# HG changeset patch
# User galaxyp
# Date 1770042529 0
# Node ID 42ad5460c1d4e46f0a54cf5564907d500884f461
# Parent  387754f0746e4d337ce431cb4ea58db4b413e74c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit bfeb0ecfd49120e3c45c403690c0f8b534513591

diff -r 387754f0746e -r 42ad5460c1d4 fragpipe.xml
--- a/fragpipe.xml	Wed Jan 21 22:25:42 2026 +0000
+++ b/fragpipe.xml	Mon Feb 02 14:28:49 2026 +0000
@@ -43,7 +43,7 @@
             ln -s \${env_location}/share/msfragger-*/MSFragger-*/ext tools/ &&
 
             ## Run FragPipe
-            '$__tool_directory__/fragpipe'
+            bash '$__tool_directory__/fragpipe'
                 --msfragger_key @MSFRAGGER_ACADEMIC_USE_KEY@
                 --ionquant_key @IONQUANT_ACADEMIC_USE_KEY@
                 --diatracer_key @DIATRACER_ACADEMIC_USE_KEY@
diff -r 387754f0746e -r 42ad5460c1d4 macros.xml
--- a/macros.xml	Wed Jan 21 22:25:42 2026 +0000
+++ b/macros.xml	Mon Feb 02 14:28:49 2026 +0000
@@ -1,7 +1,7 @@
 <macros>
     <import>msfragger_macros.xml</import>
     <token name="@TOOL_VERSION@">23.0</token>
-    <token name="@VERSION_SUFFIX@">2</token>
+    <token name="@VERSION_SUFFIX@">3</token>
     <token name="@TOOL_PROFILE@">25.1</token>
 
     <!--
@@ -18,6 +18,7 @@
     </xml>
     <xml name="required_files">
         <required_files>
+            <include path="fragpipe"/>
             <include path="generate_workflow.py"/>
             <include path="genericize_db.py"/>
             <include path="workflows/Basic-Search.workflow"/>