# HG changeset patch
# User iuc
# Date 1753451635 0
# Node ID b1a8d09e5a8209899893e4eee872fc069901c3fb
# Parent  5854d0da92b4d840920a4be72a1ecc7d3171453a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit 078ade4ee3f8566373ff88bdab4c0c766e62a347

diff -r 5854d0da92b4 -r b1a8d09e5a82 mosdepth.xml
--- a/mosdepth.xml	Mon May 06 18:41:03 2024 +0000
+++ b/mosdepth.xml	Fri Jul 25 13:53:55 2025 +0000
@@ -25,11 +25,11 @@
             </sanitizer>
             <validator type="regex">([0-9A-Za-z!#$%&amp;+./:;?@^_|~-][0-9A-Za-z!#$%&amp;*+./:;=?@^_|~-]*)?</validator>
         </xml>
-        <token name="@TOOL_VERSION@">0.3.8</token>
+        <token name="@TOOL_VERSION@">0.3.11</token>
     </macros>
     <requirements>
         <requirement type="package" version="@TOOL_VERSION@">mosdepth</requirement>
-        <requirement type="package" version="1.13">gzip</requirement>
+        <requirement type="package" version="1.14">gzip</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         #if $advanced.options == "yes" and len($advanced.quantize)
@@ -66,6 +66,7 @@
                 #end if
                 --mapq $advanced.mapq
                 $advanced.no_fast
+                $advanced.fragment_mode
                 #if str($advanced.thresholds)
                     --thresholds '$advanced.thresholds'
                 #end if
@@ -131,6 +132,7 @@
                 <param argument="--flag" name="exclude_flag" type="integer" min="0" value="0" label="Exclude reads with these bits set in FLAG" help="Exclude reads where any of these bits are set in the value of the read flags column" />
                 <param argument="--include-flag" type="integer" min="1" optional="true" label="Only include reads with these bits set in FLAG" help="Only include reads where any of these bits are set in the value of the read flags column" />
                 <param argument="--fast-mode" name="no_fast" type="boolean" truevalue="" falsevalue="-x" label="Disable fast mode" help="Fast mode doesn't look up internal cigar operations or correct mate overlaps. Disabling it is not recommended" />
+                <param argument="--fragment-mode" type="boolean" truevalue="--fragment-mode" falsevalue="" checked="false" label="Use fragment mode" help="Count the coverage of the full fragment including the full insert (proper pairs only). Note that you can use either of fast mode or fragment mode, but not both"/>
                 <param argument="--mapq" type="integer" min="0" value="0" label="Minimum mapping quality" help="Reads with a mapping quality lower than this value are ignored" />
                 <param argument="--thresholds" type="text" value="" label="Specify thresholds for output when using region output" help="The number of bases covered by these thresholds will be reported. Multiple thresholds can be separated by commas">
                     <sanitizer invalid_char="">