be prepared for other synteny formats

bebatut · Jan 9, 2024 · e6ebb03 · e6ebb03
1 parent d5ee761
commit e6ebb03
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Showing 2 changed files with 8 additions and 7 deletions.
diff --git a/tools/jbrowse2/jbrowse2.py b/tools/jbrowse2/jbrowse2.py
@@ -759,9 +759,9 @@ def process_annotations(self, track):
                 self.add_vcf(dataset_path, outputTrackConfig, zipped=True)
             elif dataset_ext == 'rest':
                 self.add_rest(track['conf']['options']['rest']['url'], outputTrackConfig)
-            elif dataset_ext == 'paf':
+            elif dataset_ext == 'synteny':
                 self.add_paf(dataset_path, outputTrackConfig,
-                             track['conf']['options']['paf'])
+                             track['conf']['options']['synteny'])
             elif dataset_ext == 'hic':
                 self.add_hic(dataset_path, outputTrackConfig,
                              track['conf']['options']['hic'])

diff --git a/tools/jbrowse2/jbrowse2.xml b/tools/jbrowse2/jbrowse2.xml
@@ -317,11 +317,11 @@ cp $output.files_path/index.html $output;
                   #end if
                     <index>${track.data_format.index}</index>
                 </gff>
-            #else if str($track.data_format.data_format_select) == "paf":
-                <paf>
+            #else if str($track.data_format.data_format_select) == "synteny":
+                <synteny>
                     <genome>${track.data_format.synteny_genome}</genome>
                     <genome_label>${track.data_format.synteny_genome.element_identifier}</genome_label>
-                </paf>
+                </synteny>
             #else if str($track.data_format.data_format_select) == "hic":
                 <hic>
                 </hic>
@@ -398,7 +398,7 @@ cp $output.files_path/index.html $output;
                 <option value="blast">Blast XML</option>
                 <option value="wiggle">BigWig XY</option>
                 <option value="vcf">VCF SNPs</option>
-                <option value="paf">Synteny</option>
+                <option value="synteny">Synteny</option>
                 <option value="hic">HiC</option>
                 <option value="sparql">SPARQL</option>
             </param>
@@ -524,11 +524,12 @@ cp $output.files_path/index.html $output;
                 <expand macro="track_visibility" />
             </when>
 
-            <when value="paf">
+            <when value="synteny">
                 <param label="Other genome sequence"
                        format="fasta"
                        name="synteny_genome"
                        type="data" />
+                <!-- TODO add .out (MashMap) .chain (UCSC), .delta (mummer) and .anchors (mcscan) inputs -->
                 <expand macro="input_conditional" label="Synteny data" format="paf" />
                 <expand macro="track_visibility" />
             </when>