Mercurial > repos > fubar > jbrowse2
diff jbrowse2.xml @ 7:b04fd993b31e draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
| author | fubar |
|---|---|
| date | Wed, 17 Jan 2024 07:50:52 +0000 |
| parents | efc64d8f4b72 |
| children | f5ce31c2f47d |
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--- a/jbrowse2.xml Tue Jan 09 06:55:34 2024 +0000 +++ b/jbrowse2.xml Wed Jan 17 07:50:52 2024 +0000 @@ -130,145 +130,9 @@ #end if <options> - <style> - <display>${track.data_format.jbstyle.track_style.display}</display> - ## TODO change this to a for loop? - #if 'show_labels' in $track.data_format.jbstyle.track_style - <trackShowLabels type="boolean">${track.data_format.jbstyle.track_style.show_labels}</trackShowLabels> - #end if - #if 'show_descriptions' in $track.data_format.jbstyle.track_style - <trackShowDescriptions type="boolean">${track.data_format.jbstyle.track_style.show_descriptions}</trackShowDescriptions> - #end if - #if 'display_mode' in $track.data_format.jbstyle.track_style - <trackDisplayMode>${track.data_format.jbstyle.track_style.display_mode}</trackDisplayMode> - #end if - #if 'max_height' in $track.data_format.jbstyle.track_style - <trackMaxHeight type="integer">${track.data_format.jbstyle.track_style.max_height}</trackMaxHeight> - #end if - #if 'autoscale' in $track.data_format.jbstyle.track_style - <autoscale>${track.data_format.jbstyle.track_style.autoscale}</autoscale> - #end if - #if 'resolution' in $track.data_format.jbstyle.track_style - <resolution type="integer">${track.data_format.jbstyle.track_style.resolution}</resolution> - #end if - #if 'summaryScoreMode' in $track.data_format.jbstyle.track_style - <summaryScoreMode>${track.data_format.jbstyle.track_style.summaryScoreMode}</summaryScoreMode> - #end if - #if 'scaleType' in $track.data_format.jbstyle.track_style - <scaleType>${track.data_format.jbstyle.track_style.scaleType}</scaleType> - #end if - #if 'filled' in $track.data_format.jbstyle.track_style - <filled type="boolean">${track.data_format.jbstyle.track_style.filled}</filled> - #end if - #if 'displayCrossHatches' in $track.data_format.jbstyle.track_style - <displayCrossHatches type="boolean">${track.data_format.jbstyle.track_style.displayCrossHatches}</displayCrossHatches> - #end if - #if 'minScore' in $track.data_format.jbstyle.track_style and $track.data_format.jbstyle.track_style.minScore - <minScore type="integer">${track.data_format.jbstyle.track_style.minScore}</minScore> - #end if - #if 'maxScore' in $track.data_format.jbstyle.track_style and $track.data_format.jbstyle.track_style.maxScore - <maxScore type="integer">${track.data_format.jbstyle.track_style.maxScore}</maxScore> - #end if - ## TODO other coloring/etc options in each renderer (e.g https://github.com/GMOD/jbrowse-components/blob/main/plugins/svg/src/SvgFeatureRenderer/configSchema.ts) - </style> - <style_labels> - ## TODO other label options: https://github.com/GMOD/jbrowse-components/blob/main/plugins/svg/src/SvgFeatureRenderer/configSchema.ts - #if 'label' in $track.data_format.jbstyle.track_style - <name>${track.data_format.jbstyle.track_style.label}</name> - #end if - #if 'description' in $track.data_format.jbstyle.track_style - <description>${track.data_format.jbstyle.track_style.description}</description> - #end if - </style_labels> - #if str($track.data_format.data_format_select) == "gene_calls" or str($track.data_format.data_format_select) == "blast" or str($track.data_format.data_format_select) == "sparql": - <scaling> - #if str($track.data_format.jbcolor_scale.color_score.color_score_select) == "none": - <method>ignore</method> - <scheme> - #if str($track.data_format.jbcolor_scale.color_score.color.color_select) == "automatic": - <color>__auto__</color> - #else - <color>${track.data_format.jbcolor_scale.color_score.color.style_color}</color> - #end if - </scheme> - #else - <method>score</method> - <algo>${track.data_format.jbcolor_scale.color_score.score_scaling}</algo> - <scales> - <type>${track.data_format.jbcolor_scale.color_score.score_scales.scale_select}</type> + - #if str($track.data_format.jbcolor_scale.color_score.score_scales.scale_select) == "manual": - <min>${track.data_format.jbcolor_scale.color_score.score_scales.minimum}</min> - <max>${track.data_format.jbcolor_scale.color_score.score_scales.maximum}</max> - #end if - </scales> - <scheme> - <type>${track.data_format.jbcolor_scale.color_score.color_scheme.score_scheme}</type> - ## auto_color - #if str($track.data_format.jbcolor_scale.color_score.color_scheme.score_scheme) == "opacity": - #if str($track.data_format.jbcolor_scale.color_score.color_scheme.color.color_select) == "automatic": - <color>__auto__</color> - #else - <color>${track.data_format.jbcolor_scale.color_score.color_scheme.color.style_color}</color> - #end if - #end if - </scheme> - #end if - </scaling> - <menus> - #for $menu_item in $track.data_format.jbmenu.track_menu: - <menu> - <action>${menu_item.menu_action}</action> - #if str($menu_item.menu_label) != "": - <label>${menu_item.menu_label}</label> - #end if - #if str($menu_item.menu_title) != "": - <title>${menu_item.menu_title}</title> - #end if - #if str($menu_item.menu_url) != "": - <url>${menu_item.menu_url.replace("&", "&").replace("\"", """)}</url> - #end if - #if str($menu_item.menu_icon) != "": - <iconClass>${menu_item.menu_icon}</iconClass> - #end if - </menu> - #end for - </menus> - #end if - - #if str($track.data_format.data_format_select) == "wiggle": - <wiggle> - <type>${track.data_format.xyplot}</type> - <variance_band>${track.data_format.var_band}</variance_band> - #if str($track.data_format.scaling.scale_select) == "auto_local": - <autoscale>local</autoscale> - #else if str($track.data_format.scaling.scale_select) == "auto_global": - <autoscale>global</autoscale> - #else: - <min>${track.data_format.scaling.minimum}</min> - <max>${track.data_format.scaling.maximum}</max> - #end if - <scale>${track.data_format.scale_select2}</scale> - - ## Wiggle tracks need special color config - #if str($track.data_format.jbcolor.color.color_select) != "automatic": - <color_pos>${track.data_format.jbcolor.color.style_pos_color}</color_pos> - <color_neg>${track.data_format.jbcolor.color.style_neg_color}</color_neg> - #else: - <color_pos>__auto__</color_pos> - <color_neg>__auto__</color_neg> - #end if - - ## Bicolor pivot config - #if str($track.data_format.jbcolor.bicolor_pivot.bicolor_pivot_select) == "zero": - <bicolor_pivot>zero</bicolor_pivot> - #else if str($track.data_format.jbcolor.bicolor_pivot.bicolor_pivot_select) == "mean": - <bicolor_pivot>mean</bicolor_pivot> - #else: - <bicolor_pivot>${track.data_format.jbcolor.bicolor_pivot.pivot_point}</bicolor_pivot> - #end if - </wiggle> - #else if str($track.data_format.data_format_select) == "pileup": + #if str($track.data_format.data_format_select) == "pileup": <pileup> <bam_indices> #for $dataset in $track.data_format.annotation: @@ -291,14 +155,12 @@ #end if <protein>${track.data_format.is_protein}</protein> <min_gap>${track.data_format.min_gap}</min_gap> - <index>${track.data_format.index}</index> </blast> #else if str($track.data_format.data_format_select) == "gene_calls": <gff> #if $track.data_format.match_part.match_part_select == "true": <match>${track.data_format.match_part.name}</match> #end if - <index>${track.data_format.index}</index> </gff> #else if str($track.data_format.data_format_select) == "synteny": <synteny> @@ -360,17 +222,17 @@ value="Default" 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"/> <repeat name="data_tracks" title="Annotation Track"> - <conditional name="data_format" label="Track Options"> + <conditional name="data_format" label="Track Data Selection Options"> <param type="select" label="Track Type" name="data_format_select"> <option value="pileup">BAM Pileup track</option> - <option value="wiggle">BigWig XY track</option> - <option value="blast">Blast XML track - converted to GFF with actual gaps between hits</option> + <option value="wiggle">BigWig track</option> + <option value="blast">Blast XML track - converted to GFF</option> <option value="cram">CRAM</option> - <option value="gene_calls" selected="true">GFF/GFF3/BED feature tracks</option> - <option value="hic">HiC binary data. Existing cool format must be converted to binary hic - hic_matrix will NOT work.</option> + <option value="gene_calls" selected="true">GFF/GFF3/BED feature track</option> + <option value="hic">HiC (compressed binary) track. Existing cool format must be converted to binary hic - hic_matrix will NOT work.</option> <option value="sparql">SPARQL</option> - <option value="synteny">Synteny</option> - <option value="vcf">VCF SNP annotation track</option> + <option value="synteny">Synteny track with PAF data</option> + <option value="vcf">VCF SNP annotation</option> </param> <when value="blast"> <expand macro="input_conditional" label="BlastXML Track Data" format="blastxml" /> @@ -393,18 +255,6 @@ name="is_protein" truevalue="true" falsevalue="false" /> - - <param label="Index this track" name="index" type="boolean" checked="false" truevalue="true" falsevalue="false" /> - - <expand macro="track_styling_feature" - classname="feature" - label="description" - description="Hit_titles" - height="600px"/> - <expand macro="color_selection" - token_scaling_lin_select="false" - token_scaling_log_select="true" /> - <expand macro="track_menu" /> <expand macro="track_visibility" /> </when> <when value="vcf"> @@ -429,68 +279,20 @@ </when> <when value="false" /> </conditional> - - <param label="Index this track" name="index" type="boolean" checked="false" truevalue="true" falsevalue="false" /> - - <expand macro="track_styling_feature" - classname="feature" - label="product,name,id" - description="note,description" - height="10px"/> - <expand macro="color_selection" /> - <expand macro="track_menu" /> <expand macro="track_visibility" /> </when> <when value="pileup"> <expand macro="input_conditional" label="BAM Track Data" format="bam" /> - <expand macro="track_styling_xam"/> <expand macro="track_visibility" /> </when> <when value="cram"> <expand macro="input_conditional" label="CRAM Track Data" format="cram" /> - <expand macro="track_styling_xam"/> <expand macro="track_visibility" /> </when> <when value="wiggle"> <expand macro="input_conditional" label="BigWig Track Data" format="bigwig" /> - - <param label="Use XYPlot" - help="instead of continuous colored band" - type="boolean" - name="xyplot" - truevalue="JBrowse/View/Track/Wiggle/XYPlot" - falsevalue="JBrowse/View/Track/Wiggle/Density" /> - <param label="Show variance band" - help="Only for XYPlots" - type="boolean" - name="var_band" - truevalue="true" - falsevalue="false" /> + <expand macro="track_visibility" /> - <conditional name="scaling" label="Scaling"> - <param type="select" label="Track Scaling" name="scale_select"> - <option value="auto_local" selected="true">Autoscale (local)</option> - <option value="auto_global">Autoscale (global)</option> - <option value="fixed">Specify Min/Max</option> - </param> - <when value="auto_local"></when> - <when value="auto_global"></when> - <when value="fixed"> - <param label="Track minimum" name="minimum" - type="integer" value="0" /> - <param label="Track maximum" name="maximum" - type="integer" value="100" /> - </when> - </conditional> - <param type="select" label="Visual Scaling" name="scale_select2"> - <option value="linear" selected="true">Linear</option> - <option value="log">Logarithmic (Dynamically Calculated)</option> - </param> - - <expand macro="color_selection_minmax" /> - - <expand macro="track_styling_bigwig"/> - <expand macro="track_visibility" /> </when> <when value="synteny"> @@ -498,7 +300,7 @@ format="fasta" name="synteny_genome" type="data" /> - <!-- TODO add .out (MashMap) .chain (UCSC), .delta (mummer) and .anchors (mcscan) inputs --> + <expand macro="input_conditional" label="Synteny data" format="paf" /> <expand macro="track_visibility" /> </when> @@ -593,7 +395,6 @@ <has_text text="trackFile path="></has_text> <has_text text="file_ext="bigwig""></has_text> <has_text text="format="wiggle""></has_text> - <has_text text="LinearWiggleDisplay"></has_text> </assert_contents> </output> </test> @@ -908,7 +709,6 @@ <conditional name="data_format"> <param name="data_format_select" value="gene_calls"/> <param name="annotation" value="gff3/1.gff"/> - <param name="index" value="true"/> <conditional name="match_part"> <param name="match_part_select" value="false"/> </conditional> @@ -928,13 +728,10 @@ <output name="output"> <assert_contents> <has_text text="With menu or index"/> - <has_text text="Some menu item"/> - <has_text text="Frame title"/> - <has_text text="dijitIconNewTask"/> + <has_text text="gene_calls"/> </assert_contents> </output> </test> - <!-- TODO add a synteny test --> <!-- TODO add a bam and a cram test --> <!-- TODO add an hic test --> @@ -955,16 +752,22 @@ Use and local viewing ===================== + A JBrowse2 history item can be opened by viewing it (the "eye" icon). -They can also be downloaded as archives ("floppy disk" icon) to share and for local viewing. -One extra step is required before they can be viewed. A local python web server must be started using a script included in each archive. -Unzip the archive (*unzip [filename].zip*) and change to the first level directory. It contains a file named "webserver.py" + +The same browser data and setup can also be downloaded as a compressed zip archive by clicking the download ("floppy disk") icon in the history. +This can be shared and viewed without Galaxy. -Assuming you have python3 installed, running: +A replacement application to serve the browser is required without Galaxy. A local python web server can be started using a script included in each archive, +assuming that Python3 is already working on your desktop - if not you will have to install it first. Unzip the archive (*unzip [filename].zip*) and change +directory to the first level in that zip archive. It contains a file named *jb2_webserver.py* -*python3 webserver.py* +With python3 installed, -will serve the unarchived JBrowse2 configuration, so it can be browsed by pointing a web browser to localhost:8080 +*python3 jb2_webserver.py* + +will serve the unarchived JBrowse2 configuration from the same directory as the python script automatically. If a new browser window does not open, +but the script appears to be running, try pointing your web browser to the default of *localhost:8080* Overview -------- @@ -973,13 +776,9 @@ JavaScript and HTML5. The JBrowse-in-Galaxy (JiG) tool was written to help build complex -JBrowse installations straight from Galaxy, taking advantage of the -latest Galaxy features such as dataset collections, sections, and colour -pickers. It allows you to build up a JBrowse instance without worrying +JBrowse installations straight from Galaxy. It allows you to build up a JBrowse instance without worrying about how to run the command line tools to format your data, and which -options need to be supplied and where. Additionally it comes with many -javascript functions to handle colouring of features which would be -nearly impossible to write without the assistance of this tool. +options need to be supplied and where. The JBrowse-in-Galaxy tool is maintained by `the Galaxy IUC <https://github.com/galaxyproject/tools-iuc/issues>`__, who you can help you @@ -988,8 +787,8 @@ Options ------- -The first option you encounter is the **Fasta Sequence(s)**. This option -now accepts multiple fasta files, allowing you to build JBrowse +The first option you encounter is the **Reference sequence(s)** to use. This option +now accepts multiple fasta files, allowing you to build JBrowse2 instances that contain data for multiple genomes or chrosomomes (generally known as "landmark features" in gff3 terminology.) @@ -1046,11 +845,6 @@ they should adjust feature locations by 3x. -VCFs/SNPs -~~~~~~~~~ - -These tracks do not support any special configuration. - @ATTRIBUTION@ ]]></help> <expand macro="citations"/>