Mercurial > repos > fubar > jbrowse2
diff jbrowse2.xml @ 62:ab0d6782a95f draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
| author | fubar |
|---|---|
| date | Thu, 28 Mar 2024 04:51:06 +0000 |
| parents | 81d535970196 |
| children | ac00dcfb5d1d |
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--- a/jbrowse2.xml Tue Mar 26 00:52:34 2024 +0000 +++ b/jbrowse2.xml Thu Mar 28 04:51:06 2024 +0000 @@ -1,4 +1,4 @@ - <tool id="jbrowse2" name="jbrowse2" version="@TOOL_VERSION@+@WRAPPER_VERSION@_7" profile="22.05"> + <tool id="jbrowse2auto" name="JBrowse2auto" version="@TOOL_VERSION@+@WRAPPER_VERSION@_8" profile="22.05"> <description>genome browser</description> <macros> <import>macros.xml</import> @@ -62,62 +62,8 @@ ]]></command> <configfiles> <configfile name="trackxml"><![CDATA[<?xml version="1.0"?> -#if $jbgen.ucol.formcoll=="form": <root> <metadata> - <genomes> - #if str($reference_genome.genome_type_select) == "uri": - <genome path="${reference_genome.uri}" label="${reference_genome.refname}" useuri="yes"> - <metadata> - <dataset - dname = "${reference_genome.refname}" /> - </metadata> - </genome> - #else if str($reference_genome.genome_type_select) == "indexed": - <genome path="${reference_genome.genome.fields.path}" label="${reference_genome.genome.fields.name}" useuri="no"> - <metadata> - <dataset - dname = "${reference_genome.genome.fields.name}" /> - </metadata> - </genome> - #else - <genome path="$reference_genome.genome" label="${reference_genome.genome.name}" useuri="no"> - <metadata> - <dataset id="${__app__.security.encode_id($reference_genome.genome.id)}" hid="${reference_genome.genome.hid}" - size="${reference_genome.genome.get_size(nice_size=True)}" - edam_format="${reference_genome.genome.datatype.edam_format}" - file_ext="${reference_genome.genome.ext}" - dname = "${reference_genome.genome.name}" /> - <history id="${__app__.security.encode_id($reference_genome.genome.history_id)}" - #if $reference_genome.genome.history.user: - user_email="${reference_genome.genome.history.user.email}" - user_id="${reference_genome.genome.history.user_id}" - display_name="${reference_genome.genome.history.get_display_name()}"/> - #else - user_email="anonymous" - user_id="-1" - display_name="Unnamed History"/> - #end if - <metadata - #for (key, value) in $reference_genome.genome.get_metadata().items(): - #if "_types" not in $key: - #if isinstance($value, list): - #set value_str = "[%s]" % ','.join([str(val) for val in value]) - ${key}="$value_str" - #else - ${key}="${value}" - #end if - #end if - #end for - /> - <tool - tool_id="${reference_genome.genome.creating_job.tool_id}" - tool_version="${reference_genome.genome.creating_job.tool_version}" - /> - </metadata> - </genome> - #end if - </genomes> <general> <defaultLocation>${jbgen.defaultLocation}</defaultLocation> <zipOut>${jbgen.zipOut}</zipOut> @@ -131,8 +77,73 @@ </general> <galaxyUrl>${__app__.config.galaxy_infrastructure_url}</galaxyUrl> </metadata> +#if $jbgen.ucol.formcoll=="form": + #for $assembly in $assemblies: + <assembly> + <metadata> + <genomes> + #if str($assembly.reference_genome.genome_type_select) == "uri": + <genome path="${assembly.reference_genome.uri}" label="${assembly.reference_genome.refname}" useuri="yes"> + <metadata> + <dataset + dname = "${assembly.reference_genome.refname}" /> + </metadata> + </genome> + #else if str($assembly.reference_genome.genome_type_select) == "indexed": + <genome path="${assembly.reference_genome.genome.fields.path}" label="${assembly.reference_genome.genome.fields.name}" useuri="no"> + <metadata> + <dataset + dname = "${assembly.reference_genome.genome.fields.name}" /> + </metadata> + </genome> + #else + <genome path="$assembly.reference_genome.genome" label="${assembly.reference_genome.genome.name}" useuri="no"> + <metadata> + #if $uglyTestingHack != "enabled": + <dataset id="${__app__.security.encode_id($assembly.reference_genome.genome.id)}" + hid="${assembly.reference_genome.genome.hid}" + size="${assembly.reference_genome.genome.get_size(nice_size=True)}" + edam_format="${assembly.reference_genome.genome.datatype.edam_format}" + file_ext="${assembly.reference_genome.genome.ext}" + dname = "${assembly.reference_genome.genome.name}" + /> + <history + #if $assembly.reference_genome.genome.history.user: + user_email="${assembly.reference_genome.genome.history.user.email}" + user_id="${assembly.reference_genome.genome.history.user_id}" + display_name="${assembly.reference_genome.genome.history.get_display_name()}"/> + #else + user_email="anonymous" + user_id="-1" + display_name="Unnamed History" + #end if + id="${__app__.security.encode_id($assembly.reference_genome.genome.history_id)}" + /> + <metadata + #for (key, value) in $assembly.reference_genome.genome.get_metadata().items(): + #if "_types" not in $key: + #if isinstance($value, list): + #set value_str = "[%s]" % ','.join([str(val) for val in value]) + ${key}="$value_str" + #else + ${key}="${value}" + #end if + #end if + #end for + /> + <tool + tool_id="${assembly.reference_genome.genome.creating_job.tool_id}" + tool_version="${assembly.reference_genome.genome.creating_job.tool_version}" + /> + #end if + </metadata> + </genome> + #end if + </genomes> + + </metadata> <tracks> - #for $tg in $track_groups: + #for $tg in $assembly.track_groups: #for $track in $tg.data_tracks: #if $track.data_format.useuri.insource == "uri": <track cat="${tg.category}" format="${track.data_format.data_format_select}" visibility="${track.data_format.track_visibility}"> @@ -151,6 +162,7 @@ #for $dataset in $track.data_format.useuri.annotation: <trackFile path="${dataset}" ext="${dataset.ext}" label="${dataset.name}" useuri="no"> <metadata> + #if $uglyTestingHack != "enabled": <dataset id="${__app__.security.encode_id($dataset.id)}" hid="${dataset.hid}" size="${dataset.get_size(nice_size=True)}" edam_format="${dataset.datatype.edam_format}" @@ -182,30 +194,32 @@ tool_id="${dataset.creating_job.tool_id}" tool_version="${dataset.creating_job.tool_version}" /> + #end if </metadata> </trackFile> #end for </files> #end if #end if + #if $uglyTestingHack != "enabled": <options> <style> - #if str($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> + #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>${track.data_format.jbstyle.track_style.show_descriptions}</trackShowDescriptions> + #end if #end if - #end if - #if str($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 + #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> @@ -264,26 +278,30 @@ </sparql> #end if </options> + #end if </track> #end for #end for </tracks> + </assembly> + #end for +#end if </root> -#end if ]]></configfile> </configfiles> - <inputs> + <repeat name="assemblies" min="1" title="Genome Assembly" help="When too many genomes are never enough"> <conditional name="reference_genome"> - <param help="Built-in references" label="Reference genome to display" name="genome_type_select" type="select"> + <param help="Select a built in, history or remote tabix URI for the reference track" + label="Reference genome source" name="genome_type_select" type="select"> <option selected="True" value="indexed">Use a built-in genome</option> <option value="history">Use a genome from history</option> - <option value="uri">URI for a reference in tabix .gz format </option> + <option value="uri">URI for a reference as tabix with predictable index file URI</option> </param> <when value="indexed"> <param - help="If your genome of interest is not listed, contact the Galaxy team" - label="Select a reference genome" + help="If not listed, add a custom genome, use a history genome or a remote URI tabix genome" + label="Select a built in reference genome or custom genome" name="genome" type="select" optional="true"> @@ -310,7 +328,7 @@ type="text"> </param> <param - label="Reference key - dbkey equivalent" + label="Reference dbkey for tracks with this genome, such as hg38 or SacCer4" name="refname" type="text"> </param> @@ -428,9 +446,8 @@ </conditional> </repeat> </repeat> - + </repeat> <expand macro="general_options" /> - <param type="hidden" name="uglyTestingHack" value="" /> </inputs> <outputs> @@ -442,115 +459,144 @@ </outputs> <tests> <test> - <param name="reference_genome|genome_type_select" value="history"/> - <param name="reference_genome|genome" value="merlin.fa"/> - <repeat name="track_groups"> - <param name="category" value="Default" /> - <repeat name="data_tracks"> - <conditional name="data_format"> - <param name="data_format_select" value="bigwig"/> - <conditional name="useuri"> - <param name="annotation" value="bw/merlin.bw"/> - <param name="insource" value="history"/> + <repeat name="assemblies"> + <conditional name="reference_genome"> + <param name="genome_type_select" value="history"/> + <param name="genome" value="merlin.fa"/> + <param name="genome.ext" value="fasta"/> + <param name="genome.name" value="Merlin"/> + </conditional> + <repeat name="track_groups"> + <param name="category" value="Default" /> + <repeat name="data_tracks"> + <conditional name="data_format"> + <param name="data_format_select" value="bigwig"/> + <conditional name="useuri"> + <param name="annotation" value="bw/merlin.bw"/> + <param name="insource" value="history"/> + </conditional> </conditional> - </conditional> - </repeat> + </repeat> + </repeat> </repeat> <param name="uglyTestingHack" value="enabled" /> <output name="output"> <assert_contents> <has_text text="genome path="></has_text> - <has_text text="dataset id="></has_text> - <has_text text="history id="></has_text> + <has_text text="label="></has_text> + <has_text text="format="></has_text> <has_text text="metadata"></has_text> - <has_text text="tool_id"></has_text> + <has_text text="useuri="></has_text> <has_text text="trackFile path="></has_text> - <has_text text="file_ext="bigwig""></has_text> + <has_text text="ext="bigwig""></has_text> <has_text text="format="bigwig""></has_text> </assert_contents> </output> </test> <test> - <param name="reference_genome|genome_type_select" value="history"/> - <param name="reference_genome|genome" value="merlin.fa"/> - <repeat name="track_groups"> - <param name="category" value="Default" /> - <repeat name="data_tracks"> - <conditional name="data_format"> - <param name="data_format_select" value="vcf"/> - <conditional name="useuri"> - <param name="insource" value="history"/> - <param name="annotation" value="vcf/merlin.vcf"/> + <repeat name="assemblies"> + <conditional name="reference_genome"> + <param name="genome_type_select" value="history"/> + <param name="genome" value="merlin.fa"/> + <param name="genome.ext" value="fasta"/> + <param name="genome.name" value="Merlin"/> + </conditional> + <repeat name="track_groups"> + <param name="category" value="Default" /> + <repeat name="data_tracks"> + <conditional name="data_format"> + <param name="data_format_select" value="vcf"/> + <conditional name="useuri"> + <param name="insource" value="history"/> + <param name="annotation" value="vcf/merlin.vcf"/> + </conditional> </conditional> - </conditional> + </repeat> </repeat> </repeat> <param name="uglyTestingHack" value="enabled" /> <output name="output"> <assert_contents> <has_text text="genome path="></has_text> - <has_text text="dataset id="></has_text> - <has_text text="history id="></has_text> + <has_text text="label="></has_text> + <has_text text="format="></has_text> <has_text text="metadata"></has_text> - <has_text text="tool_id"></has_text> + <has_text text="useuri="></has_text> <has_text text="trackFile path="></has_text> <has_text text="ext="vcf" label="merlin.vcf""></has_text> </assert_contents> </output> </test> <test> - <param name="reference_genome|genome_type_select" value="history"/> - <param name="reference_genome|genome" value="merlin.fa"/> + <repeat name="assemblies"> + <conditional name="reference_genome"> + <param name="genome_type_select" value="history"/> + <param name="genome" value="merlin.fa"/> + <param name="genome.ext" value="fasta"/> + <param name="genome.name" value="Merlin"/> + </conditional> + </repeat> <param name="uglyTestingHack" value="enabled" /> <output name="output"> <assert_contents> <has_text text="genome path="></has_text> - <has_text text="dataset id="></has_text> - <has_text text="history id="></has_text> + <has_text text="label="></has_text> + <has_text text="format="></has_text> <has_text text="metadata"></has_text> - <has_text text="tool_id"></has_text> </assert_contents> </output> </test> <test> - <param name="reference_genome|genome_type_select" value="history"/> - <param name="reference_genome|genome" value="merlin.fa"/> - <repeat name="track_groups"> - <param name="category" value="Default" /> - <repeat name="data_tracks"> - <conditional name="data_format"> - <param name="data_format_select" value="bed"/> - <conditional name="useuri"> - <param name="insource" value="history"/> - <param name="annotation" value="bed/test-3.bed"/> - </conditional> - </conditional> + <repeat name="assemblies"> + <conditional name="reference_genome"> + <param name="genome_type_select" value="history"/> + <param name="genome" value="merlin.fa"/> + <param name="genome.ext" value="fasta"/> + <param name="genome.name" value="Merlin"/> + </conditional> + <repeat name="track_groups"> + <param name="category" value="Default" /> + <repeat name="data_tracks"> + <conditional name="data_format"> + <param name="data_format_select" value="vcf"/> + <conditional name="useuri"> + <param name="insource" value="history"/> + <param name="annotation" value="vcf/merlin.vcf"/> + </conditional> + </conditional> + </repeat> </repeat> </repeat> <param name="uglyTestingHack" value="enabled" /> <output name="output"> <assert_contents> <has_text text="genome path="></has_text> - <has_text text="dataset id="></has_text> - <has_text text="history id="></has_text> + <has_text text="label="></has_text> + <has_text text="format="></has_text> <has_text text="metadata"></has_text> - <has_text text="tool_id"></has_text> + <has_text text="useuri="></has_text> <has_text text="trackFile path="></has_text> <has_text text="ext="bed" label="test-3.bed""></has_text> </assert_contents> </output> </test> <test> - <param name="reference_genome|genome_type_select" value="history"/> - <param name="reference_genome|genome" value="merlin.fa"/> - <repeat name="track_groups"> - <param name="category" value="Auto Coloured" /> - <repeat name="data_tracks"> - <conditional name="data_format"> + <repeat name="assemblies"> + <conditional name="reference_genome"> + <param name="genome_type_select" value="history"/> + <param name="genome" value="merlin.fa"/> + <param name="genome.ext" value="fasta"/> + <param name="genome.name" value="Merlin"/> + </conditional> + <repeat name="track_groups"> + <param name="category" value="Default" /> + <repeat name="data_tracks"> + <conditional name="data_format"> <param name="data_format_select" value="gff"/> - <conditional name="useuri"> - <param name="insource" value="history"/> - <param name="annotation" value="gff3/A.gff"/> + <conditional name="useuri"> + <param name="insource" value="history"/> + <param name="annotation" value="gff3/A.gff"/> + </conditional> </conditional> <conditional name="match_part"> <param name="match_part_select" value="false"/> @@ -563,7 +609,7 @@ <param name="color_select" value="automatic"/> </conditional> </section> - </conditional> + </repeat> </repeat> </repeat> @@ -770,69 +816,72 @@ </output> </test> <test> - <param name="reference_genome|genome_type_select" value="history"/> - <param name="reference_genome|genome" value="merlin.fa"/> - - <repeat name="track_groups"> - <param name="category" value="With menu or index" /> - <repeat name="data_tracks"> - <conditional name="data_format"> - <param name="data_format_select" value="gff"/> - <conditional name="useuri"> - <param name="annotation" value="gff3/1.gff"/> - <param name="insource" value= "history"/> - </conditional> - <conditional name="match_part"> - <param name="match_part_select" value="false"/> - </conditional> - <section name="jbcolor_scale"> - <conditional name="color_score"> - <param name="color_score_select" value="none"/> + <repeat name="assemblies"> + <conditional name="reference_genome"> + <param name="genome_type_select" value="history"/> + <param name="genome" value="merlin.fa"/> + <param name="genome.ext" value="fasta"/> + <param name="genome.name" value="Merlin"/> + </conditional> + <repeat name="track_groups"> + <param name="category" value="Default" /> + <repeat name="data_tracks"> + <conditional name="data_format"> + <param name="data_format_select" value="gff"/> + <conditional name="useuri"> + <param name="annotation" value="gff3/1.gff"/> + <param name="insource" value= "history"/> </conditional> - <conditional name="color"> - <param name="color_select" value="automatic"/> + <conditional name="match_part"> + <param name="match_part_select" value="false"/> </conditional> - </section> - <section name="jbmenu"> - <repeat name="track_menu"> - <param name="menu_action" value="iframeDialog"/> - <param name="menu_label" value="Some menu item"/> - <param name="menu_title" value="Frame title"/> - <param name="menu_url" value="https://example.com/#!/?id={name}&q={type}&z="{end}""/> - <param name="menu_icon" value="dijitIconNewTask"/> - </repeat> - <repeat name="track_menu"> - <param name="menu_action" value="newWindow"/> - <param name="menu_label" value="Another menu item"/> - <param name="menu_title" value="Frame title 2"/> - <param name="menu_url" value="https://example.com/#!/?id={name}&q={type}&z="{end}""/> - </repeat> - </section> - </conditional> - </repeat> - <repeat name="data_tracks"> - <conditional name="data_format"> + <section name="jbcolor_scale"> + <conditional name="color_score"> + <param name="color_score_select" value="none"/> + </conditional> + <conditional name="color"> + <param name="color_select" value="automatic"/> + </conditional> + </section> + <section name="jbmenu"> + <repeat name="track_menu"> + <param name="menu_action" value="iframeDialog"/> + <param name="menu_label" value="Some menu item"/> + <param name="menu_title" value="Frame title"/> + <param name="menu_url" value="https://example.com/#!/?id={name}&q={type}&z="{end}""/> + <param name="menu_icon" value="dijitIconNewTask"/> + </repeat> + <repeat name="track_menu"> + <param name="menu_action" value="newWindow"/> + <param name="menu_label" value="Another menu item"/> + <param name="menu_title" value="Frame title 2"/> + <param name="menu_url" value="https://example.com/#!/?id={name}&q={type}&z="{end}""/> + </repeat> + </section> + </conditional> + </repeat> + <repeat name="data_tracks"> + <conditional name="data_format"> <param name="data_format_select" value="gff"/> - <conditional name="useuri"> - <param name="annotation" value="gff3/1.gff"/> - <param name="insource" value= "history"/> - </conditional> - <param name="insource" value= "history"/> - <conditional name="match_part"> - <param name="match_part_select" value="false"/> + <conditional name="useuri"> + <param name="annotation" value="gff3/1.gff"/> + <param name="insource" value= "history"/> + </conditional> + <conditional name="match_part"> + <param name="match_part_select" value="false"/> + </conditional> + <section name="jbcolor_scale"> + <conditional name="color_score"> + <param name="color_score_select" value="none"/> + </conditional> + <conditional name="color"> + <param name="color_select" value="automatic"/> + </conditional> + </section> </conditional> - <section name="jbcolor_scale"> - <conditional name="color_score"> - <param name="color_score_select" value="none"/> - </conditional> - <conditional name="color"> - <param name="color_select" value="automatic"/> - </conditional> - </section> - </conditional> - </repeat> + </repeat> </repeat> - + </repeat> <param name="uglyTestingHack" value="enabled" /> <output name="output"> <assert_contents> @@ -841,6 +890,7 @@ </assert_contents> </output> </test> + <!-- TODO add a synteny test --> <!-- TODO add a bam and a cram test --> <!-- TODO add an hic test -->