--- a/jbrowse2.xml	Fri Mar 01 05:15:41 2024 +0000
+++ b/jbrowse2.xml	Mon Mar 04 09:47:19 2024 +0000
@@ -1,4 +1,4 @@
- <tool id="jbrowse2" name="jbrowse2" version="@TOOL_VERSION@+@WRAPPER_VERSION@_5" profile="22.05">
+ <tool id="jbrowse2" name="jbrowse2" version="@TOOL_VERSION@+@WRAPPER_VERSION@_6" profile="22.05">
     <description>genome browser</description>
     <macros>
         <import>macros.xml</import>
@@ -17,35 +17,75 @@
 
 export JBROWSE2_PATH=\$(dirname \$(which jbrowse))/../opt/jbrowse2  &&
 
-## Once that's done, we run the python script to handle the real work
-python '$__tool_directory__/jbrowse2.py'
---jbrowse2path \${JBROWSE2_PATH}
---outdir '$output.files_path'
---xml '$trackxml' &&
-#if $jbgen.zipOut == "true":
-    (cd '$output.files_path' && zip -r - . ) > '$output'
-#else
-  cp '$output.files_path/index.html' '$output'
-#end if
-## Ugly testing hack since I cannot get <extra_files> to test the files I want to test. Hmph.
-#if str($uglyTestingHack) == "enabled":
- &&   cp '$trackxml' '$output'
+#if $jbgen.ucol.formcoll=="collect":
+    python '$__tool_directory__/autogenJB2.py'
+    #for $key in $autoCollection.keys():
+        #if $autoCollection[$key].is_collection:
+            #set subCol=$autoCollection[$key]
+            #set pafs=[($subCol[x],$subcol[x].ext,x) for x in $subCol.keys() if $subCol[x].ext == 'paf']
+            #if len($pafs) > 0:
+                 --pafmeta '$pafs[0]'
+                #set refs = [($pafs[0][2],$subCol[x],x) for x in $subCol.keys() if $subCol[x].ext == 'fasta']
+                #for $ref in $refs:
+                 --pafreferencemeta '$ref'
+                #end for
+            #end if
+        #else if $autoCollection[$key].ext == 'fasta':
+          --referencemeta '$autoCollection[$key],$autoCollection[$key].ext,$key'
+        #else if $autoCollection[$key].ext in ['bed', 'bigwig', 'cool', 'gff', 'gff3', 'hic', 'maf', 'mcool', 'scool', 'vcf']
+          --trackmeta '$autoCollection[$key],$autoCollection[$key].ext,$key'
+        #else if $autoCollection[$key].ext in ['bam',]
+          --trackmeta '$autoCollection[$key],$autoCollection[$key].ext,$key,$autoCollection[$key].metadata.bam_index'
+         #else if $autoCollection[$key].ext in ['cram',]
+          --trackmeta '$autoCollection[$key],$autoCollection[$key].ext,$key,$autoCollection[$key].metadata.cram_index'
+        #end if
+    #end for
+    --outdir '$output.files_path'
+    --jbrowse2path \${JBROWSE2_PATH}
+    --sessName "Autogen JBrowse" &&
+    #if $jbgen.zipOut == "true":
+        (cd '$output.files_path' && zip -r - . ) > '$output'
+    #else
+      cp '$output.files_path/index.html' '$output'
+    #end if
+#else:
+    python '$__tool_directory__/jbrowse2.py'
+    --jbrowse2path \${JBROWSE2_PATH}
+    --outdir '$output.files_path'
+    --xml '$trackxml' &&
+    #if $jbgen.zipOut == "true":
+        (cd '$output.files_path' && zip -r - . ) > '$output'
+    #else
+      cp '$output.files_path/index.html' '$output'
+    #end if
+    ## Ugly testing hack since I cannot get <extra_files> to test the files I want to test. Hmph.
+    #if str($uglyTestingHack) == "enabled":
+       &&   cp '$trackxml' '$output'
+    #end if
 #end if
   ]]></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) == "indexed":
-              <genome path="${reference_genome.genome.fields.path}" label="${reference_genome.genome.fields.name}">
+            #if str($reference_genome.genome_type_select) == "uri":
+              <genome path="${reference_genome.uri}" label="${reference_genome.refname}" useuri="yes">
                   <metadata>
                      <dataset
-                      dname = "${reference_genome.genome.name}" />
+                      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 = "${reference_genome.genome.refname}" />
                   </metadata>
               </genome>
             #else
-              <genome path="$reference_genome.genome" label="${reference_genome.genome.name}">
+              <genome path="$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)}"
@@ -98,13 +138,14 @@
     <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":
+                #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>
-                        #for $dataset in $track.data_format.annotation:
-                               #if $dataset:
-                              <trackFile path="${dataset}" ext="${dataset.ext}" label="${dataset.name}">
+                        #for $dataset in $track.data_format.useuri.annotation:
+                              <trackFile path="${dataset}" ext="${dataset.ext}" label="${dataset.name}" useuri="no">
                                 <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}"
@@ -119,6 +160,7 @@
                                       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:
@@ -137,25 +179,20 @@
                                       />
                                 </metadata>
                               </trackFile>
-                            #end if
-
-                        #end for
+                       #end for
                     </files>
-                    #else
-                            <track cat="${tg.category}" format="sparql" visibility="off">
-                    #end if
 
                     <options>
 
                     #if str($track.data_format.data_format_select) == "bam":
                         <bam>
-                            #for $dataset in $track.data_format.annotation:
+                            #for $dataset in $track.data_format.useuri.annotation:
                                 <bam_index>${dataset.metadata.bam_index}</bam_index>
                             #end for
                         </bam>
                     #else if str($track.data_format.data_format_select) == "cram":
                         <cram>
-                            #for $dataset in $track.data_format.annotation:
+                            #for $dataset in $track.data_format.useuri.annotation:
                                 <cram_index>${dataset.metadata.cram_index}</cram_index>
                             #end for
                         </cram>
@@ -201,11 +238,25 @@
                         </sparql>
                     #end if
                     </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 for
-    #end for
+                #end if
+            #end for
+        #end for
     </tracks>
 </root>
+#end if
 ]]></configfile>
     </configfiles>
 
@@ -214,6 +265,7 @@
             <param help="Built-in references" label="Reference genome to display" 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>
             </param>
             <when value="indexed">
                 <param
@@ -236,6 +288,18 @@
                     type="data">
                 </param>
             </when>
+            <when value="uri">
+                <param
+                    label="URI pointing to tabix compressed fasta"
+                    name="uri"
+                    type="text">
+                </param>
+                <param
+                    label="Reference key - dbkey equivalent"
+                    name="refname"
+                    type="text">
+                </param>
+            </when>
         </conditional>
 
         <repeat name="track_groups" title="Track Group">
@@ -348,7 +412,7 @@
         <param type="hidden" name="uglyTestingHack" value="" />
     </inputs>
     <outputs>
-        <data format="html" name="output" label="JBrowse2 on $reference_genome.genome.name">
+        <data format="html" name="output" label="JBrowse2">
             <change_format>
                 <when input="zipOut" value="true" format="zip" />
             </change_format>
@@ -363,7 +427,10 @@
                 <repeat name="data_tracks">
                     <conditional name="data_format">
                         <param name="data_format_select" value="bigwig"/>
-                        <param name="annotation" value="bw/merlin.bw"/>
+                        <conditional name="useuri">
+                            <param name="annotation" value="bw/merlin.bw"/>
+                            <param name="insource" value="history"/>
+                        </conditional>
                     </conditional>
                 </repeat>
             </repeat>
@@ -389,7 +456,10 @@
                 <repeat name="data_tracks">
                     <conditional name="data_format">
                         <param name="data_format_select" value="vcf"/>
-                        <param name="annotation" value="vcf/merlin.vcf"/>
+                        <conditional name="useuri">
+                            <param name="insource" value="history"/>
+                            <param name="annotation" value="vcf/merlin.vcf"/>
+                        </conditional>
                     </conditional>
                 </repeat>
             </repeat>
@@ -428,7 +498,10 @@
                 <repeat name="data_tracks">
                     <conditional name="data_format">
                         <param name="data_format_select" value="gene_calls"/>
-                        <param name="annotation" value="bed/test-3.bed"/>
+                       <conditional name="useuri">
+                            <param name="insource" value="history"/>
+                            <param name="annotation" value="bed/test-3.bed"/>
+                       </conditional>
                     </conditional>
                 </repeat>
             </repeat>
@@ -453,7 +526,10 @@
                 <repeat name="data_tracks">
                     <conditional name="data_format">
                         <param name="data_format_select" value="gene_calls"/>
-                        <param name="annotation" value="gff3/A.gff"/>
+                       <conditional name="useuri">
+                            <param name="insource" value="history"/>
+                           <param name="annotation" value="gff3/A.gff"/>
+                        </conditional>
                         <conditional name="match_part">
                             <param name="match_part_select" value="false"/>
                         </conditional>
@@ -474,7 +550,10 @@
                 <repeat name="data_tracks">
                     <conditional name="data_format">
                         <param name="data_format_select" value="gene_calls"/>
+                       <conditional name="useuri">
+                            <param name="insource" value="history"/>
                         <param name="annotation" value="gff3/1.gff"/>
+                        </conditional>
                         <conditional name="match_part">
                             <param name="match_part_select" value="false"/>
                         </conditional>
@@ -496,7 +575,10 @@
                 <repeat name="data_tracks">
                     <conditional name="data_format">
                         <param name="data_format_select" value="gene_calls"/>
-                        <param name="annotation" value="gff3/C.gff"/>
+                       <conditional name="useuri">
+                            <param name="insource" value= "history"/>
+                            <param name="annotation" value="gff3/C.gff"/>
+                        </conditional>
                         <conditional name="match_part">
                             <param name="match_part_select" value="false"/>
                         </conditional>
@@ -520,8 +602,11 @@
                 <repeat name="data_tracks">
                     <conditional name="data_format">
                         <param name="data_format_select" value="gene_calls"/>
-                        <param name="annotation" value="gff3/B.gff"/>
-                        <conditional name="match_part">
+                       <conditional name="useuri">
+                            <param name="annotation" value="gff3/B.gff"/>
+                            <param name="insource" value= "history"/>
+                        </conditional>
+                       <conditional name="match_part">
                             <param name="match_part_select" value="false"/>
                         </conditional>
                         <section name="jbcolor_scale">
@@ -545,7 +630,10 @@
                 <repeat name="data_tracks">
                     <conditional name="data_format">
                         <param name="data_format_select" value="gene_calls"/>
-                        <param name="annotation" value="gff3/A.gff"/>
+                       <conditional name="useuri">
+                            <param name="annotation" value="gff3/A.gff"/>
+                            <param name="insource" value= "history"/>
+                        </conditional>
                         <conditional name="match_part">
                             <param name="match_part_select" value="false"/>
                         </conditional>
@@ -571,7 +659,10 @@
                 <repeat name="data_tracks">
                     <conditional name="data_format">
                         <param name="data_format_select" value="gene_calls"/>
-                        <param name="annotation" value="gff3/1.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>
@@ -602,7 +693,10 @@
                 <repeat name="data_tracks">
                     <conditional name="data_format">
                         <param name="data_format_select" value="gene_calls"/>
-                        <param name="annotation" value="gff3/interpro.gff"/>
+                        <conditional name="useuri">
+                            <param name="annotation" value="gff3/interpro.gff"/>
+                            <param name="insource" value= "history"/>
+                        </conditional>
                         <conditional name="match_part">
                             <param name="match_part_select" value="false"/>
                         </conditional>
@@ -619,7 +713,10 @@
                 <repeat name="data_tracks">
                     <conditional name="data_format">
                         <param name="data_format_select" value="gene_calls"/>
-                        <param name="annotation" value="gff3/2.gff"/>
+                         <conditional name="useuri">
+                            <param name="annotation" value="gff3/2.gff"/>
+                            <param name="insource" value= "history"/>
+                        </conditional>
                         <conditional name="match_part">
                             <param name="match_part_select" value="true"/>
                             <param name="name" value="cDNA_match"/>
@@ -659,7 +756,10 @@
                 <repeat name="data_tracks">
                     <conditional name="data_format">
                         <param name="data_format_select" value="gene_calls"/>
-                        <param name="annotation" value="gff3/1.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>
@@ -691,7 +791,11 @@
                 <repeat name="data_tracks">
                     <conditional name="data_format">
                         <param name="data_format_select" value="gene_calls"/>
-                        <param name="annotation" value="gff3/1.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>