add back tests + udpate todo

tools/jbrowse2/jbrowse2.xml

@@ -368,9 +368,14 @@ cp $output.files_path/index.html $output;
                 type="data" />
             </when>
         </conditional>
-        <!-- TODO auto add GC track when implemented https://github.com/GMOD/jbrowse-components/pull/2683-->
+        <!-- TODO auto add GC track when implemented
+             https://github.com/GMOD/jbrowse-components/pull/2683
+             https://github.com/GMOD/jbrowse-components/pull/3328
+        -->
 
-        <!-- TODO genetic code not yet supported in jbrowse2 https://github.com/GMOD/jbrowse-components/issues/1765 -->
+        <!-- TODO genetic code not yet supported in jbrowse2
+             https://github.com/GMOD/jbrowse-components/issues/1765
+        -->
 
         <conditional name="action">
             <param type="select" label="JBrowse-in-Galaxy Action" name="action_select">
@@ -616,7 +621,7 @@ cp $output.files_path/index.html $output;
                 </assert_contents>
             </output>
         </test>
-        <!--test>
+        <test>
             <param name="reference_genome|genome_type_select" value="history"/>
             <param name="reference_genome|genome" value="merlin.fa"/>
             <repeat name="track_groups">
@@ -641,8 +646,8 @@ cp $output.files_path/index.html $output;
                     <has_text text="NeatHTMLFeatures"></has_text>
                 </assert_contents>
             </output>
-        </test-->
-        <!--test>
+        </test>
+        <test>
             <param name="reference_genome|genome_type_select" value="history"/>
             <param name="reference_genome|genome" value="merlin.fa"/>
             <repeat name="track_groups">
@@ -846,8 +851,8 @@ cp $output.files_path/index.html $output;
                         <has_text text="2.gff"/>
                 </assert_contents>
             </output>
-        </test-->
-        <!--test>
+        </test>
+        <test>
             <param name="reference_genome|genome_type_select" value="history"/>
             <param name="reference_genome|genome" value="merlin.fa"/>
 
@@ -914,8 +919,8 @@ cp $output.files_path/index.html $output;
                     <has_text text="dijitIconNewTask"/>
                 </assert_contents>
             </output>
-        </test-->
-        <!--test>
+        </test>
+        <test>
             <param name="reference_genome|genome_type_select" value="history"/>
             <param name="reference_genome|genome" value="merlin.fa"/>
 
@@ -956,8 +961,8 @@ cp $output.files_path/index.html $output;
                     <has_text text="&lt;subParts&gt;exon&lt;/subParts&gt;"></has_text>
                 </assert_contents>
             </output>
-        </test-->
-        <!--test>
+        </test>
+        <test>
             <param name="reference_genome|genome_type_select" value="history"/>
             <param name="reference_genome|genome" value="merlin.fa"/>
 
@@ -1014,8 +1019,8 @@ cp $output.files_path/index.html $output;
                     <has_text text="style.strandArrow"/>
                 </assert_contents>
             </output>
-        </test-->
-        <!--test>
+        </test>
+        <test>
             <param name="reference_genome|genome_type_select" value="history"/>
             <param name="reference_genome|genome" value="merlin.fa"/>
 
@@ -1037,19 +1042,18 @@ cp $output.files_path/index.html $output;
                     <has_text text="bam_index"/>
                 </assert_contents>
             </output>
-        </test-->
-
-        <!--test-->
+        </test>
+        <test>
             <!-- data_table -->
-            <!--param name="reference_genome|genome_type_select" value="indexed"/>
+            <param name="reference_genome|genome_type_select" value="indexed"/>
             <param name="reference_genome|genome" value="merlin"/>
             <param name="uglyTestingHack" value="enabled" />
             <output name="output">
                 <assert_contents>
                     <has_text text="merlin.fa"/>
                 </assert_contents>
             </output>
-        </test-->
+        </test>
         <!-- TODO add a synteny test -->
         <!-- TODO add a cram test -->
         <!-- TODO add an hic test -->