changeset 3:5cd5d0947354 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit f2a83bdcd9dd514ee56a1b9e26811e65fa431c49

--- a/mosdepth.xml	Mon Nov 06 20:15:36 2023 +0000
+++ b/mosdepth.xml	Sun Feb 25 12:34:53 2024 +0000
@@ -25,7 +25,7 @@
             </sanitizer>
             <validator type="regex">([0-9A-Za-z!#$%&amp;+./:;?@^_|~-][0-9A-Za-z!#$%&amp;*+./:;=?@^_|~-]*)?</validator>
         </xml>
-        <token name="@TOOL_VERSION@">0.3.5</token>
+        <token name="@TOOL_VERSION@">0.3.6</token>
     </macros>
     <requirements>
         <requirement type="package" version="@TOOL_VERSION@">mosdepth</requirement>
@@ -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 $advanced.exclude_flag
@@ -74,7 +74,13 @@
                     --read-groups '$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
@@ -141,6 +147,8 @@
                         <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 +281,7 @@
 
 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 +289,7 @@
 * 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 +298,4 @@
     <citations>
         <citation type="doi">10.1093/bioinformatics/btx699</citation>
     </citations>
-</tool>
\ No newline at end of file
+</tool>