diff picard_EstimateLibraryComplexity.xml @ 8:e417b1d6288d draft

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

--- a/picard_EstimateLibraryComplexity.xml	Sun Nov 27 15:11:36 2016 -0500
+++ b/picard_EstimateLibraryComplexity.xml	Tue Dec 06 10:04:26 2016 -0500
@@ -6,13 +6,13 @@
   <expand macro="requirements" />
   <command detect_errors="exit_code"><![CDATA[
     @java_options@
-    
+    @symlink_element_identifier@
     picard
     EstimateLibraryComplexity
-    
-    INPUT="${inputFile}"
+
+    INPUT='$inputFile.element_identifier'
     OUTPUT="${outFile}"
-    
+
     MIN_IDENTICAL_BASES="${min_identical_bases}"
     MAX_DIFF_RATE="${max_diff_rate}"
     MIN_MEAN_QUALITY="${min_mean_quality}"
@@ -20,11 +20,11 @@
     #import pipes
     READ_NAME_REGEX=${ pipes.quote( str( $read_name_regex ) ) or "''" }
     OPTICAL_DUPLICATE_PIXEL_DISTANCE="${optical_duplicate_pixel_distance}"
-    
+
     VALIDATION_STRINGENCY="${validation_stringency}"
     QUIET=true
     VERBOSITY=ERROR
-  
+
   ]]></command>
   <inputs>
     <param format="bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset" />
@@ -42,13 +42,13 @@
     <param name="optical_duplicate_pixel_distance" type="integer" value="100" min="0" max="500" label="The maximum offset between two duplicte clusters in order to consider them optical duplicates" help="OPTICAL_DUPLICATE_PIXEL_DISTANCE; default=100"/>
 
    <expand macro="VS" />
-    
-  </inputs> 
-  
+
+  </inputs>
+
   <outputs>
     <data format="tabular" name="outFile" label="${tool.name} on ${on_string}: Library complexity report"/>
   </outputs>
-  
+
   <tests>
     <test>
       <param name="inputFile" value="picard_EstimateLibraryComplexity.bam" ftype="bam"/>
@@ -62,8 +62,8 @@
       <output name="outFile" file="picard_EstimateLibraryComplexity_test1.tab" ftype="tabular" lines_diff="4"/>
     </test>
   </tests>
-  
-  
+
+
   <help>
 
 **Purpose**
@@ -86,40 +86,40 @@
 
 @description@
 
-  MIN_IDENTICAL_BASES=Integer   The minimum number of bases at the starts of reads that must be identical for reads to be 
-                                grouped together for duplicate detection.  In effect total_reads / 4^max_id_bases reads 
-                                will be compared at a time, so lower numbers will produce more accurate results but 
-                                consume exponentially more memory and CPU.  Default value: 5. 
-  
-  MAX_DIFF_RATE=Double          The maximum rate of differences between two reads to call them identical.  Default value: 
+  MIN_IDENTICAL_BASES=Integer   The minimum number of bases at the starts of reads that must be identical for reads to be
+                                grouped together for duplicate detection.  In effect total_reads / 4^max_id_bases reads
+                                will be compared at a time, so lower numbers will produce more accurate results but
+                                consume exponentially more memory and CPU.  Default value: 5.
+
+  MAX_DIFF_RATE=Double          The maximum rate of differences between two reads to call them identical.  Default value:
                                 0.03.
-  
-  MIN_MEAN_QUALITY=Integer      The minimum mean quality of the bases in a read pair for the read to be analyzed. Reads 
-                                with lower average quality are filtered out and not considered in any calculations.  
+
+  MIN_MEAN_QUALITY=Integer      The minimum mean quality of the bases in a read pair for the read to be analyzed. Reads
+                                with lower average quality are filtered out and not considered in any calculations.
                                 Default value: 20.
-  
-  MAX_GROUP_RATIO=Integer       Do not process self-similar groups that are this many times over the mean expected group 
-                                size. I.e. if the input contains 10m read pairs and MIN_IDENTICAL_BASES is set to 5, then 
+
+  MAX_GROUP_RATIO=Integer       Do not process self-similar groups that are this many times over the mean expected group
+                                size. I.e. if the input contains 10m read pairs and MIN_IDENTICAL_BASES is set to 5, then
                                 the mean expected group size would be approximately 10 reads.  Default value: 500.
-  
-  READ_NAME_REGEX=String        Regular expression that can be used to parse read names in the incoming SAM file. Read 
-                                names are parsed to extract three variables: tile/region, x coordinate and y coordinate. 
-                                These values are used to estimate the rate of optical duplication in order to give a more 
-                                accurate estimated library size. Set this option to null to disable optical duplicate 
-                                detection. The regular expression should contain three capture groups for the three 
-                                variables, in order. It must match the entire read name. Note that if the default regex 
-                                is specified, a regex match is not actually done, but instead the read name  is split on 
-                                colon character. For 5 element names, the 3rd, 4th and 5th elements are assumed to be 
-                                tile, x and y values. For 7 element names (CASAVA 1.8), the 5th, 6th, and 7th elements 
-                                are assumed to be tile, x and y values.  Default value: 
+
+  READ_NAME_REGEX=String        Regular expression that can be used to parse read names in the incoming SAM file. Read
+                                names are parsed to extract three variables: tile/region, x coordinate and y coordinate.
+                                These values are used to estimate the rate of optical duplication in order to give a more
+                                accurate estimated library size. Set this option to null to disable optical duplicate
+                                detection. The regular expression should contain three capture groups for the three
+                                variables, in order. It must match the entire read name. Note that if the default regex
+                                is specified, a regex match is not actually done, but instead the read name  is split on
+                                colon character. For 5 element names, the 3rd, 4th and 5th elements are assumed to be
+                                tile, x and y values. For 7 element names (CASAVA 1.8), the 5th, 6th, and 7th elements
+                                are assumed to be tile, x and y values.  Default value:
                                 [a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*.
-  
-  OPTICAL_DUPLICATE_PIXEL_DISTANCE=Integer  
-                                The maximum offset between two duplicte clusters in order to consider them optical 
-                                duplicates. This should usually be set to some fairly small number (e.g. 5-10 pixels) 
-                                unless using later versions of the Illumina pipeline that multiply pixel values by 10, in 
+
+  OPTICAL_DUPLICATE_PIXEL_DISTANCE=Integer
+                                The maximum offset between two duplicte clusters in order to consider them optical
+                                duplicates. This should usually be set to some fairly small number (e.g. 5-10 pixels)
+                                unless using later versions of the Illumina pipeline that multiply pixel values by 10, in
                                 which case 50-100 is more normal.  Default value: 100.
-  
+
 
 @more_info@