Mercurial > repos > iuc > bamtools_split_ref

changeset 5:f66e109710bd draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split commit 7d29261847d2514a1ac4246e0b8bff1d32463434
author iuc
date Wed, 11 Feb 2026 14:31:36 +0000
parents 9b8feb118f9e
children
files bamtools_split_ref.xml macros.xml
diffstat 2 files changed, 8 insertions(+), 9 deletions(-) [+]
line wrap: on
line diff
--- a/bamtools_split_ref.xml	Fri Mar 15 13:49:30 2024 +0000
+++ b/bamtools_split_ref.xml	Wed Feb 11 14:31:36 2026 +0000
@@ -1,12 +1,10 @@
-<tool id="bamtools_split_ref" name="Split BAM by reference" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.09">
+<tool id="bamtools_split_ref" name="Split BAM by reference" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>into a dataset list collection</description>
     <macros>
           <import>macros.xml</import>
     </macros>
     <expand macro="xrefs"/>
-    <expand macro="requirements">
-        <requirement type="package" version="1.16.1">samtools</requirement>
-    </expand>
+    <expand macro="requirements"/>
     <command><![CDATA[
         ln -s '${input_bam}' localbam.bam &&
         ln -s '${input_bam.metadata.bam_index}' 'localbam.bam.bai' &&
@@ -35,7 +33,7 @@
 </environment_variable>
     </environment_variables>
     <configfiles>
-        <configfile name="c1">#import re
+        <configfile name="c1"><![CDATA[#import re		
 ## need to extract ref names from Galaxy's safe string representation
 #set $ref_list = [$re.sub('^.*__sq__(.+)__sq__.*$','\\1',n) if n.find('__sq__') >= 0 else n for n in str($input_bam.metadata.reference_names).split(',')]
 #if str($refs) != 'None'
@@ -44,7 +42,7 @@
 #end if
 #set $elems = [{'name': '%s: %s' % ($input_bam.name, r), 'filename': 'split_bam.REF_%s.bam' % r, 'dbkey': str($input_bam.dbkey)} for r in $ref_list]
 #import json
-#echo json.dumps({'output_bams': {'elements': $elems}})</configfile>
+#echo json.dumps({'output_bams': {'elements': $elems}})]]></configfile>
     </configfiles>
     <inputs>
         <param name="input_bam" type="data" format="bam" label="BAM dataset to split by reference"/>
--- a/macros.xml	Fri Mar 15 13:49:30 2024 +0000
+++ b/macros.xml	Wed Feb 11 14:31:36 2026 +0000
@@ -1,7 +1,8 @@
 <?xml version="1.0"?>
 <macros>
-    <token name="@TOOL_VERSION@">2.5.2</token>
-    <token name="@VERSION_SUFFIX@">2</token>
+    <token name="@TOOL_VERSION@">2.5.3</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@PROFILE@">24.2</token>
     <xml name="xrefs">
         <xrefs>
             <xref type="bio.tools">bamtools</xref>
@@ -10,7 +11,7 @@
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">bamtools</requirement>
-            <yield />
+            <requirement type="package" version="1.23">samtools</requirement>
         </requirements>
     </xml>
     <xml name="citations">