diff macros.xml @ 17:ff11d442feed draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257

--- a/macros.xml	Wed Sep 13 13:07:20 2017 -0400
+++ b/macros.xml	Wed Nov 15 15:15:27 2017 -0500
@@ -12,7 +12,7 @@
     </requirements>
   </xml>
   <token name="@DATA_DIR@">\$GALAXY_JBROWSE_SHARED_DIR</token>
-  <token name="@WRAPPER_VERSION@">0.5.3</token>
+  <token name="@WRAPPER_VERSION@">0.7.0</token>
   <xml name="stdio">
     <stdio>
       <exit_code range="1:"/>
@@ -27,6 +27,43 @@
 This Galaxy tool relies on the JBrowse, maintained by the GMOD Community. The Galaxy wrapper is developed by Eric Rasche
 ]]>
   </token>
+
+  <xml name="genome_selector"
+    token_help=""
+    token_label="Fasta sequences"
+    token_optional="False" >
+    <conditional name="reference_genome">
+        <param help="Built-in references" label="Reference genome to display" name="genome_type_select" type="select">
+            <option selected="True" value="indexed">Use a built-in genome</option>
+            <option value="history">Use a genome from history</option>
+        </param>
+        <when value="indexed">
+            <param
+              help="@HELP@"
+              label="@LABEL@"
+              name="genomes"
+              type="select"
+              optional="@OPTIONAL@"
+              >
+                <options from_data_table="all_fasta">
+                    <filter column="2" type="sort_by" />
+                    <validator message="No genomes are available for the selected input dataset" type="no_options" />
+                </options>
+            </param>
+        </when>
+        <when value="history">
+            <param
+              format="fasta"
+              label="@LABEL@"
+              help="@HELP@"
+              name="genomes"
+              type="data"
+              optional="@OPTIONAL@"
+              multiple="True" />
+        </when>
+    </conditional>
+  </xml>
+
   <xml name="auto_manual_tk"
       token_cond_label="Color"
       token_cond_name="color"
@@ -54,6 +91,14 @@
       <option value="force">Force On</option>
       <option value="always">Always On (ignores URL parameters)</option>
     </param>
+    <param type="select" label="Override Apollo Plugins" name="override_apollo_plugins" help="Disable the apollo plugin for this track, this disables the ability to make an annotation from this feature.">
+      <option value="True">Yes - Override</option>
+      <option value="False" selected="True">No - Do not Override</option>
+    </param>
+    <param type="select" label="Override Apollo Draggability" name="override_apollo_drag" help="Disable apollo's drag-to-create feature functionality.">
+      <option value="True">Yes - Override</option>
+      <option value="False" selected="True">No - Do not Override</option>
+    </param>
   </xml>
 
   <xml name="jb_color"
@@ -179,9 +224,9 @@
             <!-- Scaling -->
             <param type="select" label="JBrowse style.color function's score scaling" name="score_scaling"
                    help="How should the colors be distributed across the values? For blast results which distributes scores on the scale of approximately [1e-500, 10], it makes sense to request a logarithmic scaling of the color values. Logarithmic is indeed the default for blast. However other analysis methods may produce scores on ranges such as [0, 100] where a linear scale would be more appropriate for color distribution.">
-              <option value="linear"      selected="@SCALING_LIN_SELECT@" >Linear scaling</option>
-              <option value="logarithmic">Logarithmic scaling</option>
-              <option value="blast"       selected="@SCALING_LOG_SELECT@" >Blast scaling</option>
+              <option value="linear" selected="@SCALING_LIN_SELECT@">Linear scaling</option>
+              <option value="logarithmic" selected="false">Logarithmic scaling</option>
+              <option value="blast" selected="@SCALING_LOG_SELECT@">Blast scaling</option>
             </param>
 
             <!-- Scaling Bounds -->
@@ -219,9 +264,10 @@
   </xml>
   <xml name="track_styling"
        token_classname="feature"
-       token_label="name,id"
+       token_label="product,name,id"
        token_description="note,description"
-       token_height="100px">
+       token_height="10px"
+       token_maxheight="600">
     <section name="jbstyle" title="JBrowse Styling Options [Advanced]" expanded="false">
         <param label="JBrowse style.className" type="text"
                name="style_classname"
@@ -242,6 +288,11 @@
                name="style_height"
                value="@HEIGHT@"
                help="Height in pixels of glyphs. Default value varies from glyph to glyph. Note that the 'compact' displayMode uses style->height * 0.35 so changing style height can adjust the compact visualization."/>
+        <param label="JBrowse maxHeight"
+               type="text"
+               name="max_height"
+               value="@MAXHEIGHT@"
+               help="Maximum height that the track is permitted to reach in pixels."/>
     </section>
   </xml>