Mercurial > repos > rmarenco > hubarchivecreator

diff hubArchiveCreator.xml @ 13:25809f699cb3 draft

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 65ab931ef2b05a5acf06cbde3a746c94a0a0a4cb
author rmarenco
date Thu, 11 Aug 2016 19:02:29 -0400
parents d05236b15f81
children cbd8982c9f51
line wrap: on
line diff
--- a/hubArchiveCreator.xml	Wed Jul 27 10:43:58 2016 -0400
+++ b/hubArchiveCreator.xml	Thu Aug 11 19:02:29 2016 -0400
@@ -14,6 +14,7 @@
         <requirement type="package" version="332">ucsc-bedtobigbed</requirement>
         <requirement type="package" version="332">ucsc-fatotwobit</requirement>
         <requirement type="package" version="324">ucsc-genepredtobed</requirement>
+        <requirement type="package" version="332">ucsc-genepredtobiggenepred</requirement>
         <requirement type="package" version="324">ucsc-gff3togenepred</requirement>
         <requirement type="package" version="324">ucsc-gtftogenepred</requirement>
         <requirement type="package" version="324">ucsc-twobitinfo</requirement>
@@ -99,7 +100,13 @@
         ## Retrieve the user email
         --user_email $__user_email__
 
-        -d $__tool_directory__ -e $output.files_path -o $output;
+        -d $__tool_directory__
+
+        -e $output.files_path
+
+        $advanced_options.debug_mode
+
+        -o $output;
     ]]></command>
 
     <inputs>
@@ -184,7 +191,28 @@
                 </when>
             </conditional>
         </repeat>
-    </inputs>
+        <conditional name="advanced_options">
+            <param name="advanced_options_selector" type="select" label="Advanced options">
+                <option value="off" selected="true">Hide advanced options</option>
+                <option value="on">Display advanced options</option>
+            </param>
+            <!-- TODO: Avoid redundancy here -->
+            <when value="on">
+                <param name="debug_mode" type="boolean"
+                       label="Activate debug mode" checked="false"
+                       truevalue="--debug_mode" falsevalue="">
+                    <help>
+                        Use this option if you are a G-OnRamp developer
+                    </help>
+                </param>
+            </when>
+            <when value="off">
+                <param name="debug_mode" type="hidden"
+                       value="">
+                </param>
+            </when>
+    </conditional>
+</inputs>
 
     <outputs>
         <data format="trackhub" name="output"/>