diff macros.xml @ 46:4181e97c70a7 draft

planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a

--- a/macros.xml	Fri Mar 01 05:15:41 2024 +0000
+++ b/macros.xml	Mon Mar 04 09:47:19 2024 +0000
@@ -140,6 +140,19 @@
 
     <xml name="general_options">
         <section name="jbgen" title="General JBrowse Options [Advanced]" expanded="false">
+            <conditional name="ucol">
+                <param name="formcoll" type="select" label="Convert a collection of track files rather than filling in the tool form"
+                    help="A collection of bam/vcf and other track types will be converted into a JBrowse2 automatically">
+                    <option value="form" selected="true">Fill in the tool form to specify tracks for the output JBrowse2</option>
+                    <option value="collect">Convert a collection of suitable track files</option>
+                </param>
+                <when value="collect">
+                       <param label="Collection of bed, bam and other track files" name="autoCollection" type="data_collection" />
+                </when>
+                <when value="form">
+                </when>
+            </conditional>
+
             <param label="Create a zip archive for downloading rather than viewing " name="zipOut" help="Default is to make an interactive browser appear when the 'eye' icon is activated"
             type="boolean" checked="false" truevalue="true" falsevalue="false" />
             <param label="Subset to display to new users" type="text" name="defaultLocation" value="" help="Initial subset to be shown for users who have never visited the browser before. Example: 'ctgA:1234..5678'"/>
@@ -505,8 +518,27 @@
     </xml>
 
     <xml name="input_conditional" token_label="Track Data" token_format="data">
-        <param label="@LABEL@" format="@FORMAT@" name="annotation" optional="True" type="data" multiple="True"/>
-    </xml>
+        <conditional name="useuri">
+                <param name="insource" type="select" label="Define track data as a history file or an internet URI"
+                    help="A public URI implies that all the associated tabix files are also in place. They are created for history files">
+                    <option value="history" selected="true">Track data from a history file</option>
+                    <option value="uri" selected="true">Tabix data URI - index files must be available at corresponding URI</option>
+                </param>
+                <when value="history">
+                       <param label="@LABEL@" format="@FORMAT@" name="annotation" multiple="True" optional="true" type="data" />
+                </when>
+                <when value="uri">
+                       <param label="@LABEL@" name="annouri" multiple="false" type="text" />
+                       <param label="Short name for track display" name="annoname" type="text" >
+                             <sanitizer invalid_char="_">
+                                <valid initial="string.printable" >
+                                    <remove value="'" />
+                                </valid>
+                              </sanitizer>
+                        </param>
+                </when>
+            </conditional>
+     </xml>
     <xml name="citations">
         <citations>
         <citation type="doi">10.1186/s13059-016-0924-1</citation>