# HG changeset patch
# User fubar
# Date 1709114937 0
# Node ID 15da358c310871b8e2d35525a80d2462bcfa1f2a
# Parent  2893ef33fba9e2b57b7738f15b5d06292e9ebaa7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd-dirty

diff -r 2893ef33fba9 -r 15da358c3108 autogenJB2.py
--- a/autogenJB2.py	Sun Feb 25 04:18:53 2024 +0000
+++ b/autogenJB2.py	Wed Feb 28 10:08:57 2024 +0000
@@ -1,65 +1,66 @@
 import argparse
-import re
+import logging
 import sys
 
-from jbrowse2 import jbrowseConnector as jbC
+from jbrowse2 import JbrowseConnector as jbC
+
+logging.basicConfig(level=logging.debug)
+log = logging.getLogger("jbrowse")
 
 
-def makeDefaultLocation(jc, defLoc=None):
-
-    refName = None
-    drdict = {
-        "reversed": False,
-        "assemblyName": jc.genome_name,
-        "start": 0,
-        "end": 100000,
-    }
+def makeDefaultLocation():
 
-    if defLoc:
-        loc_match = re.search(r"^([^:]+):([\d,]*)\.*([\d,]*)$", defLoc)
-        # allow commas like 100,000 but ignore as integer
-        if loc_match:
-            refName = loc_match.group(1)
-            drdict["refName"] = refName
-            if loc_match.group(2) > "":
-                drdict["start"] = int(loc_match.group(2).replace(",", ""))
-            if loc_match.group(3) > "":
-                drdict["end"] = int(loc_match.group(3).replace(",", ""))
-        else:
-            jc.logging.info(
-                "@@@ regexp could not match contig:start..end in the supplied location %s - please fix"
-                % defLoc
-            )
-    else:
-        drdict["refName"] = jc.genome_firstcontig
-    if drdict.get("refName", None):
-        jc.logging.info("@@@ defaultlocation %s for default session" % drdict)
-        return drdict
-    else:
-        jc.logging.info("@@@ no contig name found for default session - please add one!")
-        return None
+    refName = jc.genome_firstcontig
+    defloc  = "%s:100..10000" % refName
+    print ('defloc',defloc)
+    return defloc
 
 
 if __name__ == "__main__":
     parser = argparse.ArgumentParser(description="", epilog="")
-    parser.add_argument("--sessname", help="Session name", default="AutoJBrowse")
+    parser.add_argument("--sessName", help="Session name", default="AutoJBrowse")
+    parser.add_argument(
+        "--trackmeta",
+        help="Repeatable of 'filename, filext,filepath, ... ,' for JBrowse2 tracks",
+        default=[],
+        action="append",
+    )
     parser.add_argument(
-        "--collection",
-        help="Collection of 'filepath, filename, filext' for JBrowse2",
+        "--referencemeta",
+        help="Repeatable 'filename, filext, filepath, ... ,' for JBrowse2 reference tracks",
         default=[],
-        action="extend",
+        action="append",
+    )
+    parser.add_argument(
+        "--pafmeta",
+        help="Repeatable. Each is a 'filename, filext, filepath, ... ,' for a JBrowse2 paf track",
+        default=[],
+        action="append",
     )
-    parser.add_argument("--version", "-V", action="version", version="%(prog)s 0.0.1")
+    parser.add_argument(
+        "--pafreferencemeta",
+        help="Repeatable. Each is a 'pafname,filepath,refname,filepath,refname....'. Every paf must have a corresponding one ",
+        default=[],
+        action="append",
+    )
+
+    parser.add_argument("--version", "-V", action="version", version="%(prog)s 2.10.2")
+    parser.add_argument("--outdir", help="Output directory", required=True)
     args = parser.parse_args()
-    sessName = args.sessname
-    flistList = [x.split(",") for x in args.collection]
-    if flistList:
-        listgenomes = [f for f in flistList if f[0].startswith("REFERENCE_")]
+    sessName = args.sessName
+    # --trackmeta $jbrowseme[$key],$jbrowseme[$key].ext,'$key'
+    trackList = [x.strip().split(",") for x in args.trackmeta if x > '']
+    refList = [x.strip().split(",") for x in args.referencemeta if x > '']
+    print("tracklist = %s\nreflist = %s" % (trackList,refList))
+    if len(refList) > 0:
+        listgenomes = [f for f in refList if f[1] in ['fasta', 'fasta.gz']]
+        # assume no pafs here
+        print('genomes=%s' % listgenomes)
         if len(listgenomes) > 0:
             genome_paths = [
-                x[1] for x in listgenomes
+                x[0] for x in listgenomes
             ]  # expect genome_1_genomename.fasta etc
-            genome_names = [x[0].split("REFERENCE_")[1] for x in listgenomes]
+            genome_names = [x[2] for x in listgenomes]
             jc = jbC(
                 outdir=args.outdir,
                 genomes=[
@@ -67,11 +68,13 @@
                         "path": x,
                         "meta": {
                             "name": genome_names[i],
+                            "dataset_dname": genome_names[i],
                         },
                     }
                     for i, x in enumerate(genome_paths)
                 ],
             )
+            sys.stdout.write('$$$ genome_paths:%s genome_names: %s' % (genome_paths,genome_names))
             jc.process_genomes()
             default_session_data = {
                 "visibility": {
@@ -81,42 +84,49 @@
                 "style": {},
                 "style_labels": {},
             }
-            defLoc = makeDefaultLocation(jc)
-            listtracks = [f for f in flistList if not f[0].startswith("REFERENCE_")]
+
+            listtracks = trackList
             # foo.paf must have a foo_paf.fasta or fasta.gz to match
-            tnames = [x[0] for x in listtracks]
-            texts = [x[2] for x in listtracks]
+            tnames = [x[2] for x in listtracks]
+            texts = [x[1] for x in listtracks]
             for i, track in enumerate(listtracks):
-                if track[2] == "paf":
-                    refname = track[0] + "_paf.fasta"
-                    refdat = [x[1] for x in listtracks if x[0] == refname]
+                tpath, trext, trackname = track[:3]
+                if trext == "paf":
+                    refname = trackname + "_paf.fasta"
+                    refdat = [x[2] for x in listtracks if x[2] == refname]
                     if not refdat:
                         jc.logging.warn(
                             "!! No reference file %s corresponding to paf file %s found. Not building - there must be a corresponding fasta for each paf"
-                            % (refname, tnames[i])
+                            % (refname, trackname)
                         )
                         sys.exit(3)
                     else:
                         track_conf = {
                             "conf": {
                                 "options": {
-                                    "paf": {"genome": refdat, "genome_label": track[0]}
+                                    "paf": {"genome": refdat, "genome_label": trackname}
                                 }
                             }
                         }
+                elif trext == 'bam':
+                     track_conf["conf"] = {"options": {"bam": {"bam_indices": {"bam_index": track[3]}}}}
+                elif trext == 'cram':
+                     track_conf["conf"] = {"options": {"cram": {"cram_indices": {"cram_index": track[3]}}}}
                 else:
                     track_conf = {}
-                track_conf["format"] = track[2]
-                track_conf["name"] = track[0]
-                track_conf["label"] = track[0]
-                track_conf["trackfiles"] = []
+                track_conf["format"] = trext
+                track_conf["name"] = trackname
+                track_conf["label"] = trackname
+                track_conf["trackfiles"] = [(tpath, trext, trackname,{}),]
+                track_conf["category"] = "Autogenerated"
                 keys = jc.process_annotations(track_conf)
 
                 if keys:
                     for key in keys:
-                        default_session_data["visibility"][
-                            track.attrib.get("visibility", "default_off")
-                        ].append(key)
+                        if trext in ["bigwig", "gff3", "gff", "vcf", "maf",]:
+                            default_session_data["visibility"]["default_on"].append(key)
+                        else:
+                            default_session_data["visibility"]["default_off"].append(key)
                         # if track_conf.get("style", None):
                         # default_session_data["style"][key] = track_conf[
                         # "style"
@@ -140,8 +150,10 @@
             else:
                 jc.config_json["tracks"] = jc.tracksToAdd
             jc.write_config()
-            defaultData = {"defaultLocation": defLoc, "session_name": sessName}
-            jc.add_default_session(defaultData)
+            defLoc = makeDefaultLocation()
+            default_session_data.update({"defaultLocation": defLoc, "session_name": sessName})
+            track_conf.update(default_session_data)
+            jc.add_default_session(default_session_data)
             # jc.text_index() not sure what broke here.
     else:
-        sys.stderr.write("!! empty collection supplied - nothing to process")
+        print("!! empty collection supplied - nothing to process")
diff -r 2893ef33fba9 -r 15da358c3108 autogenJB2.xml
--- a/autogenJB2.xml	Sun Feb 25 04:18:53 2024 +0000
+++ b/autogenJB2.xml	Wed Feb 28 10:08:57 2024 +0000
@@ -1,5 +1,5 @@
- <tool id="autogenjb2" name="autogenjb2" version="2.10.0_0" profile="22.05">
-    <description>Files to JBrowse2</description>
+ <tool id="autogenjb2" name="autogenjb2" version="2.10.2_0" profile="22.05">
+    <description>Track collection to JBrowse2</description>
     <macros>
         <import>macros.xml</import>
     </macros>
@@ -11,20 +11,35 @@
     <version_command>python '${__tool_directory__}/autogenJB2.py' --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
 python '$__tool_directory__/autogenJB2.py'
-#for $key in $jbrowseme.keys():
---collection '$key,$jbrowseme[$key],$jbrowseme[$key].ext'
+#for $key in $autoCollection.keys():
+    #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[$key].metadata.cram_index'
+    #end if
 #end for
---sessName "Autogen JBrowse"
+--outdir '$output.files_path'
+--sessName "Autogen JBrowse" &&
+
+  cp '$output.files_path/index.html' '$output'
+
+## Ugly testing hack since I cannot get <extra_files> to test the files I want to test. Hmph.
+
+
   ]]></command>
     <inputs>
         <param
-                    label="Collection of files specially named to become tracks"
-                    name="jbrowseme"
+                    label="Collection of files to become tracks - they must have short, informative names"
+                    name="autoCollection"
                     type="data_collection">
         </param>
     </inputs>
     <outputs>
-        <data format="html" name="output" label="JBrowse2"/>
+        <data format="html" name="output" label="AutoJBrowse2"/>
     </outputs>
 
     <help><![CDATA[
diff -r 2893ef33fba9 -r 15da358c3108 jbrowse2.py
--- a/jbrowse2.py	Sun Feb 25 04:18:53 2024 +0000
+++ b/jbrowse2.py	Wed Feb 28 10:08:57 2024 +0000
@@ -1062,59 +1062,6 @@
         self.tracksToAdd.append(trackDict)
         self.trackIdlist.append(tId)
 
-    def add_hicab(self, data, trackData, hicOpts, **kwargs):
-        rel_dest = os.path.join("data", trackData["label"] + ".hic")
-        dest = os.path.join(self.outdir, rel_dest)
-
-        self.symlink_or_copy(os.path.realpath(data), dest)
-
-        self._add_track(
-            trackData["label"],
-            trackData["key"],
-            trackData["category"],
-            rel_dest,
-            config={},
-        )
-
-    def add_sparql(self, url, query, query_refnames, trackData):
-
-        json_track_data = {
-            "type": "FeatureTrack",
-            "trackId": id,
-            "name": trackData["label"],
-            "adapter": {
-                "type": "SPARQLAdapter",
-                "endpoint": {"uri": url, "locationType": "UriLocation"},
-                "queryTemplate": query,
-            },
-            "category": [trackData["category"]],
-            "assemblyNames": [self.genome_name],
-        }
-
-        if query_refnames:
-            json_track_data["adapter"]["refNamesQueryTemplate"]: query_refnames
-
-        self.subprocess_check_call(
-            [
-                "jbrowse",
-                "add-track-json",
-                "--target",
-                os.path.join(self.outdir, "data"),
-                json_track_data,
-            ]
-        )
-
-        # Doesn't work as of 1.6.4, might work in the future
-        # self.subprocess_check_call([
-        #     'jbrowse', 'add-track',
-        #     '--trackType', 'sparql',
-        #     '--name', trackData['label'],
-        #     '--category', trackData['category'],
-        #     '--target', os.path.join(self.outdir, 'data'),
-        #     '--trackId', id,
-        #     '--config', '{"queryTemplate": "%s"}' % query,
-        #     url])
-
     def process_annotations(self, track):
         category = track["category"].replace("__pd__date__pd__", TODAY)
         for i, (
@@ -1190,7 +1137,7 @@
                     outputTrackConfig,
                 )
             elif dataset_ext == "bam":
-                real_indexes = track["conf"]["options"]["pileup"]["bam_indices"][
+                real_indexes = track["conf"]["options"]["bam"]["bam_indices"][
                     "bam_index"
                 ]
                 if not isinstance(real_indexes, list):
@@ -1199,7 +1146,7 @@
                 self.add_bam(
                     dataset_path,
                     outputTrackConfig,
-                    track["conf"]["options"]["pileup"],
+                    track["conf"]["options"]["bam"],
                     bam_index=real_indexes[i],
                 )
             elif dataset_ext == "cram":
@@ -1475,16 +1422,6 @@
                                 metadata,
                             )
                         )
-        else:
-            # For tracks without files (rest, sparql)
-            track_conf["trackfiles"].append(
-                (
-                    "",  # N/A, no path for rest or sparql
-                    track.attrib["format"],
-                    track.find("options/label").text,
-                    {},
-                )
-            )
 
         if is_multi_bigwig:
             metadata = metadata_from_node(x.find("metadata"))
diff -r 2893ef33fba9 -r 15da358c3108 jbrowse2.xml
--- 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="&#10;" target=" " />
-                                <add source="&gt;" target="__gt__" />
-                                <add source="&lt;" target="__lt__" />
-                                </mapping>
-                                <valid initial="default">
-                                <add value="|" />
-                                <add value="#" />
-                                <add value="{"/>
-                                <add value="}"/>
-                                <add value="!"/>
-                                <add value="?"/>
-                                <add value="&amp;"/>
-                                <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="&#10;" target=" " />
-                                <add source="&gt;" target="__gt__" />
-                                <add source="&lt;" target="__lt__" />
-                                </mapping>
-                                <valid initial="default">
-                                <add value="|" />
-                                <add value="#" />
-                                <add value="{"/>
-                                <add value="}"/>
-                                <add value="!"/>
-                                <add value="?"/>
-                                <add value="&amp;"/>
-                                <add value="+"/>
-                                <add value="="/>
-                                <add value="'"/>
-                                <add value='"'/>
-                                </valid>
-                            </sanitizer>
-                        </param>
-                        <expand macro="track_visibility" />
-                    </when>
                 </conditional>
             </repeat>
         </repeat>
diff -r 2893ef33fba9 -r 15da358c3108 macros.xml
--- a/macros.xml	Sun Feb 25 04:18:53 2024 +0000
+++ b/macros.xml	Wed Feb 28 10:08:57 2024 +0000
@@ -505,7 +505,7 @@
     </xml>
 
     <xml name="input_conditional" token_label="Track Data" token_format="data">
-        <param label="@LABEL@" format="@FORMAT@" name="annotation" type="data" multiple="False"/>
+        <param label="@LABEL@" format="@FORMAT@" name="annotation" type="data" multiple="True"/>
     </xml>
     <xml name="citations">
         <citations>