diff picard_MarkDuplicates.xml @ 27:fdca9493e09b draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 70d2a66c405be58d4413753792bcadf212a4da84

--- a/picard_MarkDuplicates.xml	Mon Aug 22 09:54:37 2022 +0000
+++ b/picard_MarkDuplicates.xml	Sat Feb 25 20:32:54 2023 +0000
@@ -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@">3</token>
+    <token name="@WRAPPER_VERSION@">4</token>
   </macros>
   <expand macro="requirements" />
   <command detect_errors="exit_code"><![CDATA[
@@ -56,7 +56,7 @@
     <param name="read_name_regex" type="text" value="" label="Regular expression that can be used in unusual situations to parse non-standard read names in the incoming SAM/BAM dataset" help="READ_NAME_REGEX; 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. See help below for more info; default='' (uses : separation)">
       <expand macro="sanitize_query" />
     </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="optical_duplicate_pixel_distance" type="integer" value="100" min="0" max="5000" 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. Typically 'RX' "/>
 
@@ -65,8 +65,8 @@
   </inputs>
 
   <outputs>
-    <data format="txt" name="metrics_file" label="${tool.name} on ${on_string}: MarkDuplicate metrics"/>
-    <data format="bam" name="outFile" label="${tool.name} on ${on_string}: MarkDuplicates BAM output"/>
+    <data format="txt" name="metrics_file" label="${tool.name} on ${on_string}: tabular"/>
+    <data format="bam" name="outFile" label="${tool.name} on ${on_string}: BAM"/>
   </outputs>
 
   <tests>