Mercurial > repos > fubar > jbrowse2

diff macros.xml @ 85:3b2ff9864995 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty
author fubar
date Tue, 09 Apr 2024 00:26:49 +0000
parents dff27c9f6d72
children 408781c080fc
line wrap: on
line diff
--- a/macros.xml	Wed Apr 03 02:56:39 2024 +0000
+++ b/macros.xml	Tue Apr 09 00:26:49 2024 +0000
@@ -308,6 +308,18 @@
         <param label="Max height" name="max_height" type="integer" value="600" help="Maximum height that the track is permitted to reach in pixels."/>
     </xml>
 
+    <xml name="track_styling_vgp">
+         <section name="jbstyle" title="JBrowse Styling Options [Advanced]" expanded="false">
+        <param label="Show labels" name="show_labels" type="boolean" checked="false" truevalue="true" falsevalue="false" />
+        <param label="Show descriptions" name="show_descriptions" type="boolean" checked="false" truevalue="true" falsevalue="false" />
+        <param name="display" type="select" label="Display style" help="How the track will be displayed by default">
+            <option value="LinearBasicDisplay" selected="true">LinearBasicDisplay</option>
+            <option value="LinearPileupDisplay">LinearPileupDisplay - good for dense tracks at scale</option>
+            <option value="LinearArcDisplay">LinearArcDisplay</option>
+        </param>
+        </section>
+    </xml>
+
     <xml name="track_styling_feature">
         <section name="jbstyle" title="JBrowse Styling Options [Advanced]" expanded="false">
         <conditional name="track_style">
@@ -555,20 +567,11 @@
                     <option value="uri">PAF reference comparison genome tabix .gz URI with index files at the corresponding URIs</option>
                 </param>
                 <when value="history">
-                    <repeat name="refgenomes" title="PAF reference comparison genome used to make the PAF" min="1">
-                       <param label="@LABEL@" format="@FORMAT@" name="annotation" multiple="True" optional="true" type="data" />
-                       <param label="Please provide a short name for track display" name="annoname" type="text"
-                       help="Short names take less track space. No spaces allowed here">
-                             <sanitizer invalid_char="_">
-                                <valid initial="string.printable" >
-                                    <remove value=" " />
-                                </valid>
-                              </sanitizer>
-                        </param>
-                    </repeat>
+                       <param label="@LABEL@" format="@FORMAT@" name="annotation"  type="data"
+                          help="Add all PAF reference comparison genomes used to make the PAF" multiple="true" />
                 </when>
                 <when value="uri">
-                    <repeat name="refgenomes" title="PAF reference comparison genome URI" min="1">
+                    <repeat name="refuri" title="PAF reference comparison genome URI" min="1">
                        <param label="@LABEL@" name="annotation"  type="text" />
                        <param label="Short name for this reference" name="annoname" type="text" help="Short names take less track space">
                              <sanitizer invalid_char="_">