diff picard_CollectWgsMetrics.xml @ 13:7e6fd3d0f16e draft

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

--- a/picard_CollectWgsMetrics.xml	Sun Nov 27 15:11:50 2016 -0500
+++ b/picard_CollectWgsMetrics.xml	Tue Dec 06 10:04:41 2016 -0500
@@ -6,29 +6,30 @@
   <expand macro="requirements" />
   <command detect_errors="exit_code"><![CDATA[
     @java_options@
+    @symlink_element_identifier@
     ##set up input files
 
     #set $reference_fasta_filename = "localref.fa"
-    
+
     #if str( $reference_source.reference_source_selector ) == "history":
         ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &&
     #else:
         #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
     #end if
-    
+
     picard
     CollectWgsMetrics
-    INPUT="${inputFile}"
+    INPUT='$inputFile.element_identifier'
     OUTPUT="${outFile}"
     REFERENCE_SEQUENCE="${reference_fasta_filename}"
     MINIMUM_MAPPING_QUALITY="${minimum_mapping_quality}"
     MINIMUM_BASE_QUALITY="${minimum_base_quality}"
     COVERAGE_CAP="${coverage_cap}"
-    
+
     VALIDATION_STRINGENCY="${validation_stringency}"
     QUIET=true
     VERBOSITY=ERROR
-  
+
   ]]></command>
   <inputs>
     <param format="sam,bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/>
@@ -52,15 +53,15 @@
     <param name="minimum_base_quality" type="integer" value="20" label="Minimum base quality for a base to contribute coverage" help="MINIMUM_BASE_QUALITY; default=20"/>
     <param name="coverage_cap" type="integer" value="250" label="Treat bases with coverage exceeding this value as if they had coverage at this value" help="COVERAGE_CAP; default=250"/>
 
-    
+
     <expand macro="VS" />
-    
+
   </inputs>
-  
+
   <outputs>
     <data format="tabular" name="outFile" label="${tool.name} on ${on_string}: Summary data"/>
   </outputs>
-  
+
   <tests>
     <test>
       <param name="reference_source_selector" value="history" />
@@ -70,10 +71,10 @@
       <param name="ref_file" value="picard_CollectWgsMetrics_ref.fa" />
       <param name="inputFile" value="picard_CollectWgsMetrics.bam" ftype="bam" />
       <output name="outFile" file="picard_CollectWgsMetrics_test1.tab" ftype="tabular" lines_diff="4"/>
-    </test> 
+    </test>
   </tests>
-  
-  
+
+
   <help>
 
 .. class:: infomark
@@ -87,14 +88,14 @@
 @description@
 
   MINIMUM_MAPPING_QUALITY=Integer
-  MQ=Integer                    Minimum mapping quality for a read to contribute coverage.  Default value: 20. 
+  MQ=Integer                    Minimum mapping quality for a read to contribute coverage.  Default value: 20.
 
   MINIMUM_BASE_QUALITY=Integer
-  Q=Integer                     Minimum base quality for a base to contribute coverage.  Default value: 20. 
+  Q=Integer                     Minimum base quality for a base to contribute coverage.  Default value: 20.
 
   COVERAGE_CAP=Integer
-  CAP=Integer                   Treat bases with coverage exceeding this value as if they had coverage at this value.  
-                                Default value: 250. 
+  CAP=Integer                   Treat bases with coverage exceeding this value as if they had coverage at this value.
+                                Default value: 250.
 
 @more_info@