# HG changeset patch
# User iuc
# Date 1743763069 0
# Node ID 5e03d09d5fdca675847b42d5af14965f3806b974
# Parent  98163e8ed4586dd226f9254854c29d5c646c7bea
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 2d69e621036bf155e02189d4a9a8aa9ee24536e0

diff -r 98163e8ed458 -r 5e03d09d5fdc arriba.xml
--- a/arriba.xml	Wed Sep 25 15:29:26 2024 +0000
+++ b/arriba.xml	Fri Apr 04 10:37:49 2025 +0000
@@ -507,7 +507,7 @@
 
 **INPUTS**
 
-See:  https://arriba.readthedocs.io/en/latest/input-files/
+See:  https://github.com/suhrig/arriba/wiki/04-Input-files
 
   - Alignments
 
@@ -672,14 +672,14 @@
 
 **OPTIONS**
 
-  - Arriba: https://arriba.readthedocs.io/en/latest/command-line-options/#arriba
-  - Visualization: https://arriba.readthedocs.io/en/latest/command-line-options/#draw_fusionsr
-  - RNA STAR: https://arriba.readthedocs.io/en/latest/workflow/
+  - Arriba: https://github.com/suhrig/arriba/wiki/07-Command-line-options#arriba
+  - Visualization: https://github.com/suhrig/arriba/wiki/07-Command-line-options#draw_fusionsr
+  - RNA STAR: https://github.com/suhrig/arriba/wiki/03-Workflow
 
 
 **OUTPUTS**
 
-See:  https://arriba.readthedocs.io/en/latest/output-files/
+See: https://github.com/suhrig/arriba/wiki/05-Output-files
 
   - fusions.tsv
 
@@ -732,7 +732,7 @@
 
 **VISUALIZATION**
 
-See: https://arriba.readthedocs.io/en/latest/visualization/
+See: https://github.com/suhrig/arriba/wiki/06-Visualization
 
   - fusions.pdf
 
@@ -743,11 +743,11 @@
   :height: 467
 
 
-.. _Arriba: https://arriba.readthedocs.io/en/latest/
-.. _INPUTS: https://arriba.readthedocs.io/en/latest/input-files/
-.. _OUTPUTS: https://arriba.readthedocs.io/en/latest/output-files/
-.. _VISUALIZATION: https://arriba.readthedocs.io/en/latest/visualization/
-.. _OPTIONS: https://arriba.readthedocs.io/en/latest/command-line-options/
+.. _Arriba: https://github.com/suhrig/arriba/wiki/01-Home
+.. _INPUTS: https://github.com/suhrig/arriba/wiki/04-Input-files
+.. _OUTPUTS: https://github.com/suhrig/arriba/wiki/05-Output-files
+.. _VISUALIZATION: https://github.com/suhrig/arriba/wiki/06-Visualization
+.. _OPTIONS: https://github.com/suhrig/arriba/wiki/07-Command-line-options
 
     ]]></help>
     <expand macro="citations" />
diff -r 98163e8ed458 -r 5e03d09d5fdc macros.xml
--- a/macros.xml	Wed Sep 25 15:29:26 2024 +0000
+++ b/macros.xml	Fri Apr 04 10:37:49 2025 +0000
@@ -1,6 +1,6 @@
 <macros>
-    <token name="@TOOL_VERSION@">2.4.0</token>
-    <token name="@VERSION_SUFFIX@">2</token>
+    <token name="@TOOL_VERSION@">2.5.0</token>
+    <token name="@VERSION_SUFFIX@">0</token>
     <xml name="requirements">
         <requirements>
         <requirement type="package" version="@TOOL_VERSION@">arriba</requirement>
@@ -238,6 +238,7 @@
                         </help>
                         <validator type="regex" message="">^\d+(,\d+)?$</validator>
                     </param>
+                    <param argument="--plotPanels" type="boolean" label="Plot panels" truevalue="TRUE" falsevalue="FALSE" help="The output will contain a panel for each fusion partner"/>
                 </section>
     </xml>
     <token name="@DRAW_FUSIONS@">
@@ -301,5 +302,8 @@
     #if str($visualization.options.fontSize)
         --fontSize=$visualization.options.fontSize
     #end if
+    #if $visualization.options.plotPanels
+        --plotPanels=$visualization.options.plotPanels
+    #end if
 </token>
 </macros>