diff macros.xml @ 8:ad4b9d7eae6a draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9

--- a/macros.xml	Sun Jun 26 10:50:15 2016 -0400
+++ b/macros.xml	Tue Nov 29 10:55:30 2016 -0500
@@ -2,10 +2,8 @@
 <macros>
   <xml name="requirements">
     <requirements>
-      <requirement type="package" version="1.12.0">jbrowse</requirement>
-      <requirement type="package" version="1.12.0">bundle_jbrowse</requirement>
+      <requirement type="package" version="1.12.1">jbrowse</requirement>
       <requirement type="package" version="2.7">python</requirement>
-      <requirement type="package" version="5.18.1">perl</requirement>
       <requirement type="package" version="1.66">biopython</requirement>
       <requirement type="package" version="0.6.2">bcbiogff</requirement>
       <requirement type="package" version="1.2">samtools</requirement>
@@ -13,7 +11,8 @@
       <yield/>
     </requirements>
   </xml>
-  <token name="@WRAPPER_VERSION@">1.0</token>
+  <token name="@DATA_DIR@">\$GALAXY_JBROWSE_SHARED_DIR</token>
+  <token name="@WRAPPER_VERSION@">0.5.1</token>
   <xml name="stdio">
     <stdio>
       <exit_code range="1:"/>
@@ -28,43 +27,6 @@
 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"
@@ -218,7 +180,7 @@
             <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" selected=""                     >Logarithmic scaling</option>
+              <option value="logarithmic">Logarithmic scaling</option>
               <option value="blast"       selected="@SCALING_LOG_SELECT@" >Blast scaling</option>
             </param>
 
@@ -257,8 +219,8 @@
   </xml>
   <xml name="track_styling"
        token_classname="feature"
-       token_label="prodcut,name,id"
-       token_description="note"
+       token_label="name,id"
+       token_description="note,description"
        token_height="100px">
     <section name="jbstyle" title="JBrowse Styling Options [Advanced]" expanded="false">
         <param label="JBrowse style.className" type="text"
@@ -283,7 +245,99 @@
     </section>
   </xml>
 
+  <xml name="track_menu">
+    <section name="jbmenu" title="JBrowse Contextual Menu options [Advanced]" expanded="false">
+      <repeat name="track_menu" title="Track Menu">
+          <param label="Menu action"
+                 type="select"
+                 name="menu_action"
+                 help="Action performed when user clicks on the menu">
+            <option value="iframeDialog" selected="true">iframeDialog: causes the given url to be opened in a popup dialog box within JBrowse, in an iframe element.</option>
+            <option value="newWindow">newWindow: causes the given url to be opened in a new browser window.</option>
+            <option value="navigateTo">navigateTo: opens the given url in the same browser window, navigating the user away from JBrowse.</option>
+          </param>
+          <param label="Menu label"
+                 type="text"
+                 name="menu_label"
+                 help="Will be displayed in the contextual menu on each feature ({name}, {id}, {type}, {start}, {end}, {strand} variables will be interpreted)">
+           <expand macro="menu_sanitize" />
+          </param>
+          <param label="Menu title"
+                 type="text"
+                 name="menu_title"
+                 help="Will be displayed in the popup title bar if displayed ({name}, {id}, {type}, {start}, {end}, {strand} variables will be interpreted)">
+           <expand macro="menu_sanitize" />
+          </param>
+          <param label="Menu url"
+                 type="text"
+                 name="menu_url"
+                 help="Destination URL ({name}, {id}, {type}, {start}, {end}, {strand} variables will be interpreted)">
+           <expand macro="menu_sanitize" />
+          </param>
+          <param label="Menu icon"
+                 type="select"
+                 name="menu_icon"
+                 help="Icon to display next to menu label">
+            <option value="dijitIconBookmark" selected="true">Bookmark</option>
+            <option value="dijitIconSave">Save</option>
+            <option value="dijitIconPrint">Print</option>
+            <option value="dijitIconCut">Cut</option>
+            <option value="dijitIconCopy">Copy</option>
+            <option value="dijitIconClear">Clear</option>
+            <option value="dijitIconDelete">Delete</option>
+            <option value="dijitIconUndo">Undo</option>
+            <option value="dijitIconEdit">Edit</option>
+            <option value="dijitIconNewTask">New Task</option>
+            <option value="dijitIconEditTask">Edit Task</option>
+            <option value="dijitIconEditProperty">Edit Property</option>
+            <option value="dijitIconTask">Task</option>
+            <option value="dijitIconFilter">Filter</option>
+            <option value="dijitIconConfigure">Configure</option>
+            <option value="dijitIconSearch">Search</option>
+            <option value="dijitIconApplication">Application</option>
+            <option value="dijitIconChart">Chart</option>
+            <option value="dijitIconConnector">Connector</option>
+            <option value="dijitIconDatabase">Database</option>
+            <option value="dijitIconDocuments">Documents</option>
+            <option value="dijitIconMail">Mail</option>
+            <option value="dijitLeaf">Leaf</option>
+            <option value="dijitIconFile">File</option>
+            <option value="dijitIconFunction">Function</option>
+            <option value="dijitIconKey">Key</option>
+            <option value="dijitIconPackage">Package</option>
+            <option value="dijitIconSample">Sample</option>
+            <option value="dijitIconTable">Table</option>
+            <option value="dijitIconUsers">Users</option>
+            <option value="dijitIconFolderClosed">Folder Closed</option>
+            <option value="dijitIconFolderOpen">Folder Open</option>
+            <option value="dijitIconError">Error</option>
+          </param>
+      </repeat>
+    </section>
+  </xml>
+
+  <xml name="menu_sanitize">
+    <sanitizer>
+        <valid>
+            <add value="{"/>
+            <add value="}"/>
+            <add value="!"/>
+            <add value="?"/>
+            <add value="&amp;"/>
+            <add value="+"/>
+            <add value="="/>
+            <add value="'"/>
+            <add value='"'/>
+        </valid>
+    </sanitizer>
+  </xml>
+
   <xml name="input_conditional" token_label="Track Data" token_format="data">
       <param label="@LABEL@" format="@FORMAT@" name="annotation" type="data" multiple="True"/>
   </xml>
+  <xml name="citations">
+    <citations>
+      <citation type="doi">10.1101/gr.094607.109</citation>
+    </citations>
+  </xml>
 </macros>