diff picard_CollectAlignmentSummaryMetrics.xml @ 8:e417b1d6288d draft

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

--- a/picard_CollectAlignmentSummaryMetrics.xml	Sun Nov 27 15:11:36 2016 -0500
+++ b/picard_CollectAlignmentSummaryMetrics.xml	Tue Dec 06 10:04:26 2016 -0500
@@ -6,6 +6,7 @@
   <expand macro="requirements" />
   <command detect_errors="exit_code"><![CDATA[
     @java_options@
+    @symlink_element_identifier@
     ##set up input files
 
     #set $reference_fasta_filename = "localref.fa"
@@ -18,7 +19,7 @@
 
     picard
     CollectAlignmentSummaryMetrics
-    INPUT="${inputFile}"
+    INPUT='$inputFile.element_identifier'
     OUTPUT="${outFile}"
     MAX_INSERT_SIZE=${maxinsert}
     #for $sequence in $adapters:
@@ -36,7 +37,7 @@
     VALIDATION_STRINGENCY="${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."/>
@@ -98,25 +99,25 @@
 
 @description@
 
-  MAX_INSERT_SIZE=Integer       Paired end reads above this insert size will be considered chimeric along with 
-                                inter-chromosomal pairs.  Default value: 100000.  
+  MAX_INSERT_SIZE=Integer       Paired end reads above this insert size will be considered chimeric along with
+                                inter-chromosomal pairs.  Default value: 100000.
 
-  ADAPTER_SEQUENCE=String       List of adapter sequences to use when processing the alignment metrics  This option may 
-                                be specified 0 or more times.  
+  ADAPTER_SEQUENCE=String       List of adapter sequences to use when processing the alignment metrics  This option may
+                                be specified 0 or more times.
 
   METRIC_ACCUMULATION_LEVEL=MetricAccumulationLevel
-  LEVEL=MetricAccumulationLevel The level(s) at which to accumulate metrics.    Possible values: {ALL_READS, SAMPLE, 
-                                LIBRARY, READ_GROUP} This option may be specified 0 or more times.  
+  LEVEL=MetricAccumulationLevel The level(s) at which to accumulate metrics.    Possible values: {ALL_READS, SAMPLE,
+                                LIBRARY, READ_GROUP} This option may be specified 0 or more times.
 
   IS_BISULFITE_SEQUENCED=Boolean
-  BS=Boolean                    Whether the SAM or BAM file consists of bisulfite sequenced reads.    
+  BS=Boolean                    Whether the SAM or BAM file consists of bisulfite sequenced reads.
 
 
   REFERENCE_SEQUENCE=File
-  R=File                        Reference sequence fasta  Default value: null. 
+  R=File                        Reference sequence fasta  Default value: null.
 
   ASSUME_SORTED=Boolean
-  AS=Boolean                    If true (default), then the sort order in the header file will be ignored. 
+  AS=Boolean                    If true (default), then the sort order in the header file will be ignored.
 
 @more_info@