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changeset 11:42ad5460c1d4 draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit bfeb0ecfd49120e3c45c403690c0f8b534513591
author galaxyp
date Mon, 02 Feb 2026 14:28:49 +0000
parents 387754f0746e
children
files fragpipe.xml macros.xml
diffstat 2 files changed, 3 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- 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@
--- 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"/>