diff jbrowse2.xml @ 48:460d5b6c5d98 draft

planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a-dirty

--- a/jbrowse2.xml	Wed Mar 06 00:23:02 2024 +0000
+++ b/jbrowse2.xml	Wed Mar 06 10:37:49 2024 +0000
@@ -138,7 +138,18 @@
     <tracks>
         #for $tg in $track_groups:
             #for $track in $tg.data_tracks:
-                #if $track.data_format.useuri.insource == "history":
+                #if $track.data_format.useuri.insource == "uri":
+                   <track cat="${tg.category}" format="${track.data_format.data_format_select}" visibility="${track.data_format.track_visibility}">
+                      <files>
+                        <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.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}">
                     <files>
@@ -204,7 +215,7 @@
                             <protein>${track.data_format.is_protein}</protein>
                             <min_gap>${track.data_format.min_gap}</min_gap>
                         </blast>
-                    #else if str($track.data_format.data_format_select) == "gene_calls":
+                    #else if str($track.data_format.data_format_select) == "gff":
                         <gff>
                           #if $track.data_format.match_part.match_part_select == "true":
                             <match>${track.data_format.match_part.name}</match>
@@ -229,6 +240,9 @@
                     #else if str($track.data_format.data_format_select) == "cool":
                         <cool>
                         </cool>
+                    #else if str($track.data_format.data_format_select) == "bed":
+                        <bed>
+                        </bed>
                     #else if str($track.data_format.data_format_select) == "sparql":
                         <label>${track.data_format.label}</label>
                         <sparql>
@@ -240,17 +254,6 @@
                     </options>
                   </track>
                   #end if
-                #else if track.data_format.useuri.annouri:
-                   <track cat="${tg.category}" format="${track.data_format.data_format_select}" visibility="${track.data_format.track_visibility}">
-                      <files>
-                        <trackFile path="${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.annouri}" />
-                            </metadata>
-                         </trackFile>
-                     </files>
-                    <options/>
-                </track>
                 #end if
             #end for
         #end for
@@ -312,11 +315,12 @@
                 <conditional name="data_format" label="Track Data Selection Options">
                     <param type="select" label="Track Type" name="data_format_select">
                         <option value="bam">BAM Pileup track</option>
+                        <option value="bed">BED 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="gff" selected="true">GFF/GFF3 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>
@@ -350,8 +354,8 @@
                         <expand macro="track_styling_vcf"/>
                         <expand macro="track_visibility" />
                     </when>
-                    <when value="gene_calls">
-                        <expand macro="input_conditional" label="GFF/GFF3/BED Track Data" format="gff,gff3,bed" />
+                    <when value="gff">
+                        <expand macro="input_conditional" label="GFF/GFF3 Track Data" format="gff,gff3" />
                         <conditional name="match_part" label="match/match_part data">
                         <param help="Match part data selection " label="This is match/match_part data" name="match_part_select" type="select">
                             <option selected="True" value="false">Not match/match part data</option>
@@ -373,6 +377,10 @@
                         <expand macro="input_conditional" label="BAM Track Data" format="bam" />
                         <expand macro="track_visibility" />
                     </when>
+                    <when value="bed">
+                        <expand macro="input_conditional" label="BED Track Data" format="bed" />
+                        <expand macro="track_visibility" />
+                    </when>
                     <when value="cram">
                         <expand macro="input_conditional" label="CRAM Track Data" format="cram" />
                         <expand macro="track_visibility" />
@@ -497,7 +505,7 @@
                 <param name="category" value="Default" />
                 <repeat name="data_tracks">
                     <conditional name="data_format">
-                        <param name="data_format_select" value="gene_calls"/>
+                        <param name="data_format_select" value="bed"/>
                        <conditional name="useuri">
                             <param name="insource" value="history"/>
                             <param name="annotation" value="bed/test-3.bed"/>
@@ -525,7 +533,7 @@
                 <param name="category" value="Auto Coloured" />
                 <repeat name="data_tracks">
                     <conditional name="data_format">
-                        <param name="data_format_select" value="gene_calls"/>
+                        <param name="data_format_select" value="gff"/>
                        <conditional name="useuri">
                             <param name="insource" value="history"/>
                            <param name="annotation" value="gff3/A.gff"/>
@@ -549,7 +557,7 @@
                 <param name="category" value="Ignore Scale" />
                 <repeat name="data_tracks">
                     <conditional name="data_format">
-                        <param name="data_format_select" value="gene_calls"/>
+                        <param name="data_format_select" value="gff"/>
                        <conditional name="useuri">
                             <param name="insource" value="history"/>
                         <param name="annotation" value="gff3/1.gff"/>
@@ -574,7 +582,7 @@
                 <param name="category" value="Scaled Colour" />
                 <repeat name="data_tracks">
                     <conditional name="data_format">
-                        <param name="data_format_select" value="gene_calls"/>
+                        <param name="data_format_select" value="gff"/>
                        <conditional name="useuri">
                             <param name="insource" value= "history"/>
                             <param name="annotation" value="gff3/C.gff"/>
@@ -601,7 +609,7 @@
                 </repeat>
                 <repeat name="data_tracks">
                     <conditional name="data_format">
-                        <param name="data_format_select" value="gene_calls"/>
+                        <param name="data_format_select" value="gff"/>
                        <conditional name="useuri">
                             <param name="annotation" value="gff3/B.gff"/>
                             <param name="insource" value= "history"/>
@@ -629,7 +637,7 @@
                 </repeat>
                 <repeat name="data_tracks">
                     <conditional name="data_format">
-                        <param name="data_format_select" value="gene_calls"/>
+                        <param name="data_format_select" value="gff"/>
                        <conditional name="useuri">
                             <param name="annotation" value="gff3/A.gff"/>
                             <param name="insource" value= "history"/>
@@ -658,7 +666,7 @@
                 </repeat>
                 <repeat name="data_tracks">
                     <conditional name="data_format">
-                        <param name="data_format_select" value="gene_calls"/>
+                        <param name="data_format_select" value="gff"/>
                         <conditional name="useuri">
                             <param name="annotation" value="gff3/1.gff"/>
                             <param name="insource" value= "history"/>
@@ -692,7 +700,7 @@
                 <param name="category" value="Realistic" />
                 <repeat name="data_tracks">
                     <conditional name="data_format">
-                        <param name="data_format_select" value="gene_calls"/>
+                        <param name="data_format_select" value="gff"/>
                         <conditional name="useuri">
                             <param name="annotation" value="gff3/interpro.gff"/>
                             <param name="insource" value= "history"/>
@@ -712,7 +720,7 @@
                 </repeat>
                 <repeat name="data_tracks">
                     <conditional name="data_format">
-                        <param name="data_format_select" value="gene_calls"/>
+                        <param name="data_format_select" value="gff"/>
                          <conditional name="useuri">
                             <param name="annotation" value="gff3/2.gff"/>
                             <param name="insource" value= "history"/>
@@ -755,7 +763,7 @@
                 <param name="category" value="With menu or index" />
                 <repeat name="data_tracks">
                     <conditional name="data_format">
-                        <param name="data_format_select" value="gene_calls"/>
+                        <param name="data_format_select" value="gff"/>
                         <conditional name="useuri">
                             <param name="annotation" value="gff3/1.gff"/>
                             <param name="insource" value= "history"/>
@@ -790,7 +798,7 @@
                 </repeat>
                 <repeat name="data_tracks">
                     <conditional name="data_format">
-                        <param name="data_format_select" value="gene_calls"/>
+                        <param name="data_format_select" value="gff"/>
                          <conditional name="useuri">
                             <param name="annotation" value="gff3/1.gff"/>
                             <param name="insource" value= "history"/>
@@ -815,7 +823,7 @@
             <output name="output">
                 <assert_contents>
                     <has_text text="With menu or index"/>
-                    <has_text text="gene_calls"/>
+                    <has_text text="gff"/>
                 </assert_contents>
             </output>
         </test>