diff macros.xml @ 9:1455d3e7f191 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 02d7c1a0439315c2868c0e66d74fd567e89cca02

--- a/macros.xml	Fri Oct 17 16:22:03 2025 +0000
+++ b/macros.xml	Fri Jan 16 09:34:00 2026 +0000
@@ -1,7 +1,8 @@
 <macros>
     <import>msfragger_macros.xml</import>
     <token name="@TOOL_VERSION@">23.0</token>
-    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@VERSION_SUFFIX@">1</token>
+    <token name="@TOOL_PROFILE@">25.1</token>
 
     <!--
         These keys were generated ONLY for use by the Galaxy tool wrapper, and only after
@@ -15,6 +16,19 @@
             <requirement type="package" version="@TOOL_VERSION@">fragpipe</requirement>
         </requirements>
     </xml>
+    <xml name="required_files">
+        <required_files>
+            <include path="generate_workflow.py"/>
+            <include path="genericize_db.py"/>
+            <include path="workflows/Basic-Search.workflow"/>
+            <include path="workflows/DIA_SpecLib_Quant.workflow"/>
+            <include path="workflows/LFQ-MBR.workflow"/>
+            <include path="workflows/Nonspecific-HLA.workflow"/>
+            <include path="workflows/Open.workflow"/>
+            <include path="workflows/TMT10.workflow"/>
+            <include path="workflows/TMT11.workflow"/>
+        </required_files>
+    </xml>
 
     <!-- TMT-n uses the following n first labels from TMT-18 -->
     <token name="@TMT_LABELS@">['126', '127N', '127C', '128N', '128C', '129N', '129C', '130N', '130C', '131N', '131C', '132N', '132C', '133N', '133C', '134N', '134C', '135N']</token>
@@ -347,21 +361,7 @@
     <xml name="workflow_configfile">
         <configfile name="workflow_configfile"><![CDATA[#slurp
             ## Create a fragpipe params dictionary from a file
-            #set $comments = []
             #set $wfdict = {}
-            #set $wfpath = $__tool_directory__ + '/workflows/' + str($wf.workflow_name) + '.workflow'
-            #set $fh = open($wfpath, 'r')
-            #for $line in $fh:
-                #if $line.startswith('#')
-                    #silent $comments.append($line)
-                #elif $line.strip() != ''
-                    #set $kv = $line.strip().split('=')
-                    #if len($kv) < 2
-                        #silent $kv.append('')
-                    #end if
-                    #set $wfdict[$kv[0]] = '='.join($kv[1:])
-                #end if
-            #end for
 
             #set $wfdict['database.db-path'] = 'final_db.fas'
             #set $wfdict['msfragger.misc.slice-db'] = $num_slices
@@ -436,11 +436,6 @@
                 #set $wfdict["ptmshepherd.use_msfragger_localization"] = "true"
             #end if
 
-            ## Populate the workflow with configuration and comment dictionary entries populated by tool params.
-            #for $comment in $comments
-$comment
-            #end for
-
             #for $k in sorted($wfdict.keys())
               #set $kv = $k + '=' + str($wfdict[$k])
 $kv