diff picard_CollectInsertSizeMetrics.xml @ 8:e417b1d6288d draft

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

--- a/picard_CollectInsertSizeMetrics.xml	Sun Nov 27 15:11:36 2016 -0500
+++ b/picard_CollectInsertSizeMetrics.xml	Tue Dec 06 10:04:26 2016 -0500
@@ -8,27 +8,28 @@
   </expand>
   <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( $reference_source.ref_file.fields.path )
     #end if
-    
+
     picard
     CollectInsertSizeMetrics
-    INPUT="${inputFile}"
+    INPUT='$inputFile.element_identifier'
     OUTPUT="${outFile}"
     HISTOGRAM_FILE="${histFile}"
     DEVIATIONS="${deviations}"
-    
+
     #if str( $hist_width ):
       HISTOGRAM_WIDTH="${hist_width}"
     #end if
-    
+
     MINIMUM_PCT="${min_pct}"
     REFERENCE_SEQUENCE="${reference_fasta_filename}"
     ASSUME_SORTED="${assume_sorted}"
@@ -37,7 +38,7 @@
     VALIDATION_STRINGENCY="${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."/>
@@ -67,16 +68,16 @@
       <option value="LIBRARY">Library</option>
       <option value="READ_GROUP">Read group</option>
     </param>
-    
+
     <expand macro="VS" />
-    
+
   </inputs>
-  
+
   <outputs>
     <data format="tabular" name="outFile"/>
     <data format="pdf" name="histFile"/>
   </outputs>
-  
+
   <tests>
     <test>
       <param name="metric_accumulation_level" value="ALL_READS"/>
@@ -90,8 +91,8 @@
       <output name="outFile" file="picard_CollectInsertSizeMetrics_test1.tab" ftype="tabular" lines_diff="4"/>
     </test>
   </tests>
-  
-  
+
+
   <help>
 
 .. class:: infomark
@@ -104,30 +105,30 @@
 
 @description@
 
- 
-  DEVIATIONS=Double             Generate mean, sd and plots by trimming the data down to MEDIAN + 
-                                DEVIATIONS*MEDIAN_ABSOLUTE_DEVIATION. This is done because insert size data typically 
-                                includes enough anomalous values from chimeras and other artifacts to make the mean and 
-                                sd grossly misleading regarding the real distribution.  Default value: 10.0. 
+
+  DEVIATIONS=Double             Generate mean, sd and plots by trimming the data down to MEDIAN +
+                                DEVIATIONS*MEDIAN_ABSOLUTE_DEVIATION. This is done because insert size data typically
+                                includes enough anomalous values from chimeras and other artifacts to make the mean and
+                                sd grossly misleading regarding the real distribution.  Default value: 10.0.
 
   HISTOGRAM_WIDTH=Integer
-  W=Integer                     Explicitly sets the Histogram width, overriding automatic truncation of Histogram tail. 
-                                Also, when calculating mean and standard deviation, only bins &lt;= Histogram_WIDTH will be 
-                                included.  Default value: not set. 
+  W=Integer                     Explicitly sets the Histogram width, overriding automatic truncation of Histogram tail.
+                                Also, when calculating mean and standard deviation, only bins &lt;= Histogram_WIDTH will be
+                                included.  Default value: not set.
 
   MINIMUM_PCT=Float
-  M=Float                       When generating the Histogram, discard any data categories (out of FR, TANDEM, RF) that 
-                                have fewer than this percentage of overall reads. (Range: 0 to 1).  Default value: 0.05. 
+  M=Float                       When generating the Histogram, discard any data categories (out of FR, TANDEM, RF) that
+                                have fewer than this percentage of overall reads. (Range: 0 to 1).  Default value: 0.05.
 
   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.
+
   ASSUME_SORTED=Boolean
-  AS=Boolean                    If true (default), then the sort order in the header file will be ignored.  Default 
-                                value: true. This option can be set to 'null' to clear the default value. Possible 
+  AS=Boolean                    If true (default), then the sort order in the header file will be ignored.  Default
+                                value: true. This option can be set to 'null' to clear the default value. Possible
                                 values: {true, false}
-                                
+
 @more_info@
 
   </help>