changeset 25:7d34178f2812 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit a0fcbda330469051d130fd0802c55960ae948e3b

--- a/picard_MarkDuplicates.xml	Fri May 31 03:21:52 2019 -0400
+++ b/picard_MarkDuplicates.xml	Tue Jun 11 02:36:54 2019 -0400
@@ -2,7 +2,7 @@
   <description>examine aligned records in BAM datasets to locate duplicate molecules</description>
   <macros>
     <import>picard_macros.xml</import>
-    <token name="@WRAPPER_VERSION@">1</token>
+    <token name="@WRAPPER_VERSION@">2</token>
   </macros>
   <expand macro="requirements" />
   <command detect_errors="exit_code"><![CDATA[
@@ -29,7 +29,6 @@
     #end if
     OPTICAL_DUPLICATE_PIXEL_DISTANCE='${optical_duplicate_pixel_distance}'
 
-    # Optional arguments
     #if $barcode_tag:
       BARCODE_TAG='${barcode_tag}'
     #end if
@@ -58,7 +57,7 @@
     </param>
     <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"/>
 
-    <param name="barcode_tag" type="text" optional="True" label="Barcode Tag" help="Barcode SAM tag. This tag can be utilized when you have data from an assay that includes Unique Molecular Indices."/>
+    <param name="barcode_tag" type="text" optional="True" label="Barcode Tag" help="Barcode SAM tag. This tag can be utilized when you have data from an assay that includes Unique Molecular Indices. Typically 'RX' "/>
 
    <expand macro="VS" />
 
@@ -92,6 +91,18 @@
       <param name="validation_stringency" value="LENIENT"/>
       <output name="outFile" file="picard_MarkDuplicates_test2.bam" ftype="bam" lines_diff="4"/>
     </test>
+    <test>
+      <param name="inputFile" value="picard_MarkDuplicates.bam" ftype="bam"/>
+      <param name="comment" value="test-run"/>
+      <param name="assume_sorted" value="True"/>
+      <param name="remove_duplicates" value="False"/>
+      <param name="read_name_regex" value=""/>
+      <param name="optical_duplicate_pixel_distance" value="100"/>
+      <param name="duplicate_scoring_strategy" value="SUM_OF_BASE_QUALITIES"/>
+      <param name="validation_stringency" value="LENIENT"/>
+      <param name='barcode_tag' value="RX"/>
+      <output name="outFile" file="picard_MarkDuplicates_test2.bam" ftype="bam" lines_diff="4"/>
+    </test>
   </tests>