diff fgbio_group_reads_by_umi.xml @ 1:568816308859 draft

"planemo upload commit 692ea558cbbefee93859dc2b005fab5ac4970eb8"

--- a/fgbio_group_reads_by_umi.xml	Sun Feb 21 23:40:34 2021 +0000
+++ b/fgbio_group_reads_by_umi.xml	Wed Feb 24 13:02:09 2021 +0000
@@ -51,10 +51,10 @@
                 </help>
             </param>
             <param argument="--min-map-q" type="integer" value="" optional="true" label="Minimum mapping quality" help="Default: 30"/>
-            <param argument="--raw-tag" type="text" value="" label="The tag containing the raw UMI" help="Default: RX"> 
+            <param argument="--raw-tag" type="text" value="" optional="true" label="The tag containing the raw UMI" help="Default: RX"> 
                 <expand macro="sam_tag_validator"/>
             </param>
-            <param argument="--assign-tag" type="text" value="" label="The output tag for UMI grouping" help="Default: MI"> 
+            <param argument="--assign-tag" type="text" value="" optional="true" label="The output tag for UMI grouping" help="Default: MI"> 
                 <expand macro="sam_tag_validator"/>
             </param>
             <param argument="--include-non-pf-reads" type="select" value="true" optional="true" label="Include non-PF reads">
@@ -68,8 +68,14 @@
     <outputs>
         <data name="family_size_histogram" format="tabular" >
             <filter>output_counts == True</filter>
+            <actions>
+                <action name="comment_lines" type="metadata" default="1" />
+                <action name="column_names" type="metadata" default="family_size,count,fraction,fraction_gt_or_eq_family_size" />
+            </actions>
         </data>
-        <data name="output" format="bam" />
+        <data name="output" format="unsorted.bam" >
+            <expand macro="sort_order_change_format" />
+        </data>
     </outputs>
     <help><![CDATA[
 **fgbio GroupReadsByUmi**