# HG changeset patch
# User iuc
# Date 1762776926 0
# Node ID a387f00796c0427a14693257391ce3da550abe43
# Parent  b08cd2e5e61acc237b9269bca5d436dd9adc5397
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/mosdepth commit 42dc2863caa2105d8467575366147d1164945157

diff -r b08cd2e5e61a -r a387f00796c0 mosdepth.xml
--- a/mosdepth.xml	Mon Jul 31 06:09:19 2023 +0000
+++ b/mosdepth.xml	Mon Nov 10 12:15:26 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@">0.3.4</token>
+        <token name="@TOOL_VERSION@">0.3.12</token>
     </macros>
     <requirements>
         <requirement type="package" version="@TOOL_VERSION@">mosdepth</requirement>
-        <requirement type="package" version="1.12">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)
@@ -56,7 +56,7 @@
             $per_base_coverage 
             #if $advanced.options == "yes"
                 #if str($advanced.chrom)
-                --chrom '$advanced.chrom'
+                    --chrom '$advanced.chrom'
                 #end if
                 #if $advanced.exclude_flag
                     --flag $advanced.exclude_flag
@@ -66,6 +66,7 @@
                 #end if
                 --mapq $advanced.mapq
                 $advanced.no_fast
+                $advanced.fragment_mode
                 #if str($advanced.thresholds)
                     --thresholds '$advanced.thresholds'
                 #end if
@@ -74,7 +75,13 @@
                     --read-groups '$read_groups'
                 #end if
                 #if len($advanced.quantize)
-                --quantize '$quant_groups_depths_str'
+                    --quantize '$quant_groups_depths_str'
+                #end if
+                #if str($advanced.min_frag_len):
+                    --min-frag-len $advanced.min_frag_len
+                #end if
+                #if str($advanced.max_frag_len):
+                    --max-frag-len $advanced.max_frag_len
                 #end if
             #end if 
             output input_alignment
@@ -125,6 +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="">
@@ -141,6 +149,8 @@
                         <add value=" " />
                     </expand>
                 </param>
+                <param argument="--min-frag-len" type="integer" min="0" optional="true" label="Reads with a smaller insert size than this are ignored" />
+                <param argument="--max-frag-len" type="integer" min="0" optional="true" label="Reads with a larger insert size than this are ignored" />                
                 <repeat name="quantize" title="Read depth thresholds for depth-defined regions">
                     <param name="quant_group_mindepth" type="integer" min="0" value="0" label="Minimum depth for depth-defined region" help="Regions with this depth or lower will be included in this depth-defined region" />
                     <param name="quant_group_name" type="text" label="Depth-defined region name" help="Name include in BED output for regions in this depth-defined region">
@@ -273,7 +283,7 @@
 
 It can compute:
 
-* mean (or median) depth in fixed sized windows
+* mean (or median) depth in fixed-sized windows
 * mean (or median) depth in regions specified by a BED file
 * per base depths
 * a histogram of read depths
@@ -281,7 +291,7 @@
 * a distribution of proportion of based covered over a particular threshold
 * a BED format report on regions that are defined by coverage thresholds
 
-By default only a summary and depth histogram is computed, but the other options mentioned above can
+By default, only a summary and depth histogram is computed, but the other options mentioned above can
 be enabled using different options in the "Compute depth by region" selector and some of the Advanced
 options.
 
@@ -290,4 +300,4 @@
     <citations>
         <citation type="doi">10.1093/bioinformatics/btx699</citation>
     </citations>
-</tool>
\ No newline at end of file
+</tool>
diff -r b08cd2e5e61a -r a387f00796c0 test-data/output_region_distribution.tabular
--- a/test-data/output_region_distribution.tabular	Mon Jul 31 06:09:19 2023 +0000
+++ b/test-data/output_region_distribution.tabular	Mon Nov 10 12:15:26 2025 +0000
@@ -1,4 +1,4 @@
-sample	999	0.40
+sample	511	0.40
 sample	300	0.40
 sample	299	0.40
 sample	298	0.40
@@ -300,7 +300,7 @@
 sample	2	1.00
 sample	1	1.00
 sample	0	1.00
-total	999	0.40
+total	511	0.40
 total	300	0.40
 total	299	0.40
 total	298	0.40
diff -r b08cd2e5e61a -r a387f00796c0 test-data/output_region_distribution_median.tabular
--- a/test-data/output_region_distribution_median.tabular	Mon Jul 31 06:09:19 2023 +0000
+++ b/test-data/output_region_distribution_median.tabular	Mon Nov 10 12:15:26 2025 +0000
@@ -1,4 +1,4 @@
-sample	999	0.40
+sample	511	0.40
 sample	300	0.40
 sample	299	0.40
 sample	298	0.40
@@ -300,7 +300,7 @@
 sample	2	0.80
 sample	1	1.00
 sample	0	1.00
-total	999	0.40
+total	511	0.40
 total	300	0.40
 total	299	0.40
 total	298	0.40