diff picard_ReplaceSamHeader.xml @ 8:e417b1d6288d draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e

--- a/picard_ReplaceSamHeader.xml	Sun Nov 27 15:11:36 2016 -0500
+++ b/picard_ReplaceSamHeader.xml	Tue Dec 06 10:04:26 2016 -0500
@@ -6,32 +6,32 @@
   <expand macro="requirements" />
   <command detect_errors="exit_code"><![CDATA[
     @java_options@
-    
-  
-    ## Two lines below are due to the fact that picard likes fasta files to have extension .fa  
+    @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}" "${fasta_file}" &&    
-    
+    ln -s "${inputFile}" "${fasta_file}" &&
+
     picard
     ReplaceSamHeader
-    
-    INPUT="${inputFile}"
+
+    INPUT='$inputFile.element_identifier'
     HEADER="${header}"
     OUTPUT="${outFile}"
-    
+
     QUIET=true
     VERBOSITY=ERROR
-  
+
   ]]></command>
   <inputs>
     <param format="sam,bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection (header recepient dataset)" help="If empty, upload or import a SAM/BAM dataset"/>
     <param name="header" type="data" format="sam,bam" label="SAM/BAM dataset from which Header will be read (header source dataset)" help="HEADER; If empty, upload or import a SAM/BAM dataset"/>
-  </inputs> 
-  
+  </inputs>
+
   <outputs>
     <data format="bam" name="outFile" label="${tool.name} on ${on_string}: BAM file with replaced header"/>
   </outputs>
-  
+
   <tests>
     <test>
       <param name="inputFile" value="picard_ReplaceSamHeader.bam" ftype="bam"/>
@@ -39,8 +39,8 @@
       <output name="outFile" file="picard_ReplaceSamHeader_test1.bam" ftype="bam"/>
     </test>
   </tests>
-  
-  
+
+
   <help>
 
 **Purpose**
@@ -50,7 +50,7 @@
 
 @description@
 
-  HEADER=File                   SAM file from which SAMFileHeader will be read.  Required. 
+  HEADER=File                   SAM file from which SAMFileHeader will be read.  Required.
 
 @more_info@