diff picard_ReplaceSamHeader.xml @ 33:3f254c5ced1d draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8

--- a/picard_ReplaceSamHeader.xml	Mon Sep 25 08:32:17 2023 +0000
+++ b/picard_ReplaceSamHeader.xml	Sun Mar 03 16:06:11 2024 +0000
@@ -1,51 +1,46 @@
-<tool name="ReplaceSamHeader" id="picard_ReplaceSamHeader" version="@TOOL_VERSION@.@WRAPPER_VERSION@">
+<tool name="ReplaceSamHeader" id="picard_ReplaceSamHeader" version="@TOOL_VERSION@.@WRAPPER_VERSION@" profile="@PROFILE@">
     <description>replace header in a SAM/BAM dataset</description>
     <macros>
         <import>picard_macros.xml</import>
-        <token name="@WRAPPER_VERSION@">1</token>
+        <token name="@WRAPPER_VERSION@">0</token>
     </macros>
     <xrefs>
         <xref type="bio.tools">picard_replacesamheader</xref>
     </xrefs>
-    <expand macro="requirements" />
+    <expand macro="requirements"/>
     <command detect_errors="exit_code"><![CDATA[
     @java_options@
     @symlink_element_identifier@
 
     ## Two lines below are due to the fact that picard likes fasta files to have extension .fa
     #set $fasta_file="local_fasta.fa"
-    ln -s "${inputFile}" "${fasta_file}" &&
+    ln -sf '${inputFile}' '${fasta_file}' &&
 
-    picard
-    ReplaceSamHeader
+    picard ReplaceSamHeader
 
-    INPUT='$escaped_element_identifier'
-    HEADER="${header}"
-    OUTPUT="${outFile}"
+    --INPUT '$escaped_element_identifier'
+    --HEADER '${header}'
+    --OUTPUT '${outFile}'
 
-    QUIET=true
-    VERBOSITY=ERROR
+    --QUIET true
+    --VERBOSITY ERROR
 
   ]]></command>
-  <inputs>
-    <param format="sam,bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection (header recepient dataset)" help="If empty, upload or import a SAM/BAM dataset"/>
-    <param name="header" type="data" format="sam,bam" label="SAM/BAM dataset from which Header will be read (header source dataset)" help="HEADER; If empty, upload or import a SAM/BAM dataset"/>
-  </inputs>
-
-  <outputs>
-    <data format="bam" name="outFile" label="${tool.name} on ${on_string}: BAM file with replaced header"/>
-  </outputs>
-
-  <tests>
-    <test>
-      <param name="inputFile" value="picard_ReplaceSamHeader.bam" ftype="bam"/>
-      <param name="header" value="picard_ReplaceSamHeader_header.bam" ftype="bam"/>
-      <output name="outFile" file="picard_ReplaceSamHeader_test1.bam" ftype="bam"/>
-    </test>
-  </tests>
-
-
-  <help>
+    <inputs>
+        <param format="sam,bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection (header recepient dataset)" help="If empty, upload or import a SAM/BAM dataset"/>
+        <param name="header" type="data" format="sam,bam" label="SAM/BAM dataset from which Header will be read (header source dataset)" help="HEADER; If empty, upload or import a SAM/BAM dataset"/>
+    </inputs>
+    <outputs>
+        <data format="bam" name="outFile" label="${tool.name} on ${on_string}: BAM file with replaced header"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="inputFile" value="picard_ReplaceSamHeader.bam" ftype="bam"/>
+            <param name="header" value="picard_ReplaceSamHeader_header.bam" ftype="bam"/>
+            <output name="outFile" file="picard_ReplaceSamHeader_test1.bam" ftype="bam"/>
+        </test>
+    </tests>
+    <help>
 
 **Purpose**
 
@@ -59,5 +54,5 @@
 @more_info@
 
   </help>
-  <expand macro="citations" />
+    <expand macro="citations"/>
 </tool>