changeset 12:a459ead5ab75 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit a55cff7dfc145ed17ec2ee9f6a70d51c6f9d74b6

--- a/picard_CollectRnaSeqMetrics.xml	Wed Feb 08 12:41:25 2017 -0500
+++ b/picard_CollectRnaSeqMetrics.xml	Thu Apr 13 19:09:04 2017 -0400
@@ -219,12 +219,12 @@
    9. A new dataset will appear in the current Galaxy history
    10. Use this dataset as the input for **Gene annotations in refFlat form** dropdown of this tool
 
-.. _refFlat: http://genome.ucsc.edu/goldenPath/gbdDescriptionsOld.html#RefFlat
+.. _refFlat: https://genome.ucsc.edu/FAQ/FAQformat.html#format9
 
 @description@
 
    REF_FLAT=File                 Gene annotations in refFlat form.  Format described here:
-                                 http://genome.ucsc.edu/goldenPath/gbdDescriptionsOld.html#RefFlat  Required.
+                                 https://genome.ucsc.edu/FAQ/FAQformat.html#format9  Required.
 
    RIBOSOMAL_INTERVALS=File      Location of rRNA sequences in genome, in interval_list format.  If not specified no bases
                                  will be identified as being ribosomal. Format described here:

--- a/picard_MarkDuplicates.xml	Wed Feb 08 12:41:25 2017 -0500
+++ b/picard_MarkDuplicates.xml	Thu Apr 13 19:09:04 2017 -0400
@@ -1,4 +1,4 @@
-<tool name="MarkDuplicates" id="picard_MarkDuplicates" version="@TOOL_VERSION@.0">
+<tool name="MarkDuplicates" id="picard_MarkDuplicates" version="@TOOL_VERSION@.1">
   <description>examine aligned records in BAM datasets to locate duplicate molecules</description>
   <macros>
     <import>picard_macros.xml</import>
@@ -11,22 +11,28 @@
     MarkDuplicates
 
     INPUT='$escaped_element_identifier'
-    OUTPUT="${outFile}"
+    OUTPUT='${outFile}'
 
-    METRICS_FILE="${metrics_file}"
+    METRICS_FILE='${metrics_file}'
     #for $element in $comments:
-      COMMENT="${element.comment}"
+      COMMENT='${element.comment}'
     #end for
-    REMOVE_DUPLICATES="${remove_duplicates}"
-    ASSUME_SORTED="${assume_sorted}"
 
-    DUPLICATE_SCORING_STRATEGY="${duplicate_scoring_strategy}"
+    REMOVE_DUPLICATES='${remove_duplicates}'
+    ASSUME_SORTED='${assume_sorted}'
+
+    DUPLICATE_SCORING_STRATEGY='${duplicate_scoring_strategy}'
 
     #import pipes
     READ_NAME_REGEX=${ pipes.quote( str( $read_name_regex ) ) or "''" }
-    OPTICAL_DUPLICATE_PIXEL_DISTANCE="${optical_duplicate_pixel_distance}"
+    OPTICAL_DUPLICATE_PIXEL_DISTANCE='${optical_duplicate_pixel_distance}'
 
-    VALIDATION_STRINGENCY="${validation_stringency}"
+    # Optional arguments
+    #if $barcode_tag:
+    BARCODE_TAG='${barcode_tag}'
+    #end if
+
+    VALIDATION_STRINGENCY='${validation_stringency}'
     QUIET=true
     VERBOSITY=ERROR
 
@@ -53,6 +59,8 @@
     </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."/>
+
    <expand macro="VS" />
 
   </inputs>
@@ -116,6 +124,8 @@
                                 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.
 
+  BARCODE_TAG=String            Barcode SAM tag (ex. BC for 10X Genomics)  Default value: null.
+
 @more_info@
 
   </help>