a35e1245fa5e62f4be6116a725b9e4d9c353a
| author | fubar |
|---|---|
| date | Mon, 25 Mar 2024 02:10:05 +0000 |
| parents | f807e219cec3 |
| children | ab0d6782a95f |
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--- a/jbrowse2.xml Fri Mar 22 22:04:08 2024 +0000 +++ b/jbrowse2.xml Mon Mar 25 02:10:05 2024 +0000 @@ -11,12 +11,8 @@ <version_command>python '${__tool_directory__}/jbrowse2.py' --version</version_command> <command detect_errors="aggressive"><![CDATA[ mkdir -p '$output.files_path' && -## Copy the XML file into the directory, mostly for debugging -## but nice if users want to reproduce locally cp '$trackxml' '$output.files_path/galaxy.xml' && - export JBROWSE2_PATH=\$(dirname \$(which jbrowse))/../opt/jbrowse2 && - #if $jbgen.ucol.formcoll=="collect": python '$__tool_directory__/autogenJB2.py' #for $key in $autoCollection.keys(): @@ -139,17 +135,15 @@ #for $tg in $track_groups: #for $track in $tg.data_tracks: #if $track.data_format.useuri.insource == "uri": - <track cat="${tg.category}" format="paf" visibility="${track.data_format.track_visibility}"> + <track cat="${tg.category}" format="${track.data_format.data_format_select}" visibility="${track.data_format.track_visibility}"> <files> - <trackFile path="${ $track.data_format.useuri.insource.annouri}" ext="paf" - label="${track.data_format.useuri.insource.annoname}" useuri="yes"> + <trackFile path="${track.data_format.useuri.annouri}" ext="${track.data_format.data_format_select}" + label="${track.data_format.useuri.annoname}" useuri="yes"> <metadata> - <dataset id = "${track.data_format.useuri.insource.annouri}" /> + <dataset id = "${track.data_format.useuri.annouri}" /> </metadata> </trackFile> </files> - <options/> - </track> #else if $track.data_format.useuri.insource == "history": #if $track.data_format.useuri.annotation: <track cat="${tg.category}" format="${track.data_format.data_format_select}" visibility="${track.data_format.track_visibility}"> @@ -157,7 +151,6 @@ #for $dataset in $track.data_format.useuri.annotation: <trackFile path="${dataset}" ext="${dataset.ext}" label="${dataset.name}" useuri="no"> <metadata> - <dataset id="${__app__.security.encode_id($dataset.id)}" hid="${dataset.hid}" size="${dataset.get_size(nice_size=True)}" edam_format="${dataset.datatype.edam_format}" @@ -193,23 +186,27 @@ </trackFile> #end for </files> - - <options> - <style> - #if str($track.data_format.data_format_select) in ["gff", "bed", "vcf", "maf", "blastxml"]: - <type>${track.data_format.jbstyle.track_style.display}</type> - #if str($track.data_format.jbstyle.track_style.display) in ["LinearBasicDisplay", "LinearVariantDisplay"]: - <trackShowLabels>${track.data_format.jbstyle.track_style.show_labels}</trackShowLabels> - <trackShowDescriptions>${track.data_format.jbstyle.track_style.show_descriptions}</trackShowDescriptions> - #end if + #end if + #end if + <options> + <style> + #if str($track.data_format.data_format_select) in ["gff", "bed", "vcf", "maf", "blastxml"]: + <type>${track.data_format.jbstyle.track_style.display}</type> + #if str($track.data_format.jbstyle.track_style.display) in ["LinearBasicDisplay", "LinearVariantDisplay"]: + <trackShowLabels>${track.data_format.jbstyle.track_style.show_labels}</trackShowLabels> + <trackShowDescriptions>${track.data_format.jbstyle.track_style.show_descriptions}</trackShowDescriptions> #end if - #if str($track.data_format.data_format_select) in ["bam", "cram"]: - <type>LinearAlignmentsDisplay</type> - #end if - #if str($track.data_format.data_format_select) in ["paf"]: - <type>LinearBasicDisplay</type> - #end if - </style> + #end if + #if str($track.data_format.data_format_select) in ["bam", "cram"]: + <type>LinearAlignmentsDisplay</type> + #end if + #if str($track.data_format.data_format_select) in ["paf"]: + <type>LinearBasicDisplay</type> + #end if + #if str($track.data_format.data_format_select) in ["hic"]: + <type>LinearHicDisplay</type> + #end if + </style> #if str($track.data_format.data_format_select) == "bam": <bam> #for $dataset in $track.data_format.useuri.annotation: @@ -268,8 +265,6 @@ #end if </options> </track> - #end if - #end if #end for #end for </tracks>