diff picard_QualityScoreDistribution.xml @ 13:7e6fd3d0f16e draft

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

--- a/picard_QualityScoreDistribution.xml	Sun Nov 27 15:11:50 2016 -0500
+++ b/picard_QualityScoreDistribution.xml	Tue Dec 06 10:04:41 2016 -0500
@@ -9,31 +9,31 @@
   <command detect_errors="exit_code"><![CDATA[
     @java_options@
     ##set up input files
-
+    @symlink_element_identifier@
     #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( $reference_source.ref_file.fields.path )
     #end if
-    
+
     picard
     QualityScoreDistribution
-    INPUT="${inputFile}"
+    INPUT='$inputFile.element_identifier'
     OUTPUT="${outFile}"
     CHART_OUTPUT="${pdfFile}"
     REFERENCE_SEQUENCE="${reference_fasta_filename}"
     ALIGNED_READS_ONLY="${aligned_reads_only}"
     PF_READS_ONLY="${pf_reads_only}"
     INCLUDE_NO_CALLS="${include_no_calls}"
-  
+
     ASSUME_SORTED="${assume_sorted}"
-    
+
     VALIDATION_STRINGENCY="${validation_stringency}"
     QUIET=true
     VERBOSITY=ERROR
-  
+
   ]]></command>
   <inputs>
     <param format="sam,bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/>
@@ -57,16 +57,16 @@
     <param name="pf_reads_only" type="boolean" truevalue="true" falsevalue="false" label="If set to true calculate mean quality over reads passing quality filter" help="PF_READS_ONLY; default=False"/>
     <param name="include_no_calls" type="boolean" label="If set to true, include quality for no-call bases in the distribution" help="INCLUDE_NO_CALLS; default=False"/>
     <param name="assume_sorted" type="boolean" label="Assume the input file is already sorted" checked="true" truevalue="true" falsevalue="false" help="ASSUME_SORTED; default=True"/>
-    
+
     <expand macro="VS" />
-    
+
   </inputs>
-  
+
   <outputs>
     <data format="tabular" name="outFile" label="${tool.name} on ${on_string}: Summary data"/>
     <data format="pdf" name="pdfFile" label="${tool.name} on ${on_string}: Chart PDF"/>
   </outputs>
-  
+
   <tests>
     <test>
       <param name="assume_sorted" value="true" />
@@ -77,10 +77,10 @@
       <param name="ref_file" value="picard_QualityScoreDistribution_ref.fa" />
       <param name="inputFile" value="picard_QualityScoreDistribution.bam" ftype="bam" />
       <output name="outFile" file="picard_QualityScoreDistribution_test1.tab" ftype="tabular" lines_diff="4"/>
-    </test> 
+    </test>
   </tests>
-  
-  
+
+
   <help>
 
 .. class:: infomark
@@ -93,17 +93,17 @@
 
 @description@
 
-  ALIGNED_READS_ONLY=Boolean    If set to true, calculate the base distribution over aligned reads only.  Default value: 
-                                false. Possible values: {true, false} 
+  ALIGNED_READS_ONLY=Boolean    If set to true, calculate the base distribution over aligned reads only.  Default value:
+                                false. Possible values: {true, false}
 
-  PF_READS_ONLY=Boolean         If set to true calculate the base distribution over PF reads only.  Default value: false. 
+  PF_READS_ONLY=Boolean         If set to true calculate the base distribution over PF reads only.  Default value: false.
                                 Possible values: {true, false}
-                                
-  INCLUDE_NO_CALLS=Boolean      If set to true, include quality for no-call bases in the distribution.  Default value: 
-                                false. Possible values: {true, false} 
+
+  INCLUDE_NO_CALLS=Boolean      If set to true, include quality for no-call bases in the distribution.  Default value:
+                                false. Possible values: {true, false}
 
   ASSUME_SORTED=Boolean
-  AS=Boolean                    If true (default), then the sort order in the header file will be ignored.  Default: True 
+  AS=Boolean                    If true (default), then the sort order in the header file will be ignored.  Default: True
 
 @more_info@