Mercurial > repos > fubar > jbrowse2
diff jbrowse2.xml @ 35:15da358c3108 draft
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd-dirty
| author | fubar |
|---|---|
| date | Wed, 28 Feb 2024 10:08:57 +0000 |
| parents | 2893ef33fba9 |
| children | 5f39f745682f |
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--- a/jbrowse2.xml Sun Feb 25 04:18:53 2024 +0000 +++ b/jbrowse2.xml Wed Feb 28 10:08:57 2024 +0000 @@ -93,107 +93,110 @@ <tracks> #for $tg in $track_groups: #for $track in $tg.data_tracks: - <track cat="${tg.category}" format="${track.data_format.data_format_select}" visibility="${track.data_format.track_visibility}"> - #if $track.data_format.data_format_select != "sparql": - <files> - #set dataset = $track.data_format.annotation - <trackFile path="${dataset}" ext="${dataset.ext}" label="${dataset.name}"> - <metadata> - <dataset id="${__app__.security.encode_id($dataset.id)}" hid="${dataset.hid}" - size="${dataset.get_size(nice_size=True)}" - edam_format="${dataset.datatype.edam_format}" - file_ext="${dataset.ext}" /> - <history id="${__app__.security.encode_id($dataset.history_id)}" - #if $dataset.history.user: - user_email="${dataset.history.user.email}" - user_id="${dataset.history.user_id}" - display_name="${dataset.history.get_display_name()}"/> - #else - user_email="anonymous" - user_id="-1" - display_name="Unnamed History"/> - #end if - <metadata - #for (key, value) in $dataset.get_metadata().items(): - #if "_types" not in $key and $value is not None and len(str($value)) < 5000: - #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="${dataset.creating_job.tool_id}" - tool_version="${dataset.creating_job.tool_version}" - /> - </metadata> - </trackFile> - </files> - #else - <track cat="${tg.category}" format="sparql" visibility="off"> - #end if + <track cat="${tg.category}" format="${track.data_format.data_format_select}" visibility="${track.data_format.track_visibility}"> + #if $track.data_format.data_format_select != "sparql": + #for $dataset in $track.data_format.annotation: + <files> + <trackFile path="${dataset}" ext="${dataset.ext}" label="${dataset.name}"> + <metadata> + <dataset id="${__app__.security.encode_id($dataset.id)}" hid="${dataset.hid}" + size="${dataset.get_size(nice_size=True)}" + edam_format="${dataset.datatype.edam_format}" + file_ext="${dataset.ext}" /> + <history id="${__app__.security.encode_id($dataset.history_id)}" + #if $dataset.history.user: + user_email="${dataset.history.user.email}" + user_id="${dataset.history.user_id}" + display_name="${dataset.history.get_display_name()}"/> + #else + user_email="anonymous" + user_id="-1" + display_name="Unnamed History"/> + #end if + <metadata + #for (key, value) in $dataset.get_metadata().items(): + #if "_types" not in $key and $value is not None and len(str($value)) < 5000: + #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="${dataset.creating_job.tool_id}" + tool_version="${dataset.creating_job.tool_version}" + /> + </metadata> + </trackFile> + </files> + #end for + #else + <track cat="${tg.category}" format="sparql" visibility="off"> + #end if - <options> + <options> - #if str($track.data_format.data_format_select) == "pileup": - <pileup> - <bam_indices> - <bam_index>${dataset.metadata.bam_index}</bam_index> - </bam_indices> - </pileup> - #else if str($track.data_format.data_format_select) == "cram": - <cram> - <cram_indices> - <cram_index>${dataset.metadata.cram_index}</cram_index> - </cram_indices> - </cram> - #else if str($track.data_format.data_format_select) == "blast": - <blast> - #if str($track.data_format.blast_parent) != "": - <parent>${track.data_format.blast_parent}</parent> - #end if - <protein>${track.data_format.is_protein}</protein> - <min_gap>${track.data_format.min_gap}</min_gap> - </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 - </gff> - #else if str($track.data_format.data_format_select) == "paf": - <paf> - <genome> - #for gnome in $track.data_format.synteny_genome: - $gnome, - #end for - </genome> - <genome_label> - #for gnome in $track.data_format.synteny_genome: - $gnome.name, - #end for - </genome_label> - </paf> - #else if str($track.data_format.data_format_select) == "hic": - <hic> - </hic> - #else if str($track.data_format.data_format_select) == "cool": - <cool> - </cool> - #else if str($track.data_format.data_format_select) == "sparql": - <label>${track.data_format.label}</label> - <sparql> - <url>${track.data_format.url}</url> - <query>${track.data_format.query}</query> - <query_refnames>${track.data_format.query_refnames}</query_refnames> - </sparql> - #end if - </options> - </track> - #end for + #if str($track.data_format.data_format_select) == "bam": + <pileup> + #for $dataset in $track.data_format.annotation: + <bam_index>${dataset.metadata.bam_index}</bam_index> + #end for + </pileup> + #else if str($track.data_format.data_format_select) == "cram": + <cram> + <cram_indices> + #for $dataset in $track.data_format.annotation: + <cram_index>${dataset.metadata.cram_index}</cram_index> + #end for + </cram_indices> + </cram> + #else if str($track.data_format.data_format_select) == "blastxml": + <blast> + #if str($track.data_format.blast_parent) != "": + <parent>${track.data_format.blast_parent}</parent> + #end if + <protein>${track.data_format.is_protein}</protein> + <min_gap>${track.data_format.min_gap}</min_gap> + </blast> + #else if str($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 + </gff> + #else if str($track.data_format.data_format_select) == "paf": + <paf> + <genome> + #for gnome in $track.data_format.synteny_genome: + $gnome, + #end for + </genome> + <genome_label> + #for gnome in $track.data_format.synteny_genome: + $gnome.name, + #end for + </genome_label> + </paf> + #else if str($track.data_format.data_format_select) == "hic": + <hic> + </hic> + #else if str($track.data_format.data_format_select) == "cool": + <cool> + </cool> + #else if str($track.data_format.data_format_select) == "sparql": + <label>${track.data_format.label}</label> + <sparql> + <url>${track.data_format.url}</url> + <query>${track.data_format.query}</query> + <query_refnames>${track.data_format.query_refnames}</query_refnames> + </sparql> + #end if + </options> + </track> + #end for #end for </tracks> </root> @@ -238,19 +241,18 @@ <repeat name="data_tracks" title="Annotation Track"> <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 track</option> - <option value="blast">Blast XML track - converted to GFF</option> + <option value="bam">BAM Pileup track</option> + <option value="bigwig">BigWig track</option> + <option value="blastxml">Blast XML track - converted to GFF</option> <option value="cool">HiC as cool/mcool/scool format files</option> <option value="cram">CRAM</option> <option value="gene_calls" selected="true">GFF/GFF3/BED feature track</option> <option value="hic">HiC as juicebox_hic format file. Tabular hic_matrix will NOT work.</option> <option value="maf">Multiple alignment format. Reference name must match the MAF name exactly to work correctly</option> <option value="paf">PAF - approximate mapping positions between two set of sequences</option> - <option value="sparql">SPARQL</option> <option value="vcf">VCF SNP</option> </param> - <when value="blast"> + <when value="blastxml"> <expand macro="input_conditional" label="BlastXML Track Data" format="blastxml" /> <param label="Features used in Blast Search" @@ -297,7 +299,7 @@ </conditional> <expand macro="track_visibility" /> </when> - <when value="pileup"> + <when value="bam"> <expand macro="input_conditional" label="BAM Track Data" format="bam" /> <expand macro="track_visibility" /> </when> @@ -309,12 +311,12 @@ <expand macro="input_conditional" label="MAF Track Data" format="maf" /> <expand macro="track_visibility" /> </when> - <when value="wiggle"> + <when value="bigwig"> <expand macro="input_conditional" label="BigWig Track Data" format="bigwig" /> <expand macro="track_visibility" /> </when> <when value="paf"> - <param label="Comparison genome sequence" help="Paf from these as the references, using the real reference as the reads to map" + <param label="Comparison genome sequence" help="Paf from these as the reference(s), using the common reference as the reads to map" format="fasta" name="synteny_genome" type="data" @@ -331,55 +333,6 @@ <expand macro="input_conditional" label="HiC data in cool/mcool/scool format" format="cool,mcool,scool" /> <expand macro="track_visibility" /> </when> - <when value="sparql"> - <param type="text" label="SPARQL Server URL" name="url" /> - <param type="text" label="Track Label" name="label" value="SPARQL Genes" /> - <param type="text" label="SPARQL Query" name="query" area="true"> - <sanitizer> - <mapping initial="galaxy.util.mapped_chars"> - <add source=" " target=" " /> - <add source=">" target="__gt__" /> - <add source="<" target="__lt__" /> - </mapping> - <valid initial="default"> - <add value="|" /> - <add value="#" /> - <add value="{"/> - <add value="}"/> - <add value="!"/> - <add value="?"/> - <add value="&"/> - <add value="+"/> - <add value="="/> - <add value="'"/> - <add value='"'/> - </valid> - </sanitizer> - </param> - <param type="text" label="SPARQL reference names query" help="This query should return a line for each reference name in a `refName` column" name="query_refnames" area="true"> - <sanitizer> - <mapping initial="galaxy.util.mapped_chars"> - <add source=" " target=" " /> - <add source=">" target="__gt__" /> - <add source="<" target="__lt__" /> - </mapping> - <valid initial="default"> - <add value="|" /> - <add value="#" /> - <add value="{"/> - <add value="}"/> - <add value="!"/> - <add value="?"/> - <add value="&"/> - <add value="+"/> - <add value="="/> - <add value="'"/> - <add value='"'/> - </valid> - </sanitizer> - </param> - <expand macro="track_visibility" /> - </when> </conditional> </repeat> </repeat>