diff jbrowse2.xml @ 85:3b2ff9864995 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty

--- a/jbrowse2.xml	Wed Apr 03 02:56:39 2024 +0000
+++ b/jbrowse2.xml	Tue Apr 09 00:26:49 2024 +0000
@@ -1,4 +1,4 @@
- <tool id="jbrowse2" name="JBrowse2" version="@TOOL_VERSION@+@WRAPPER_VERSION@_11" profile="22.05">
+ <tool id="jbrowse2" name="JBrowse2" version="@TOOL_VERSION@+@WRAPPER_VERSION@_12" profile="22.05">
     <description>genome browser</description>
     <macros>
         <import>macros.xml</import>
@@ -204,34 +204,42 @@
                   #if $uglyTestingHack != "enabled":
                   <options>
                     <style>
-                        #if str($track.data_format.data_format_select) in ["gff", "bed", "vcf", "maf", "blastxml"]:
+                        #if str($track.data_format.data_format_select) in ["gff", "bed", "maf", "blastxml"]:
+                            <type>${track.data_format.jbstyle.display}</type>
+                            #if str($track.data_format.jbstyle.display) in ["LinearBasicDisplay", "LinearVariantDisplay"]:
+                                <trackShowLabels>${track.data_format.jbstyle.show_labels}</trackShowLabels>
+                                <trackShowDescriptions>${track.data_format.jbstyle.show_descriptions}</trackShowDescriptions>
+                            #end if
+                        #else if str($track.data_format.data_format_select) == "vcf":
                             <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
                         #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($track.data_format.data_format_select) in ["hic"]:
+                        #if str($track.data_format.data_format_select) in ["hic", "cool", "mcool", "scool"]:
                             <type>LinearHicDisplay</type>
                         #end if
                     </style>
                     #if str($track.data_format.data_format_select) == "bam":
                         <bam>
+                        <bam_index>
                             #for $dataset in $track.data_format.useuri.annotation:
-                                <bam_index>${dataset.metadata.bam_index}</bam_index>
+                                ${dataset.name},${dataset.metadata.bam_index}
                             #end for
+                        </bam_index>
                         </bam>
                     #else if str($track.data_format.data_format_select) == "cram":
                         <cram>
+                        <cram_index>
                             #for $dataset in $track.data_format.useuri.annotation:
-                                <cram_index>${dataset.metadata.cram_index}</cram_index>
+                                ${dataset.name},${dataset.metadata.cram_index}
                             #end for
+                        </cram_index>
                         </cram>
                     #else if str($track.data_format.data_format_select) == "blastxml":
                         <blast>
@@ -249,16 +257,29 @@
                         </gff>
                     #else if str($track.data_format.data_format_select) == "paf":
                         <paf>
+                            #if $track.data_format.pafuseuri.insource == "history":
                             <genome>
-                            #for refgenome in $track.data_format.pafuseuri.refgenomes:
-                                $refgenome.annotation,
-                            #end for
+                                #for $anno in $track.data_format.pafuseuri.annotation:
+                                    ${anno},
+                                #end for
                             </genome>
                             <genome_label>
-                            #for refgenome in $track.data_format.pafuseuri.refgenomes:
-                                $refgenome.annoname,
-                            #end for
+                                #for $anno in $track.data_format.pafuseuri.annotation:
+                                        ${anno.name},
+                                #end for
                             </genome_label>
+                            #else:
+                            <genome>
+                                #for $refgenome in $track.data_format.pafuseuri.refuri:
+                                    $refgenome.annotation,
+                                #end for
+                            </genome>
+                            <genome_label>
+                                #for $refgenome in $track.data_format.pafuseuri.refuri:
+                                    ${refgenome.annoname},
+                                #end for
+                            </genome_label>
+                            #end if
                         </paf>
                     #else if str($track.data_format.data_format_select) == "hic":
                         <hic>
@@ -377,7 +398,7 @@
                             name="is_protein"
                             truevalue="true"
                             falsevalue="false" />
-                        <expand macro="track_styling_feature" />
+                        <expand macro="track_styling_vgp" />
                         <expand macro="track_visibility" />
                     </when>
                     <when value="vcf">
@@ -402,7 +423,7 @@
                             </when>
                             <when value="false" />
                         </conditional>
-                        <expand macro="track_styling_feature" />
+                        <expand macro="track_styling_vgp" />
                         <expand macro="track_visibility" />
                     </when>
                     <when value="bam">
@@ -411,7 +432,7 @@
                     </when>
                     <when value="bed">
                         <expand macro="input_conditional" label="BED Track Data" format="bed" />
-                        <expand macro="track_styling_feature" />
+                        <expand macro="track_styling_vgp" />
                         <expand macro="track_visibility" />
                     </when>
                     <when value="cram">
@@ -420,7 +441,7 @@
                     </when>
                     <when value="maf">
                         <expand macro="input_conditional" label="MAF Track Data" format="maf" />
-                        <expand macro="track_styling_feature" />
+                        <expand macro="track_styling_vgp" />
                         <expand macro="track_visibility" />
                     </when>
                     <when value="bigwig">