clustal as input format

galaxyproject · Oct 15, 2014 · d771be1 · d771be1
1 parent 845e928
commit d771be1
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Showing 2 changed files with 19 additions and 2 deletions.
diff --git a/visualizations/biojs-msa/config/biojs-msa.xml b/visualizations/biojs-msa/config/biojs-msa.xml
@@ -7,6 +7,11 @@
             <test type="isinstance" test_attr="datatype" result_type="datatype">sequence.Fasta</test>
             <to_param param_attr="id">dataset_id</to_param>
         </data_source>
+         <data_source>
+            <model_class>HistoryDatasetAssociation</model_class>
+            <test type="isinstance" test_attr="datatype" result_type="datatype">sequences</test>
+            <to_param param_attr="id">dataset_id</to_param>
+        </data_source>
     </data_sources>
     <params>
         <param type="dataset" var_name_in_template="hda" required="true">dataset_id</param>

diff --git a/visualizations/biojs-msa/templates/biojs-msa.mako b/visualizations/biojs-msa/templates/biojs-msa.mako
@@ -32,19 +32,31 @@ ${h.javascript_link( root + 'plugins/visualizations/biojs-msa/static/msa.min.js'
 
 <script type="text/javascript">
     var config  = ${h.dumps( config )};
+    var hdaJson = ${h.dumps( trans.security.encode_dict_ids( hda.to_dict() ), indent=2 )};
+
+    var title   = "${title or default_title}";
     var url = "/api/datasets/"+config.dataset_id+"?data_type=raw_data&provider=base";
 	var xhr = require("nets");
 	xhr(url, function(err, response,text){
 		var data = JSON.parse(text).data;
-		var seqs = require("biojs-io-fasta").parse.parse(data);
+
+        if(hdaJson.data_type == "galaxy.datatypes.sequence.Fasta"){
+		  var seqs = require("biojs-io-fasta").parse.parse(data);
+        }else{
+          // it could be clustal
+          var seqs = require("biojs-io-clustal").parse(data); 
+        }
 
         var msa = require("biojs-vis-msa");
         
-        // msa opts
         var opts = {};
+        
         opts.el = document.getElementById('msa_menu');
         opts.seqs = seqs;
+        
+        //opts.zoomer = { textVisible: false};
         opts.vis = {overviewbox: true};
+        //opts.columns = {hidden: [1,2,3]};
         var m = new msa.msa(opts);
         
         // the menu is independent to the MSA container